The Enzyme Database

Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)

Proposed Changes to the Enzyme List

The entries below are proposed additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC-IUBMB by Kristian Axelsen, Richard Cammack, Ron Caspi, Masaaki Kotera, Andrew McDonald, Gerry Moss, Dietmar Schomburg, Ida Schomburg and Keith Tipton. Comments and suggestions on these draft entries should be sent to Dr Andrew McDonald (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland). The date on which an enzyme will be made official is appended after the EC number. To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.

An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.


Contents

EC 1.1.1.307 D-xylose reductase
EC 1.1.99.36 alcohol dehydrogenase (nicotinoprotein)
EC 1.1.99.37 methanol dehydrogenase (nicotinoprotein)
*EC 1.2.1.24 succinate-semialdehyde dehydrogenase (NAD+)
EC 1.2.1.79 succinate-semialdehyde dehydrogenase (NADP+)
*EC 1.13.11.39 biphenyl-2,3-diol 1,2-dioxygenase
EC 1.14.14.8 anthranilate 3-monooxygenase (FAD)
EC 1.14.99.41 all-trans-8′-apo-β-carotenal 15,15′-oxygenase
EC 2.1.1.48 transferred
EC 2.1.1.51 transferred
*EC 2.1.1.148 thymidylate synthase (FAD)
EC 2.1.1.175 tricin synthase
EC 2.1.1.176 16S rRNA (cytosine967-C5)-methyltransferase
EC 2.1.1.177 23S rRNA (pseudouridine1915-N3)-methyltransferase
EC 2.1.1.178 16S rRNA (cytosine1407-C5)-methyltransferase
EC 2.1.1.179 16S rRNA (guanine1405-N7)-methyltransferase
EC 2.1.1.180 16S rRNA (adenine1408-N1)-methyltransferase
EC 2.1.1.181 23S rRNA (adenine1618-N6)-methyltransferase
EC 2.1.1.182 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
EC 2.1.1.183 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase
EC 2.1.1.184 23S rRNA (adenine2085-N6)-dimethyltransferase
EC 2.1.1.185 23S rRNA (guanosine2251-2′-O)-methyltransferase
EC 2.1.1.186 23S rRNA (cytidine2498-2′-O)-methyltransferase
EC 2.1.1.187 23S rRNA (guanine745-N1)-methyltransferase
EC 2.1.1.188 23S rRNA (guanine748-N1)-methyltransferase
EC 2.1.1.189 23S rRNA (uracil747-C5)-methyltransferase
EC 2.1.1.190 23S rRNA (uracil1939-C5)-methyltransferase
EC 2.1.1.191 23S rRNA (cytosine1962-C5)-methyltransferase
EC 2.1.1.192 23S rRNA (adenine2503-C2)-methyltransferase
EC 2.1.1.193 16S rRNA (uracil1498-N3)-methyltransferase
EC 2.1.1.194 23S rRNA (adenine2503-C2,C8)-dimethyltransferase
*EC 2.4.1.94 protein N-acetylglucosaminyltransferase
*EC 2.5.1.10 (2E,6E)-farnesyl diphosphate synthase
EC 2.5.1.11 transferred
*EC 2.5.1.30 heptaprenyl diphosphate synthase
*EC 2.5.1.31 ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
EC 2.5.1.33 transferred
*EC 2.5.1.68 (2Z,6E)-farnesyl diphosphate synthase
EC 2.5.1.81 geranylfarnesyl diphosphate synthase
EC 2.5.1.82 hexaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific]
EC 2.5.1.83 hexaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
EC 2.5.1.84 all-trans-nonaprenyl-diphosphate synthase [geranyl-diphosphate specific]
EC 2.5.1.85 all-trans-nonaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific]
EC 2.5.1.86 trans,polycis-decaprenyl diphosphate synthase
EC 2.5.1.87 ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific]
EC 2.5.1.88 trans,polycis-polyprenyl diphosphate synthase [(2Z,6E)-farnesyl diphosphate specific]
EC 2.5.1.89 tritrans,polycis-undecaprenyl-diphosphate synthase [geranylgeranyl-diphosphate specific]
EC 2.5.1.90 all-trans-octaprenyl-diphosphate synthase
EC 2.5.1.91 all-trans-decaprenyl-diphosphate synthase
EC 2.5.1.92 (2Z,6Z)-farnesyl diphosphate synthase
EC 2.7.7.69 GDP-L-galactose phosphorylase
EC 2.7.8.30 undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
*EC 3.6.1.40 guanosine-5′-triphosphate,3′-diphosphate phosphatase
*EC 4.1.99.14 spore photoproduct lyase
EC 4.1.99.15 deleted
EC 4.2.3.50 (+)-α-santalene synthase [(2Z,6Z)-farnesyl diphosphate cyclizing]
EC 4.2.3.51 β-phellandrene synthase (neryl-diphosphate-cyclizing)
EC 4.2.3.52 (4S)-β-phellandrene synthase (geranyl-diphosphate-cyclizing)
EC 4.2.3.53 (+)-endo-β-bergamotene synthase [(2Z,6Z)-farnesyl diphosphate cyclizing]
EC 4.2.3.54 (-)-endo-α-bergamotene synthase [(2Z,6Z)-farnesyl diphosphate cyclizing]
EC 6.1.2 acid—alcohol ligases (ester synthases)
EC 6.1.2.1 D-alanine—(R)-lactate ligase
*EC 6.3.2.13 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—2,6-diaminopimelate ligase
EC 6.3.2.35 D-alanine—D-serine ligase
EC 6.3.5.11 cobyrinate a,c-diamide synthase


EC 1.1.1.307
Accepted name: D-xylose reductase
Reaction: xylitol + NAD(P)+ = D-xylose + NAD(P)H + H+
Other name(s): XylR; XyrA; msXR; dsXR; monospecific xylose reductase; dual specific xylose reductase; NAD(P)H-dependent xylose reductase; xylose reductase
Systematic name: xylitol:NAD(P)+ oxidoreductase
Comments: Xylose reductase catalyses the initial reaction in the xylose utilization pathway, the NAD(P)H dependent reduction of xylose to xylitol.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Neuhauser, W., Haltrich, D., Kulbe, K.D. and Nidetzky, B. NAD(P)H-dependent aldose reductase from the xylose-assimilating yeast Candida tenuis. Isolation, characterization and biochemical properties of the enzyme. Biochem. J. 326 (1997) 683–692. [PMID: 9307017]
2.  Nidetzky, B., Bruggler, K., Kratzer, R. and Mayr, P. Multiple forms of xylose reductase in Candida intermedia: comparison of their functional properties using quantitative structure-activity relationships, steady-state kinetic analysis, and pH studies. J. Agric. Food Chem. 51 (2003) 7930–7935. [PMID: 14690376]
3.  Iablochkova, E.N., Bolotnikova, O.I., Mikhailova, N.P., Nemova, N.N. and Ginak, A.I. The activity of xylose reductase and xylitol dehydrogenase in yeasts. Mikrobiologiia 72 (2003) 466–469. [PMID: 14526534] (in Russian)
4.  Chen, L.C., Huang, S.C., Chuankhayan, P., Chen, C.D., Huang, Y.C., Jeyakanthan, J., Pang, H.F., Men, L.C., Chen, Y.C., Wang, Y.K., Liu, M.Y., Wu, T.K. and Chen, C.J. Purification, crystallization and preliminary X-ray crystallographic analysis of xylose reductase from Candida tropicalis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 65 (2009) 419–421. [PMID: 19342796]
5.  Verduyn, C., Van Kleef, R., Frank, J., Schreuder, H., Van Dijken, J.P. and Scheffers, W.A. Properties of the NAD(P)H-dependent xylose reductase from the xylose-fermenting yeast Pichia stipitis. Biochem. J. 226 (1985) 669–677. [PMID: 3921014]
6.  Fernandes, S., Tuohy, M.G. and Murray, P.G. Xylose reductase from the thermophilic fungus Talaromyces emersonii: cloning and heterologous expression of the native gene (Texr) and a double mutant (TexrK271R + N273D) with altered coenzyme specificity. J. Biosci. 34 (2009) 881–890. [PMID: 20093741]
7.  Lee, J.K., Koo, B.S. and Kim, S.Y. Cloning and characterization of the xyl1 gene, encoding an NADH-preferring xylose reductase from Candida parapsilosis, and its functional expression in Candida tropicalis. Appl. Environ. Microbiol. 69 (2003) 6179–6188. [PMID: 14532079]
8.  Woodyer, R., Simurdiak, M., van der Donk, W.A. and Zhao, H. Heterologous expression, purification, and characterization of a highly active xylose reductase from Neurospora crassa. Appl. Environ. Microbiol. 71 (2005) 1642–1647. [PMID: 15746370]
[EC 1.1.1.307 created 2010]
 
 
EC 1.1.99.36
Accepted name: alcohol dehydrogenase (nicotinoprotein)
Reaction: ethanol + acceptor = acetaldehyde + reduced acceptor
Other name(s): NDMA-dependent alcohol dehydrogenase; nicotinoprotein alcohol dehydrogenase; np-ADH; ethanol:N,N-dimethyl-4-nitrosoaniline oxidoreductase
Systematic name: ethanol:acceptor oxidoreductase
Comments: Contains Zn2+. Nicotinoprotein alcohol dehydrogenases are unique medium-chain dehydrogenases/reductases (MDR) alcohol dehydrogenases that have a tightly bound NAD+/NADH cofactor that does not dissociate during the catalytic process. Instead, the cofactor is regenerated by a second substrate or electron carrier. While the in vivo electron acceptor is not known, N,N-dimethyl-4-nitrosoaniline (NDMA), which is reduced to 4-(hydroxylamino)-N,N-dimethylaniline, can serve this function in vitro. The enzyme from the Gram-positive bacterium Amycolatopsis methanolica can accept many primary alcohols as substrates, including benzylalcohol [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Van Ophem, P.W., Van Beeumen, J. and Duine, J.A. Nicotinoprotein [NAD(P)-containing] alcohol/aldehyde oxidoreductases. Purification and characterization of a novel type from Amycolatopsis methanolica. Eur. J. Biochem. 212 (1993) 819–826. [PMID: 8385013]
2.  Piersma, S.R., Visser, A.J., de Vries, S. and Duine, J.A. Optical spectroscopy of nicotinoprotein alcohol dehydrogenase from Amycolatopsis methanolica: a comparison with horse liver alcohol dehydrogenase and UDP-galactose epimerase. Biochemistry 37 (1998) 3068–3077. [PMID: 9485460]
3.  Schenkels, P. and Duine, J.A. Nicotinoprotein (NADH-containing) alcohol dehydrogenase from Rhodococcus erythropolis DSM 1069: an efficient catalyst for coenzyme-independent oxidation of a broad spectrum of alcohols and the interconversion of alcohols and aldehydes. Microbiology 146 (2000) 775–785. [PMID: 10784035]
4.  Piersma, S.R., Norin, A., de Vries, S., Jornvall, H. and Duine, J.A. Inhibition of nicotinoprotein (NAD+-containing) alcohol dehydrogenase by trans-4-(N,N-dimethylamino)-cinnamaldehyde binding to the active site. J. Protein Chem. 22 (2003) 457–461. [PMID: 14690248]
5.  Norin, A., Piersma, S.R., Duine, J.A. and Jornvall, H. Nicotinoprotein (NAD+ -containing) alcohol dehydrogenase: structural relationships and functional interpretations. Cell. Mol. Life Sci. 60 (2003) 999–1006. [PMID: 12827287]
[EC 1.1.99.36 created 2010]
 
 
EC 1.1.99.37
Accepted name: methanol dehydrogenase (nicotinoprotein)
Reaction: methanol + acceptor = formaldehyde + reduced acceptor
Other name(s): NDMA-dependent methanol dehydrogenase; nicotinoprotein methanol dehydrogenase; methanol:N,N-dimethyl-4-nitrosoaniline oxidoreductase
Systematic name: methanol:acceptor oxidoreductase
Comments: Contains Zn2+ and Mg2+. Nicotinoprotein methanol dehydrogenases have a tightly bound NADP+/NADPH cofactor that does not dissociate during the catalytic process. Instead, the cofactor is regenerated by a second substrate or electron carrier. While the in vivo electron acceptor is not known, N,N-dimethyl-4-nitrosoaniline (NDMA), which is reduced to 4-(hydroxylamino)-N,N-dimethylaniline, can serve this function in vitro. The enzyme has been detected in several Gram-positive methylotrophic bacteria, including Amycolatopsis methanolica, Rhodococcus rhodochrous and Rhodococcus erythropolis [1-3]. These enzymes are decameric, and possess a 5-fold symmetry [4]. Some of the enzymes can also dismutate formaldehyde to methanol and formate [5].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Vonck, J., Arfman, N., De Vries, G.E., Van Beeumen, J., Van Bruggen, E.F. and Dijkhuizen, L. Electron microscopic analysis and biochemical characterization of a novel methanol dehydrogenase from the thermotolerant Bacillus sp. C1. J. Biol. Chem. 266 (1991) 3949–3954. [PMID: 1995642]
2.  Van Ophem, P.W., Van Beeumen, J. and Duine, J.A. Nicotinoprotein [NAD(P)-containing] alcohol/aldehyde oxidoreductases. Purification and characterization of a novel type from Amycolatopsis methanolica. Eur. J. Biochem. 212 (1993) 819–826. [PMID: 8385013]
3.  Bystrykh, L.V., Vonck, J., van Bruggen, E.F., van Beeumen, J., Samyn, B., Govorukhina, N.I., Arfman, N., Duine, J.A. and Dijkhuizen, L. Electron microscopic analysis and structural characterization of novel NADP(H)-containing methanol: N,N′-dimethyl-4-nitrosoaniline oxidoreductases from the gram-positive methylotrophic bacteria Amycolatopsis methanolica and Mycobacterium gastri MB19. J. Bacteriol. 175 (1993) 1814–1822. [PMID: 8449887]
4.  Hektor, H.J., Kloosterman, H. and Dijkhuizen, L. Identification of a magnesium-dependent NAD(P)(H)-binding domain in the nicotinoprotein methanol dehydrogenase from Bacillus methanolicus. J. Biol. Chem. 277 (2002) 46966–46973. [PMID: 12351635]
5.  Park, H., Lee, H., Ro, Y.T. and Kim, Y.M. Identification and functional characterization of a gene for the methanol : N,N′-dimethyl-4-nitrosoaniline oxidoreductase from Mycobacterium sp. strain JC1 (DSM 3803). Microbiology 156 (2010) 463–471. [PMID: 19875438]
[EC 1.1.99.37 created 2010]
 
 
*EC 1.2.1.24
Accepted name: succinate-semialdehyde dehydrogenase (NAD+)
Reaction: succinate semialdehyde + NAD+ + H2O = succinate + NADH + 2 H+
For diagram of arginine catabolism, click here and for diagram of the citric acid cycle, click here
Other name(s): succinate semialdehyde dehydrogenase (NAD+); succinic semialdehyde dehydrogenase (NAD+); succinyl semialdehyde dehydrogenase (NAD+); succinate semialdehyde:NAD+ oxidoreductase
Systematic name: succinate-semialdehyde:NAD+ oxidoreductase
Comments: This enzyme participates in the degradation of glutamate and 4-aminobutyrate. It is similar to EC 1.2.1.79 [succinate-semialdehyde dehydrogenase (NADP+)], and EC 1.2.1.16 [succinate-semialdehyde dehydrogenase (NAD(P)+)], but is specific for NAD+.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 9028-95-9
References:
1.  Albers, R.W. and Koval, G.J. Succinic semialdehyde dehydrogenase : purification and properties of the enzyme from monkey brain. Biochim. Biophys. Acta 52 (1961) 29–35. [PMID: 13860092]
2.  Ryzlak, M.T. and Pietruszko, R. Human brain "high Km" aldehyde dehydrogenase: purification, characterization, and identification as NAD+ -dependent succinic semialdehyde dehydrogenase. Arch. Biochem. Biophys. 266 (1988) 386–396. [PMID: 3190233]
3.  Busch, K.B. and Fromm, H. Plant succinic semialdehyde dehydrogenase. Cloning, purification, localization in mitochondria, and regulation by adenine nucleotides. Plant Physiol. 121 (1999) 589–597. [PMID: 10517851]
[EC 1.2.1.24 created 1972, modified 2010]
 
 
EC 1.2.1.79
Accepted name: succinate-semialdehyde dehydrogenase (NADP+)
Reaction: succinate semialdehyde + NADP+ + H2O = succinate + NADPH + 2 H+
For diagram of the citric acid cycle, click here
Other name(s): succinic semialdehyde dehydrogenase (NADP+); succinyl semialdehyde dehydrogenase (NADP+); succinate semialdehyde:NADP+ oxidoreductase; NADP-dependent succinate-semialdehyde dehydrogenase; GabD
Systematic name: succinate-semialdehyde:NADP+ oxidoreductase
Comments: This enzyme participates in the degradation of glutamate and 4-aminobutyrate. It is similar to EC 1.2.1.24 [succinate-semialdehyde dehydrogenase (NAD+)], and EC 1.2.1.16 [succinate-semialdehyde dehydrogenase (NAD(P)+)], but is specific for NADP+. The enzyme from Escherichia coli is 20-fold more active with NADP+ than NAD+ [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Bartsch, K., von Johnn-Marteville, A. and Schulz, A. Molecular analysis of two genes of the Escherichia coli gab cluster: nucleotide sequence of the glutamate:succinic semialdehyde transaminase gene (gabT) and characterization of the succinic semialdehyde dehydrogenase gene (gabD). J. Bacteriol. 172 (1990) 7035–7042. [PMID: 2254272]
2.  Jaeger, M., Rothacker, B. and Ilg, T. Saturation transfer difference NMR studies on substrates and inhibitors of succinic semialdehyde dehydrogenases. Biochem. Biophys. Res. Commun. 372 (2008) 400–406. [PMID: 18474219]
[EC 1.2.1.79 created 2010]
 
 
*EC 1.13.11.39
Accepted name: biphenyl-2,3-diol 1,2-dioxygenase
Reaction: biphenyl-2,3-diol + O2 = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
Other name(s): 2,3-dihydroxybiphenyl dioxygenase; biphenyl-2,3-diol dioxygenase; bphC (gene name); biphenyl-2,3-diol:oxygen 1,2-oxidoreductase (decyclizing)
Systematic name: biphenyl-2,3-diol:oxygen 1,2-oxidoreductase (ring-opening)
Comments: Contains Fe2+ or Mn2+ [3]. This enzyme participates in the degradation pathway of biphenyl and PCB (poly chlorinated biphenyls), and catalyses the first ring cleavage step by incorporating two oxygen atoms into the catechol ring formed by EC 1.3.1.56, cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase.The enzyme from the bacterium Burkholderia xenovorans LB400 can also process catechol, 3-methylcatechol, and 4-methylcatechol, but less efficiently [1]. The enzyme from the carbazole-degrader Pseudomonas resinovorans strain CA10 also accepts 2′-aminobiphenyl-2,3-diol [5]. The enzyme from Ralstonia sp. SBUG 290 can also accept 1,2-dihydroxydibenzofuran and 1,2-dihydroxynaphthalene [4]. The enzyme is strongly inhibited by the substrate [1].Not identical with EC 1.13.11.2 catechol 2,3-dioxygenase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, UM-BBD, CAS registry number: 103679-58-9
References:
1.  Eltis, L.D., Hofmann, B., Hecht, H.J., Lunsdorf, H. and Timmis, K.N. Purification and crystallization of 2,3-dihydroxybiphenyl 1,2-dioxygenase. J. Biol. Chem. 268 (1993) 2727–2732. [PMID: 8428946]
2.  Uragami, Y., Senda, T., Sugimoto, K., Sato, N., Nagarajan, V., Masai, E., Fukuda, M. and Mitsu, Y. Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase. J. Inorg. Biochem. 83 (2001) 269–279. [PMID: 11293547]
3.  Hatta, T., Mukerjee-Dhar, G., Damborsky, J., Kiyohara, H. and Kimbara, K. Characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8. J. Biol. Chem. 278 (2003) 21483–21492. [PMID: 12672826]
4.  Wesche, J., Hammer, E., Becher, D., Burchhardt, G. and Schauer, F. The bphC gene-encoded 2,3-dihydroxybiphenyl-1,2-dioxygenase is involved in complete degradation of dibenzofuran by the biphenyl-degrading bacterium Ralstonia sp. SBUG 290. J. Appl. Microbiol. 98 (2005) 635–645. [PMID: 15715866]
5.  Iwata, K., Nojiri, H., Shimizu, K., Yoshida, T., Habe, H. and Omori, T. Expression, purification, and characterization of 2′-aminobiphenyl-2,3-diol 1,2-dioxygenase from carbazole-degrader Pseudomonas resinovorans strain CA10. Biosci. Biotechnol. Biochem. 67 (2003) 300–307. [PMID: 12728990]
[EC 1.13.11.39 created 1989]
 
 
EC 1.14.14.8
Accepted name: anthranilate 3-monooxygenase (FAD)
Reaction: anthranilate + FADH2 + O2 = 3-hydroxyanthranilate + FAD + H2O
Glossary: anthranilate = 2-aminobenzoate
Other name(s): anthranilate 3-hydroxylase; anthranilate hydroxylase
Systematic name: anthranilate,FADH2:oxygen oxidoreductase (3-hydroxylating)
Comments: This enzyme, isolated from the bacterium Geobacillus thermodenitrificans, participates in the pathway of tryptophan degradation. The enzyme is part of a system that also includes a bifunctional riboflavin kinase/FMN adenylyltransferase and an FAD reductase, which ensures ample supply of FAD to the monooxygenase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Liu, X., Dong, Y., Li, X., Ren, Y., Li, Y., Wang, W., Wang, L. and Feng, L. Characterization of the anthranilate degradation pathway in Geobacillus thermodenitrificans NG80-2. Microbiology 156 (2010) 589–595. [PMID: 19942660]
[EC 1.14.14.8 created 2010]
 
 
EC 1.14.99.41
Transferred entry: all-trans-8′-apo-β-carotenal 15,15′-oxygenase. Now EC 1.13.11.75, all-trans-8′-apo-β-carotenal 15,15′-oxygenase
[EC 1.14.99.41 created 2010, deleted 2013]
 
 
EC 2.1.1.48
Transferred entry: rRNA (adenine-N6-)-methyltransferase. Now covered by EC 2.1.1.181 [23S rRNA (adenine1618-N6)-methyltransferase], EC 2.1.1.182 [16S rRNA adenine1518-N6/adenine1519-N6)-dimethyltransferase], EC 2.1.1.183 [18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase] and EC 2.1.1.184 [23S rRNA (adenine2085-N6)-dimethyltransferase]
[EC 2.1.1.48 created 1976, deleted 2010]
 
 
EC 2.1.1.51
Transferred entry: rRNA (guanine-N1-)-methyltransferase. Now covered by EC 2.1.1.187 [23S rRNA (guanine745-N1)-methyltransferase] and EC 2.1.1.188 [23S rRNA (guanine748-N1)-methyltransferase].
[EC 2.1.1.51 created 1976, deleted 2010]
 
 
*EC 2.1.1.148
Accepted name: thymidylate synthase (FAD)
Reaction: 5,10-methylenetetrahydrofolate + dUMP + NADPH + H+ = dTMP + tetrahydrofolate + NADP+
For diagram of C1 metabolism, click here
Other name(s): Thy1; ThyX
Systematic name: 5,10-methylenetetrahydrofolate,FADH2:dUMP C-methyltransferase
Comments: Contains FAD. All thymidylate synthases catalyse a reductive methylation involving the transfer of the methylene group of 5,10-methylenetetrahydrofolate to the C5 position of dUMP and a two electron reduction of the methylene group to a methyl group. Unlike the classical thymidylate synthase, ThyA (EC 2.1.1.45), which uses folate as both a 1-carbon donor and a source of reducing equivalents, this enzyme uses a flavin coenzyme as a source of reducing equivalents, which are derived from NADPH.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 850167-13-4
References:
1.  Myllykallio, H., Lipowski, G., Leduc, D., Filee, J., Forterre, P. and Liebl, U. An alternative flavin-dependent mechanism for thymidylate synthesis. Science 297 (2002) 105–107. [PMID: 12029065]
2.  Griffin, J., Roshick, C., Iliffe-Lee, E. and McClarty, G. Catalytic mechanism of Chlamydia trachomatis flavin-dependent thymidylate synthase. J. Biol. Chem. 280 (2005) 5456–5467. [PMID: 15591067]
3.  Graziani, S., Bernauer, J., Skouloubris, S., Graille, M., Zhou, C.Z., Marchand, C., Decottignies, P., van Tilbeurgh, H., Myllykallio, H. and Liebl, U. Catalytic mechanism and structure of viral flavin-dependent thymidylate synthase ThyX. J. Biol. Chem. 281 (2006) 24048–24057. [PMID: 16707489]
4.  Koehn, E.M., Fleischmann, T., Conrad, J.A., Palfey, B.A., Lesley, S.A., Mathews, I.I. and Kohen, A. An unusual mechanism of thymidylate biosynthesis in organisms containing the thyX gene. Nature 458 (2009) 919–923. [PMID: 19370033]
5.  Koehn, E.M. and Kohen, A. Flavin-dependent thymidylate synthase: a novel pathway towards thymine. Arch. Biochem. Biophys. 493 (2010) 96–102. [PMID: 19643076]
6.  Mishanina, T.V., Yu, L., Karunaratne, K., Mondal, D., Corcoran, J.M., Choi, M.A. and Kohen, A. An unprecedented mechanism of nucleotide methylation in organisms containing thyX. Science 351 (2016) 507–510. [PMID: 26823429]
[EC 2.1.1.148 created 2003, modified 2010]
 
 
EC 2.1.1.175
Accepted name: tricin synthase
Reaction: 2 S-adenosyl-L-methionine + tricetin = 2 S-adenosyl-L-homocysteine + 3′,5′-O-dimethyltricetin (overall reaction)
(1a) S-adenosyl-L-methionine + tricetin = S-adenosyl-L-homocysteine + 3′-O-methyltricetin
(1b) S-adenosyl-L-methionine + 3′-O-methyltricetin = S-adenosyl-L-homocysteine + 3′,5′-O-dimethyltricetin
Glossary: tricin = 3′,5′-O-dimethyltricetin
Other name(s): ROMT-17; ROMT-15; HvOMT1; ZmOMT1
Systematic name: S-adenosyl-L-methionine:tricetin 3′,5′-O-dimethyltransferase
Comments: The enzymes from Oryza sativa (ROMT-15 and ROMT-17) catalyses the stepwise methylation of tricetin to its 3′-mono- and 3′,5′-dimethyl ethers. In contrast with the wheat enzyme (EC 2.1.1.169, tricetin 3′,4′,5′-O-trimethyltransferase), tricetin dimethyl ether is not converted to its 3′,4′,5′-trimethylated ether derivative [1]. The enzymes from Hordeum vulgare (HvOMT1) and from Zea mays (ZmOMT1) form the 3′,5′-dimethyl derivative as the major product [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Lee, Y.J., Kim, B.G., Chong, Y., Lim, Y. and Ahn, J.H. Cation dependent O-methyltransferases from rice. Planta 227 (2008) 641–647. [PMID: 17943312]
2.  Zhou, J.-M., Fukushi, Y., Wollenweber, E., Ibrahim, R.K. Characterization of two O-methyltransferase-like genes in barley and maize. Pharm. Biol. 46 (2008) 26–34.
[EC 2.1.1.175 created 2010]
 
 
EC 2.1.1.176
Accepted name: 16S rRNA (cytosine967-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytosine967 in 16S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine967 in 16S rRNA
Other name(s): rsmB (gene name); fmu (gene name); 16S rRNA m5C967 methyltransferase
Systematic name: S-adenosyl-L-methionine:16S rRNA (cytosine967-C5)-methyltransferase
Comments: The enzyme specifically methylates cytosine967 at C5 in 16S rRNA.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Tscherne, J.S., Nurse, K., Popienick, P., Michel, H., Sochacki, M. and Ofengand, J. Purification, cloning, and characterization of the 16S RNA m5C967 methyltransferase from Escherichia coli. Biochemistry 38 (1999) 1884–1892. [PMID: 10026269]
2.  Gu, X.R., Gustafsson, C., Ku, J., Yu, M. and Santi, D.V. Identification of the 16S rRNA m5C967 methyltransferase from Escherichia coli. Biochemistry 38 (1999) 4053–4057. [PMID: 10194318]
3.  Foster, P.G., Nunes, C.R., Greene, P., Moustakas, D. and Stroud, R.M. The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate. Structure 11 (2003) 1609–1620. [PMID: 14656444]
[EC 2.1.1.176 created 2010]
 
 
EC 2.1.1.177
Accepted name: 23S rRNA (pseudouridine1915-N3)-methyltransferase
Reaction: S-adenosyl-L-methionine + pseudouridine1915 in 23S rRNA = S-adenosyl-L-homocysteine + N3-methylpseudouridine1915 in 23S rRNA
Other name(s): YbeA; RlmH; pseudouridine methyltransferase; m3Ψ methyltransferase; Ψ1915-specific methyltransferase; rRNA large subunit methyltransferase H
Systematic name: S-adenosyl-L-methionine:23S rRNA (pseudouridine1915-N3)-methyltransferase
Comments: YbeA does not methylate uridine at position 1915 [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ero, R., Peil, L., Liiv, A. and Remme, J. Identification of pseudouridine methyltransferase in Escherichia coli. RNA 14 (2008) 2223–2233. [PMID: 18755836]
2.  Purta, E., Kaminska, K.H., Kasprzak, J.M., Bujnicki, J.M. and Douthwaite, S. YbeA is the m3Ψ methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. RNA 14 (2008) 2234–2244. [PMID: 18755835]
[EC 2.1.1.177 created 2010]
 
 
EC 2.1.1.178
Accepted name: 16S rRNA (cytosine1407-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytosine1407 in 16S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
Other name(s): RNA m5C methyltransferase YebU; RsmF; YebU
Systematic name: S-adenosyl-L-methionine:16S rRNA (cytosine1407-C5)-methyltransferase
Comments: The enzyme specifically methylates cytosine1407 at C5 in 16S rRNA.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Andersen, N.M. and Douthwaite, S. YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407. J. Mol. Biol. 359 (2006) 777–786. [PMID: 16678201]
2.  Hallberg, B.M., Ericsson, U.B., Johnson, K.A., Andersen, N.M., Douthwaite, S., Nordlund, P., Beuscher, A.E., 4th and Erlandsen, H. The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain. J. Mol. Biol. 360 (2006) 774–787. [PMID: 16793063]
[EC 2.1.1.178 created 2010]
 
 
EC 2.1.1.179
Accepted name: 16S rRNA (guanine1405-N7)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine1405 in 16S rRNA = S-adenosyl-L-homocysteine + N7-methylguanine1405 in 16S rRNA
Other name(s): methyltransferase Sgm; m7G1405 Mtase; Sgm Mtase; Sgm; sisomicin-gentamicin methyltransferase; sisomicin-gentamicin methylase; GrmA; RmtB; RmtC; ArmA
Systematic name: S-adenosyl-L-methionine:16S rRNA (guanine1405-N7)-methyltransferase
Comments: The enzyme from the antibiotic-producing bacterium Micromonospora zionensis specifically methylates guanine1405 at N7 in 16S rRNA, thereby rendering the ribosome resistant to 4,6-disubstituted deoxystreptamine aminoglycosides, which include gentamicins and kanamycins [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Husain, N., Tkaczuk, K.L., Tulsidas, S.R., Kaminska, K.H., Cubrilo, S., Maravic-Vlahovicek, G., Bujnicki, J.M. and Sivaraman, J. Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m7G methyltransferases. Nucleic Acids Res. 38 (2010) 4120–4132. [PMID: 20194115]
2.  Savic, M., Lovric, J., Tomic, T.I., Vasiljevic, B. and Conn, G.L. Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics. Nucleic Acids Res. 37 (2009) 5420–5431. [PMID: 19589804]
3.  Tomic, T.I., Moric, I., Conn, G.L. and Vasiljevic, B. Aminoglycoside resistance genes sgm and kgmB protect bacterial but not yeast small ribosomal subunits in vitro despite high conservation of the rRNA A-site. Res. Microbiol. 159 (2008) 658–662. [PMID: 18930134]
4.  Savic, M., Ilic-Tomic, T., Macmaster, R., Vasiljevic, B. and Conn, G.L. Critical residues for cofactor binding and catalytic activity in the aminoglycoside resistance methyltransferase Sgm. J. Bacteriol. 190 (2008) 5855–5861. [PMID: 18586937]
5.  Maravic Vlahovicek, G., Cubrilo, S., Tkaczuk, K.L. and Bujnicki, J.M. Modeling and experimental analyses reveal a two-domain structure and amino acids important for the activity of aminoglycoside resistance methyltransferase Sgm. Biochim. Biophys. Acta 1784 (2008) 582–590. [PMID: 18343347]
6.  Kojic, M., Topisirovic, L. and Vasiljevic, B. Cloning and characterization of an aminoglycoside resistance determinant from Micromonospora zionensis. J. Bacteriol. 174 (1992) 7868–7872. [PMID: 1447159]
7.  Schmitt, E., Galimand, M., Panvert, M., Courvalin, P. and Mechulam, Y. Structural bases for 16 S rRNA methylation catalyzed by ArmA and RmtB methyltransferases. J. Mol. Biol. 388 (2009) 570–582. [PMID: 19303884]
8.  Wachino, J., Shibayama, K., Kimura, K., Yamane, K., Suzuki, S. and Arakawa, Y. RmtC introduces G1405 methylation in 16S rRNA and confers high-level aminoglycoside resistance on Gram-positive microorganisms. FEMS Microbiol. Lett. 311 (2010) 56–60. [PMID: 20722735]
9.  Liou, G.F., Yoshizawa, S., Courvalin, P. and Galimand, M. Aminoglycoside resistance by ArmA-mediated ribosomal 16S methylation in human bacterial pathogens. J. Mol. Biol. 359 (2006) 358–364. [PMID: 16626740]
[EC 2.1.1.179 created 2010]
 
 
EC 2.1.1.180
Accepted name: 16S rRNA (adenine1408-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenine1408 in 16S rRNA = S-adenosyl-L-homocysteine + N1-methyladenine1408 in 16S rRNA
Other name(s): kanamycin-apramycin resistance methylase; 16S rRNA:m1A1408 methyltransferase; KamB; NpmA; 16S rRNA m1A1408 methyltransferase
Systematic name: S-adenosyl-L-methionine:16S rRNA (adenine1408-N1)-methyltransferase
Comments: The enzyme provides a panaminoglycoside-resistant nature through interference with the binding of aminoglycosides toward the A site of 16S rRNA through N1-methylation at position adenine1408 [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Beauclerk, A.A. and Cundliffe, E. Sites of action of two ribosomal RNA methylases responsible for resistance to aminoglycosides. J. Mol. Biol. 193 (1987) 661–671. [PMID: 2441068]
2.  Koscinski, L., Feder, M. and Bujnicki, J.M. Identification of a missing sequence and functionally important residues of 16S rRNA:m1A1408 methyltransferase KamB that causes bacterial resistance to aminoglycoside antibiotics. Cell Cycle 6 (2007) 1268–1271. [PMID: 17495534]
3.  Holmes, D.J., Drocourt, D., Tiraby, G. and Cundliffe, E. Cloning of an aminoglycoside-resistance-encoding gene, kamC, from Saccharopolyspora hirsuta: comparison with kamB from Streptomyces tenebrarius. Gene 102 (1991) 19–26. [PMID: 1840536]
4.  Wachino, J., Shibayama, K., Kurokawa, H., Kimura, K., Yamane, K., Suzuki, S., Shibata, N., Ike, Y. and Arakawa, Y. Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse aminoglycosides. Antimicrob. Agents Chemother. 51 (2007) 4401–4409. [PMID: 17875999]
[EC 2.1.1.180 created 2010]
 
 
EC 2.1.1.181
Accepted name: 23S rRNA (adenine1618-N6)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenine1618 in 23S rRNA = S-adenosyl-L-homocysteine + N6-methyladenine1618 in 23S rRNA
Other name(s): rRNA large subunit methyltransferase F; YbiN protein; rlmF (gene name); m6A1618 methyltransferase
Systematic name: S-adenosyl-L-methionine:23S rRNA (adenine1618-N6)-methyltransferase
Comments: The recombinant YbiN protein is able to methylate partially deproteinized 50 S ribosomal subunit, but neither the completely assembled 50 S subunits nor completely deproteinized 23 S rRNA [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sergiev, P.V., Serebryakova, M.V., Bogdanov, A.A. and Dontsova, O.A. The ybiN gene of Escherichia coli encodes adenine-N6 methyltransferase specific for modification of A1618 of 23 S ribosomal RNA, a methylated residue located close to the ribosomal exit tunnel. J. Mol. Biol. 375 (2008) 291–300. [PMID: 18021804]
[EC 2.1.1.181 created 1976 as EC 2.1.1.48, part transferred 2010 to EC 2.1.1.181]
 
 
EC 2.1.1.182
Accepted name: 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
Reaction: 4 S-adenosyl-L-methionine + adenine1518/adenine1519 in 16S rRNA = 4 S-adenosyl-L-homocysteine + N6-dimethyladenine1518/N6-dimethyladenine1519 in 16S rRNA
Other name(s): S-adenosylmethionine-6-N′,N′-adenosyl (rRNA) dimethyltransferase; KsgA; ksgA methyltransferase
Systematic name: S-adenosyl-L-methionine:16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
Comments: KsgA introduces the most highly conserved ribosomal RNA modification, the dimethylation of adenine1518 and adenine1519 in 16S rRNA. Strains lacking the methylase are resistant to kasugamycin [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Helser, T.L., Davies, J.E. and Dahlberg, J.E. Change in methylation of 16S ribosomal RNA associated with mutation to kasugamycin resistance in Escherichia coli. Nat. New Biol. 233 (1971) 12–14. [PMID: 4329247]
2.  Helser, T.L., Davies, J.E. and Dahlberg, J.E. Mechanism of kasugamycin resistance in Escherichia coli. Nat. New Biol. 235 (1972) 6–9. [PMID: 4336392]
3.  van Buul, C.P. and van Knippenberg, P.H. Nucleotide sequence of the ksgA gene of Escherichia coli: comparison of methyltransferases effecting dimethylation of adenosine in ribosomal RNA. Gene 38 (1985) 65–72. [PMID: 3905517]
4.  Formenoy, L.J., Cunningham, P.R., Nurse, K., Pleij, C.W. and Ofengand, J. Methylation of the conserved A1518-A1519 in Escherichia coli 16S ribosomal RNA by the ksgA methyltransferase is influenced by methylations around the similarly conserved U1512.G1523 base pair in the 3′ terminal hairpin. Biochimie 76 (1994) 1123–1128. [PMID: 7538324]
5.  O'Farrell, H.C., Scarsdale, J.N. and Rife, J.P. Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli. J. Mol. Biol. 339 (2004) 337–353. [PMID: 15136037]
6.  Poldermans, B., Roza, L. and Van Knippenberg, P.H. Studies on the function of two adjacent N6,N6-dimethyladenosines near the 3′ end of 16 S ribosomal RNA of Escherichia coli. III. Purification and properties of the methylating enzyme and methylase-30 S interactions. J. Biol. Chem. 254 (1979) 9094–9100. [PMID: 383712]
7.  Demirci, H., Belardinelli, R., Seri, E., Gregory, S.T., Gualerzi, C., Dahlberg, A.E. and Jogl, G. Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5′-methylthioadenosine. J. Mol. Biol. 388 (2009) 271–282. [PMID: 19285505]
8.  Tu, C., Tropea, J.E., Austin, B.P., Court, D.L., Waugh, D.S. and Ji, X. Structural basis for binding of RNA and cofactor by a KsgA methyltransferase. Structure 17 (2009) 374–385. [PMID: 19278652]
[EC 2.1.1.182 created 1976 as EC 2.1.1.48, part transferred 2010 to EC 2.1.1.182]
 
 
EC 2.1.1.183
Accepted name: 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase
Reaction: 4 S-adenosyl-L-methionine + adenine1779/adenine1780 in 18S rRNA = 4 S-adenosyl-L-homocysteine + N6-dimethyladenine1779/N6-dimethyladenine1780 in 18S rRNA
Other name(s): 18S rRNA dimethylase Dim1p; Dim1p; ScDim1; m2(6)A dimethylase; KIDIM1
Systematic name: S-adenosyl-L-methionine:18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase
Comments: DIM1 is involved in pre-rRNA processing [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Lafontaine, D., Vandenhaute, J. and Tollervey, D. The 18S rRNA dimethylase Dim1p is required for pre-ribosomal RNA processing in yeast. Genes Dev. 9 (1995) 2470–2481. [PMID: 7590228]
2.  Lafontaine, D.L., Preiss, T. and Tollervey, D. Yeast 18S rRNA dimethylase Dim1p: a quality control mechanism in ribosome synthesis. Mol. Cell Biol. 18 (1998) 2360–2370. [PMID: 9528805]
3.  Pulicherla, N., Pogorzala, L.A., Xu, Z., O'Farrell, H.C., Musayev, F.N., Scarsdale, J.N., Sia, E.A., Culver, G.M. and Rife, J.P. Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases. J. Mol. Biol. 391 (2009) 884–893. [PMID: 19520088]
4.  Lafontaine, D., Delcour, J., Glasser, A.L., Desgres, J. and Vandenhaute, J. The DIM1 gene responsible for the conserved m6(2)Am6(2)A dimethylation in the 3′-terminal loop of 18 S rRNA is essential in yeast. J. Mol. Biol. 241 (1994) 492–497. [PMID: 8064863]
5.  O'Farrell, H.C., Pulicherla, N., Desai, P.M. and Rife, J.P. Recognition of a complex substrate by the KsgA/Dim1 family of enzymes has been conserved throughout evolution. RNA 12 (2006) 725–733. [PMID: 16540698]
[EC 2.1.1.183 created 1976 as EC 2.1.1.48, part transferred 2010 to EC 2.1.1.183]
 
 
EC 2.1.1.184
Accepted name: 23S rRNA (adenine2085-N6)-dimethyltransferase
Reaction: 2 S-adenosyl-L-methionine + adenine2085 in 23S rRNA = 2 S-adenosyl-L-homocysteine + N6-dimethyladenine2085 in 23S rRNA
Other name(s): ErmC′ methyltransferase; ermC methylase; ermC 23S rRNA methyltransferase; rRNA:m6A methyltransferase ErmC′; ErmC′; rRNA methyltransferase ErmC′
Systematic name: S-adenosyl-L-methionine:23S rRNA (adenine2085-N6)-dimethyltransferase
Comments: ErmC is a methyltransferase that confers resistance to the macrolide-lincosamide-streptogramin B group of antibiotics by catalysing the methylation of 23S rRNA at adenine2085.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Zhong, P., Pratt, S.D., Edalji, R.P., Walter, K.A., Holzman, T.F., Shivakumar, A.G. and Katz, L. Substrate requirements for ErmC′ methyltransferase activity. J. Bacteriol. 177 (1995) 4327–4332. [PMID: 7543473]
2.  Denoya, C. and Dubnau, D. Mono- and dimethylating activities and kinetic studies of the ermC 23 S rRNA methyltransferase. J. Biol. Chem. 264 (1989) 2615–2624. [PMID: 2492520]
3.  Denoya, C.D. and Dubnau, D. Site and substrate specificity of the ermC 23S rRNA methyltransferase. J. Bacteriol. 169 (1987) 3857–3860. [PMID: 2440853]
4.  Bussiere, D.E., Muchmore, S.W., Dealwis, C.G., Schluckebier, G., Nienaber, V.L., Edalji, R.P., Walter, K.A., Ladror, U.S., Holzman, T.F. and Abad-Zapatero, C. Crystal structure of ErmC′, an rRNA methyltransferase which mediates antibiotic resistance in bacteria. Biochemistry 37 (1998) 7103–7112. [PMID: 9585521]
5.  Schluckebier, G., Zhong, P., Stewart, K.D., Kavanaugh, T.J. and Abad-Zapatero, C. The 2.2 Å structure of the rRNA methyltransferase ErmC′ and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism. J. Mol. Biol. 289 (1999) 277–291. [PMID: 10366505]
6.  Maravic, G., Bujnicki, J.M., Feder, M., Pongor, S. and Flogel, M. Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC′ redefines the substrate-binding site and suggests a model for protein-RNA interactions. Nucleic Acids Res. 31 (2003) 4941–4949. [PMID: 12907737]
[EC 2.1.1.184 created 1976 as EC 2.1.1.48, part transferred 2010 to EC 2.1.1.184]
 
 
EC 2.1.1.185
Accepted name: 23S rRNA (guanosine2251-2′-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanosine2251 in 23S rRNA = S-adenosyl-L-homocysteine + 2′-O-methylguanosine2251 in 23S rRNA
Other name(s): rlmB (gene name); yifH (gene name)
Systematic name: S-adenosyl-L-methionine:23S rRNA (guanosine2251-2′-O-)-methyltransferase
Comments: The enzyme catalyses the methylation of guanosine2251, a modification conserved in the peptidyltransferase domain of 23S rRNA.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Lovgren, J.M. and Wikstrom, P.M. The rlmB gene is essential for formation of Gm2251 in 23S rRNA but not for ribosome maturation in Escherichia coli. J. Bacteriol. 183 (2001) 6957–6960. [PMID: 11698387]
2.  Michel, G., Sauve, V., Larocque, R., Li, Y., Matte, A. and Cygler, M. The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot. Structure 10 (2002) 1303–1315. [PMID: 12377117]
[EC 2.1.1.185 created 2010]
 
 
EC 2.1.1.186
Accepted name: 23S rRNA (cytidine2498-2′-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytidine2498 in 23S rRNA = S-adenosyl-L-homocysteine + 2′-O-methylcytidine2498 in 23S rRNA
Other name(s): YgdE; rRNA large subunit methyltransferase M; RlmM
Systematic name: S-adenosyl-L-methionine:23S rRNA (cytidine2498-2′-O-)-methyltransferase
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Purta, E., O'Connor, M., Bujnicki, J.M. and Douthwaite, S. YgdE is the 2′-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA. Mol. Microbiol. 72 (2009) 1147–1158. [PMID: 19400805]
[EC 2.1.1.186 created 2010]
 
 
EC 2.1.1.187
Accepted name: 23S rRNA (guanine745-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine745 in 23S rRNA = S-adenosyl-L-homocysteine + N1-methylguanine745 in 23S rRNA
Other name(s): Rlma(I); Rlma1; 23S rRNA m1G745 methyltransferase; YebH; RlmAI methyltransferase; ribosomal RNA(m1G)-methylase (ambiguous); rRNA(m1G)methylase (ambiguous); RrmA (ambiguous); 23S rRNA:m1G745 methyltransferase
Systematic name: S-adenosyl-L-methionine:23S rRNA (guanine745-N1)-methyltransferase
Comments: The enzyme specifically methylates guanine745 at N1 in 23S rRNA.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Liu, M., Novotny, G.W. and Douthwaite, S. Methylation of 23S rRNA nucleotide G745 is a secondary function of the RlmAI methyltransferase. RNA 10 (2004) 1713–1720. [PMID: 15388872]
2.  Gustafsson, C. and Persson, B.C. Identification of the rrmA gene encoding the 23S rRNA m1G745 methyltransferase in Escherichia coli and characterization of an m1G745-deficient mutant. J. Bacteriol. 180 (1998) 359–365. [PMID: 9440525]
3.  Das, K., Acton, T., Chiang, Y., Shih, L., Arnold, E. and Montelione, G.T. Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site. Proc. Natl. Acad. Sci. USA 101 (2004) 4041–4046. [PMID: 14999102]
4.  Hansen, L.H., Kirpekar, F. and Douthwaite, S. Recognition of nucleotide G745 in 23 S ribosomal RNA by the rrmA methyltransferase. J. Mol. Biol. 310 (2001) 1001–1010. [PMID: 11501991]
5.  Liu, M. and Douthwaite, S. Methylation at nucleotide G745 or G748 in 23S rRNA distinguishes Gram-negative from Gram-positive bacteria. Mol. Microbiol. 44 (2002) 195–204. [PMID: 11967079]
[EC 2.1.1.187 created 1976 as EC 2.1.1.51, part transferred 2010 to EC 2.1.1.187]
 
 
EC 2.1.1.188
Accepted name: 23S rRNA (guanine748-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine748 in 23S rRNA = S-adenosyl-L-homocysteine + N1-methylguanine748 in 23S rRNA
Other name(s): Rlma(II); Rlma2; 23S rRNA m1G748 methyltransferase; RlmaII; Rlma II; tylosin-resistance methyltransferase RlmA(II); TlrB; rRNA large subunit methyltransferase II
Systematic name: S-adenosyl-L-methionine:23S rRNA (guanine748-N1)-methyltransferase
Comments: The enzyme specifically methylates guanine748 at N1 in 23S rRNA. The methyltransferase RlmAII confers resistance to the macrolide antibiotic tylosin in the drug-producing strain Streptomyces fradiae [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Douthwaite, S., Crain, P.F., Liu, M. and Poehlsgaard, J. The tylosin-resistance methyltransferase RlmAII (TlrB) modifies the N-1 position of 23S rRNA nucleotide G748. J. Mol. Biol. 337 (2004) 1073–1077. [PMID: 15046978]
2.  Liu, M., Kirpekar, F., Van Wezel, G.P. and Douthwaite, S. The tylosin resistance gene tlrB of Streptomyces fradiae encodes a methyltransferase that targets G748 in 23S rRNA. Mol. Microbiol. 37 (2000) 811–820. [PMID: 10972803]
3.  Lebars, I., Yoshizawa, S., Stenholm, A.R., Guittet, E., Douthwaite, S. and Fourmy, D. Structure of 23S rRNA hairpin 35 and its interaction with the tylosin-resistance methyltransferase RlmAII. EMBO J. 22 (2003) 183–192. [PMID: 12514124]
4.  Lebars, I., Husson, C., Yoshizawa, S., Douthwaite, S. and Fourmy, D. Recognition elements in rRNA for the tylosin resistance methyltransferase RlmAII. J. Mol. Biol. 372 (2007) 525–534. [PMID: 17673230]
5.  Douthwaite, S., Jakobsen, L., Yoshizawa, S. and Fourmy, D. Interaction of the tylosin-resistance methyltransferase RlmAII at its rRNA target differs from the orthologue RlmAI. J. Mol. Biol. 378 (2008) 969–975. [PMID: 18406425]
6.  Liu, M. and Douthwaite, S. Methylation at nucleotide G745 or G748 in 23S rRNA distinguishes Gram-negative from Gram-positive bacteria. Mol. Microbiol. 44 (2002) 195–204. [PMID: 11967079]
[EC 2.1.1.188 created 1976 as EC 2.1.1.51, part transferred 2010 to EC 2.1.1.188]
 
 
EC 2.1.1.189
Accepted name: 23S rRNA (uracil747-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + uracil747 in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Other name(s): YbjF; RumB; RNA uridine methyltransferase B
Systematic name: S-adenosyl-L-methionine:23S rRNA (uracil747-C5)-methyltransferase
Comments: The enzyme specifically methylates uracil747 at C5 in 23S rRNA.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Madsen, C.T., Mengel-Jorgensen, J., Kirpekar, F. and Douthwaite, S. Identifying the methyltransferases for m5U747 and m5U1939 in 23S rRNA using MALDI mass spectrometry. Nucleic Acids Res. 31 (2003) 4738–4746. [PMID: 12907714]
[EC 2.1.1.189 created 2010]
 
 
EC 2.1.1.190
Accepted name: 23S rRNA (uracil1939-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + uracil1939 in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil1939 in 23S rRNA
Other name(s): RumA; RNA uridine methyltransferase A; YgcA
Systematic name: S-adenosyl-L-methionine:23S rRNA (uracil1939-C5)-methyltransferase
Comments: The enzyme specifically methylates uracil1939 at C5 in 23S rRNA [1]. The enzyme contains an [4Fe-4S] cluster coordinated by four conserved cysteine residues [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Agarwalla, S., Kealey, J.T., Santi, D.V. and Stroud, R.M. Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from Escherichia coli. J. Biol. Chem. 277 (2002) 8835–8840. [PMID: 11779873]
2.  Lee, T.T., Agarwalla, S. and Stroud, R.M. Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase. Structure 12 (2004) 397–407. [PMID: 15016356]
3.  Madsen, C.T., Mengel-Jorgensen, J., Kirpekar, F. and Douthwaite, S. Identifying the methyltransferases for m5U747 and m5U1939 in 23S rRNA using MALDI mass spectrometry. Nucleic Acids Res. 31 (2003) 4738–4746. [PMID: 12907714]
4.  Persaud, C., Lu, Y., Vila-Sanjurjo, A., Campbell, J.L., Finley, J. and O'Connor, M. Mutagenesis of the modified bases, m5U1939 and Ψ2504, in Escherichia coli 23S rRNA. Biochem. Biophys. Res. Commun. 392 (2010) 223–227. [PMID: 20067766]
5.  Agarwalla, S., Stroud, R.M. and Gaffney, B.J. Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies. J. Biol. Chem. 279 (2004) 34123–34129. [PMID: 15181002]
6.  Lee, T.T., Agarwalla, S. and Stroud, R.M. A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. Cell 120 (2005) 599–611. [PMID: 15766524]
[EC 2.1.1.190 created 2010]
 
 
EC 2.1.1.191
Accepted name: 23S rRNA (cytosine1962-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytosine1962 in 23S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine1962 in 23S rRNA
Other name(s): RlmI; rRNA large subunit methyltransferase I; YccW
Systematic name: S-adenosyl-L-methionine:23S rRNA (cytosine1962-C5)-methyltransferase
Comments: The enzyme specifically methylates cytosine1962 at C5 in 23S rRNA.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Purta, E., O'Connor, M., Bujnicki, J.M. and Douthwaite, S. YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962. J. Mol. Biol. 383 (2008) 641–651. [PMID: 18786544]
2.  Sunita, S., Tkaczuk, K.L., Purta, E., Kasprzak, J.M., Douthwaite, S., Bujnicki, J.M. and Sivaraman, J. Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes. J. Mol. Biol. 383 (2008) 652–666. [PMID: 18789337]
[EC 2.1.1.191 created 2010]
 
 
EC 2.1.1.192
Accepted name: 23S rRNA (adenine2503-C2)-methyltransferase
Reaction: (1) 2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin = S-adenosyl-L-homocysteine + L-methionine + 5′-deoxyadenosine + 2-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
(2) 2 S-adenosyl-L-methionine + adenine37 in tRNA + 2 reduced [2Fe-2S] ferredoxin = S-adenosyl-L-homocysteine + L-methionine + 5′-deoxyadenosine + 2-methyladenine37 in tRNA + 2 oxidized [2Fe-2S] ferredoxin
Other name(s): RlmN; YfgB; Cfr
Systematic name: S-adenosyl-L-methionine:23S rRNA (adenine2503-C2)-methyltransferase
Comments: Contains an [4Fe-4S] cluster [2]. This enzyme is a member of the ’AdoMet radical’ (radical SAM) family. S-Adenosyl-L-methionine acts as both a radical generator and as the source of the appended methyl group. RlmN first transfers an CH2 group to a conserved cysteine (Cys355 in Escherichia coli) [6], the generated radical from a second S-adenosyl-L-methionine then attacks the methyl group, exctracting a hydrogen. The formed radical forms a covalent intermediate with the adenine group of the tRNA [9]. RlmN is an endogenous enzyme used by the cell to refine functions of the ribosome in protein synthesis [2]. The enzyme methylates adenosine by a radical mechanism with CH2 from the S-adenosyl-L-methionine and retention of the hydrogen at C-2 of adenosine2503 of 23S rRNA. It will also methylate 8-methyladenosine2503 of 23S rRNA. cf. EC 2.1.1.224 [23S rRNA (adenine2503-C8)-methyltransferase].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Toh, S.M., Xiong, L., Bae, T. and Mankin, A.S. The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA. RNA 14 (2008) 98–106. [PMID: 18025251]
2.  Yan, F., LaMarre, J.M., Röhrich, R., Wiesner, J., Jomaa, H., Mankin, A.S. and Fujimori, D.G. RlmN and Cfr are radical SAM enzymes involved in methylation of ribosomal RNA. J. Am. Chem. Soc. 132 (2010) 3953–3964. [PMID: 20184321]
3.  Yan, F. and Fujimori, D.G. RNA methylation by radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift. Proc. Natl. Acad. Sci. USA 108 (2011) 3930–3934. [PMID: 21368151]
4.  Grove, T.L., Benner, J.S., Radle, M.I., Ahlum, J.H., Landgraf, B.J., Krebs, C. and Booker, S.J. A radically different mechanism for S-adenosylmethionine-dependent methyltransferases. Science 332 (2011) 604–607. [PMID: 21415317]
5.  Boal, A.K., Grove, T.L., McLaughlin, M.I., Yennawar, N.H., Booker, S.J. and Rosenzweig, A.C. Structural basis for methyl transfer by a radical SAM enzyme. Science 332 (2011) 1089–1092. [PMID: 21527678]
6.  Grove, T.L., Radle, M.I., Krebs, C. and Booker, S.J. Cfr and RlmN contain a single [4Fe-4S] cluster, which directs two distinct reactivities for S-adenosylmethionine: methyl transfer by SN2 displacement and radical generation. J. Am. Chem. Soc. 133 (2011) 19586–19589. [PMID: 21916495]
7.  McCusker, K.P., Medzihradszky, K.F., Shiver, A.L., Nichols, R.J., Yan, F., Maltby, D.A., Gross, C.A. and Fujimori, D.G. Covalent intermediate in the catalytic mechanism of the radical S-adenosyl-L-methionine methyl synthase RlmN trapped by mutagenesis. J. Am. Chem. Soc. 134 (2012) 18074–18081. [PMID: 23088750]
8.  Benitez-Paez, A., Villarroya, M. and Armengod, M.E. The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy. RNA 18 (2012) 1783–1795. [PMID: 22891362]
9.  Silakov, A., Grove, T.L., Radle, M.I., Bauerle, M.R., Green, M.T., Rosenzweig, A.C., Boal, A.K. and Booker, S.J. Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN. J. Am. Chem. Soc. 136 (2014) 8221–8228. [PMID: 24806349]
[EC 2.1.1.192 created 2010, modified 2011, modified 2014]
 
 
EC 2.1.1.193
Accepted name: 16S rRNA (uracil1498-N3)-methyltransferase
Reaction: S-adenosyl-L-methionine + uracil1498 in 16S rRNA = S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
For diagram of fumitremorgin alkaloid biosynthesis (part 1), click here
Other name(s): DUF558 protein; YggJ; RsmE; m3U1498 specific methyltransferase
Systematic name: S-adenosyl-L-methionine:16S rRNA (uracil1498-N3)-methyltransferase
Comments: The enzyme specifically methylates uracil1498 at N3 in 16S rRNA.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Basturea, G.N., Rudd, K.E. and Deutscher, M.P. Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family. RNA 12 (2006) 426–434. [PMID: 16431987]
2.  Basturea, G.N. and Deutscher, M.P. Substrate specificity and properties of the Escherichia coli 16S rRNA methyltransferase, RsmE. RNA 13 (2007) 1969–1976. [PMID: 17872509]
[EC 2.1.1.193 created 2010]
 
 
EC 2.1.1.194
Deleted entry: 23S rRNA (adenine2503-C2,C8)-dimethyltransferase. A mixture of EC 2.1.1.192 (23S rRNA (adenine2503-C2)-methyltransferase) and EC 2.1.1.224 (23S rRNA (adenine2503-C8)-methyltransferase)
[EC 2.1.1.194 created 2010, deleted 2011]
 
 
*EC 2.4.1.94
Accepted name: protein N-acetylglucosaminyltransferase
Reaction: UDP-N-acetyl-D-glucosamine + [protein]-L-asparagine = UDP + [protein]-N4-(N-acetyl-D-glucosaminyl)-L-asparagine
Other name(s): uridine diphosphoacetylglucosamine-protein acetylglucosaminyltransferase; uridine diphospho-N-acetylglucosamine:polypeptide β-N-acetylglucosaminyltransferase; N-acetylglucosaminyltransferase I
Systematic name: UDP-N-acetyl-D-glucosamine:[protein]-L-asparagine β-N-acetyl-D-glucosaminyl-transferase
Comments: The acceptor is the asparagine residue in a sequence of the form Asn-Xaa-Thr or Asn-Xaa-Ser.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 72319-34-7
References:
1.  Khalkhali, Z. and Marshall, R.D. Glycosylation of ribonuclease A catalysed by rabbit liver extracts. Biochem. J. 146 (1975) 299–307. [PMID: 1156375]
2.  Khalkhali, Z. and Marshall, R.D. UDP-N-acetyl-D-glucosamine-asparagine sequon N-acetyl-β-D-glucosaminyl-transferase-activity in human serum. Carbohydr. Res. 49 (1976) 455–473. [PMID: 986874]
3.  Khalkhali, Z., Marshall, R.D., Reuvers, F., Habets-Willems, C. and Boer, P. Glycosylation in vitro of an asparagine sequon catalysed by preparations of yeast cell membranes. Biochem. J. 160 (1976) 37–41. [PMID: 795426]
[EC 2.4.1.94 created 1978, modified 2010]
 
 
*EC 2.5.1.10
Accepted name: (2E,6E)-farnesyl diphosphate synthase
Reaction: geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2E,6E)-farnesyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): farnesyl-diphosphate synthase; geranyl transferase I; prenyltransferase; farnesyl pyrophosphate synthetase; farnesylpyrophosphate synthetase; geranyltranstransferase
Systematic name: geranyl-diphosphate:isopentenyl-diphosphate geranyltranstransferase
Comments: Some forms of this enzyme will also use dimethylallyl diphosphate as a substrate. The enzyme will not accept larger prenyl diphosphates as efficient donors.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 37277-79-5
References:
1.  Lynen, F., Agranoff, B.W., Eggerer, H., Henning, V. and Möslein, E.M. Zur Biosynthese der Terpene. VI. γ,γ-Dimethyl-allyl-pyrophosphat und Geranyl-pyrophosphat, biologische Vorstufen des Squalens. Angew. Chem. 71 (1959) 657–663.
2.  Ogura, K., Nishino, T. and Seto, S. The purification of prenyltransferase and isopentenyl pyrophosphate isomerase of pumpkin fruit and their some properties. J. Biochem. (Tokyo) 64 (1968) 197–203. [PMID: 4303505]
3.  Reed, B.C. and Rilling, H. Crystallization and partial characterization of prenyltransferase from avian liver. Biochemistry 14 (1975) 50–54. [PMID: 1109590]
4.  Takahashi, I. and Ogura, K. Farnesyl pyrophosphate synthetase from Bacillus subtilis. J. Biochem. (Tokyo) 89 (1981) 1581–1587. [PMID: 6792191]
5.  Takahashi, I. and Ogura, K. Prenyltransferases of Bacillus subtilis: undecaprenyl pyrophosphate synthetase and geranylgeranyl pyrophosphate synthetase. J. Biochem. (Tokyo) 92 (1982) 1527–1537. [PMID: 6818223]
[EC 2.5.1.10 created 1972, modified 2010]
 
 
EC 2.5.1.11
Transferred entry: trans-octaprenyltranstransferase. Now covered by EC 2.5.1.84 (all-trans-nonaprenyl-diphosphate synthase [geranyl-diphosphate specific]) and EC 2.5.1.85 (all-trans-nonaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific])
[EC 2.5.1.11 created 1972, deleted 2010]
 
 
*EC 2.5.1.30
Accepted name: heptaprenyl diphosphate synthase
Reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): all-trans-heptaprenyl-diphosphate synthase; heptaprenyl pyrophosphate synthase; heptaprenyl pyrophosphate synthetase; HepPP synthase; HepPS; heptaprenylpyrophosphate synthetase
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 4 isopentenyl units)
Comments: This enzyme catalyses the condensation reactions resulting in the formation of all-trans-heptaprenyl diphosphate, the isoprenoid side chain of ubiquinone-7 and menaquinone-7. The enzyme adds four isopentenyl diphosphate molecules sequentially to farnesyl diphosphate with trans stereochemistry.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 74506-59-5
References:
1.  Takahashi, I., Ogura, K. and Seto, S. Heptaprenyl pyrophosphate synthetase from Bacillus subtilis. J. Biol. Chem. 255 (1980) 4539–4543. [PMID: 6768722]
2.  Zhang, Y.W., Koyama, T., Marecak, D.M., Prestwich, G.D., Maki, Y. and Ogura, K. Two subunits of heptaprenyl diphosphate synthase of Bacillus subtilis form a catalytically active complex. Biochemistry 37 (1998) 13411–13420. [PMID: 9748348]
3.  Zhang, Y.W., Li, X.Y., Sugawara, H. and Koyama, T. Site-directed mutagenesis of the conserved residues in component I of Bacillus subtilis heptaprenyl diphosphate synthase. Biochemistry 38 (1999) 14638–14643. [PMID: 10545188]
4.  Suzuki, T., Zhang, Y.W., Koyama, T., Sasaki, D.Y. and Kurihara, K. Direct observation of substrate-enzyme complexation by surface forces measurement. J. Am. Chem. Soc. 128 (2006) 15209–15214. [PMID: 17117872]
[EC 2.5.1.30 created 1984, modified 2010]
 
 
*EC 2.5.1.31
Accepted name: ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
Reaction: (2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate = 8 diphosphate + ditrans,octacis-undecaprenyl diphosphate
For diagram of di- and tritrans,polycis-polyprenol biosynthesis, click here
Other name(s): di-trans,poly-cis-undecaprenyl-diphosphate synthase; undecaprenyl-diphosphate synthase; bactoprenyl-diphosphate synthase; UPP synthetase; undecaprenyl diphosphate synthetase; undecaprenyl pyrophosphate synthetase; di-trans,poly-cis-decaprenylcistransferase
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 8 isopentenyl units)
Comments: Undecaprenyl pyrophosphate synthase catalyses the consecutive condensation reactions of a farnesyl diphosphate with eight isopentenyl diphosphates, in which new cis-double bonds are formed, to generate undecaprenyl diphosphate that serves as a lipid carrier for peptidoglycan synthesis of bacterial cell wall [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 52350-87-5
References:
1.  Muth, J.D. and Allen, C.M. Undecaprenyl pyrophosphate synthetase from Lactobacillus plantarum: a dimeric protein. Arch. Biochem. Biophys. 230 (1984) 49–60. [PMID: 6712246]
2.  Takahashi, I. and Ogura, K. Prenyltransferases of Bacillus subtilis: undecaprenyl pyrophosphate synthetase and geranylgeranyl pyrophosphate synthetase. J. Biochem. (Tokyo) 92 (1982) 1527–1537. [PMID: 6818223]
3.  Guo, R.T., Ko, T.P., Chen, A.P., Kuo, C.J., Wang, A.H. and Liang, P.H. Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate, and farnesyl thiopyrophosphate: roles of the metal ion and conserved residues in catalysis. J. Biol. Chem. 280 (2005) 20762–20774. [PMID: 15788389]
4.  Ko, T.P., Chen, Y.K., Robinson, H., Tsai, P.C., Gao, Y.G., Chen, A.P., Wang, A.H. and Liang, P.H. Mechanism of product chain length determination and the role of a flexible loop in Escherichia coli undecaprenyl-pyrophosphate synthase catalysis. J. Biol. Chem. 276 (2001) 47474–47482. [PMID: 11581264]
5.  Fujikura, K., Zhang, Y.W., Fujihashi, M., Miki, K. and Koyama, T. Mutational analysis of allylic substrate binding site of Micrococcus luteus B-P 26 undecaprenyl diphosphate synthase. Biochemistry 42 (2003) 4035–4041. [PMID: 12680756]
6.  Fujihashi, M., Zhang, Y.W., Higuchi, Y., Li, X.Y., Koyama, T. and Miki, K. Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase. Proc. Natl. Acad. Sci. USA 98 (2001) 4337–4342. [PMID: 11287651]
7.  Pan, J.J., Chiou, S.T. and Liang, P.H. Product distribution and pre-steady-state kinetic analysis of Escherichia coli undecaprenyl pyrophosphate synthase reaction. Biochemistry 39 (2000) 10936–10942. [PMID: 10978182]
8.  Kharel, Y., Zhang, Y.W., Fujihashi, M., Miki, K. and Koyama, T. Significance of highly conserved aromatic residues in Micrococcus luteus B-P 26 undecaprenyl diphosphate synthase. J. Biochem. 134 (2003) 819–826. [PMID: 14769870]
[EC 2.5.1.31 created 1984, modified 2011]
 
 
EC 2.5.1.33
Transferred entry: trans-pentaprenyltranstransferase. Now covered by EC 2.5.1.82 (hexaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific]) and EC 2.5.1.83 (hexaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific])
[EC 2.5.1.33 created 1984, deleted 2010]
 
 
*EC 2.5.1.68
Accepted name: (2Z,6E)-farnesyl diphosphate synthase
Reaction: geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2Z,6E)-farnesyl diphosphate
For diagram of trans-polycis-polyprenol diphosphate biosynthesis, click here
Other name(s): (Z)-farnesyl diphosphate synthase; Z-farnesyl diphosphate synthase
Systematic name: geranyl-diphosphate:isopentenyl-diphosphate geranylcistransferase
Comments: Requires Mg2+ or Mn2+ for activity. The product of this reaction is an intermediate in the synthesis of decaprenyl phosphate, which plays a central role in the biosynthesis of most features of the mycobacterial cell wall, including peptidoglycan, linker unit galactan and arabinan. Neryl diphosphate can also act as substrate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Schulbach, M.C., Mahapatra, S., Macchia, M., Barontini, S., Papi, C., Minutolo, F., Bertini, S., Brennan, P.J. and Crick, D.C. Purification, enzymatic characterization, and inhibition of the Z-farnesyl diphosphate synthase from Mycobacterium tuberculosis. J. Biol. Chem. 276 (2001) 11624–11630. [PMID: 11152452]
[EC 2.5.1.68 created 2007, modified 2010]
 
 
EC 2.5.1.81
Accepted name: geranylfarnesyl diphosphate synthase
Reaction: geranylgeranyl diphosphate + isopentenyl diphosphate = (2E,6E,10E,14E)-geranylfarnesyl diphosphate + diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): FGPP synthase; (all-E) geranylfarnesyl diphosphate synthase; GFPS; Fgs
Systematic name: geranylgeranyl-diphosphate:isopentenyl-diphosphate transtransferase (adding 1 isopentenyl unit)
Comments: The enzyme from Methanosarcina mazei is involved in biosynthesis of the polyprenyl side-chain of methanophenazine, an electron carrier utilized for methanogenesis. It prefers geranylgeranyl diphosphate and farnesyl diphosphate as allylic substrate [1]. The enzyme from Aeropyrum pernix prefers farnesyl diphosphate as allylic substrate. The enzyme is involved in the biosynthesis of C25-C25 membrane lipids [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ogawa, T., Yoshimura, T. and Hemmi, H. Geranylfarnesyl diphosphate synthase from Methanosarcina mazei: Different role, different evolution. Biochem. Biophys. Res. Commun. 393 (2010) 16–20. [PMID: 20097171]
2.  Tachibana, A., Yano, Y., Otani, S., Nomura, N., Sako, Y. and Taniguchi, M. Novel prenyltransferase gene encoding farnesylgeranyl diphosphate synthase from a hyperthermophilic archaeon, Aeropyrum pernix. Molecular evolution with alteration in product specificity. Eur. J. Biochem. 267 (2000) 321–328. [PMID: 10632701]
3.  Tachibana, A. A novel prenyltransferase, farnesylgeranyl diphosphate synthase, from the haloalkaliphilic archaeon, Natronobacterium pharaonis. FEBS Lett. 341 (1994) 291–294. [PMID: 8137956]
4.  Lee, P.C., Mijts, B.N., Petri, R., Watts, K.T. and Schmidt-Dannert, C. Alteration of product specificity of Aeropyrum pernix farnesylgeranyl diphosphate synthase (Fgs) by directed evolution. Protein Eng. Des. Sel. 17 (2004) 771–777. [PMID: 15548566]
[EC 2.5.1.81 created 2010]
 
 
EC 2.5.1.82
Accepted name: hexaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific]
Reaction: geranylgeranyl diphosphate + 2 isopentenyl diphosphate = 2 diphosphate + all-trans-hexaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): HexPS(ambiguous); (all-E) hexaprenyl diphosphate synthase; (all-trans) hexaprenyl diphosphate synthase; hexaprenyl pyrophosphate synthase (ambiguous); HexPPs (ambiguous); hexaprenyl diphosphate synthase (ambiguous)
Systematic name: geranylgeranyl-diphosphate:isopentenyl-diphosphate transferase (adding 2 isopentenyl units)
Comments: The enzyme prefers geranylgeranyl diphosphate to farnesyl diphosphate as an allylic substrate and does not show activity for geranyl diphosphate and dimethylallyl diphosphate. Requires Mg2+ [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Hemmi, H., Ikejiri, S., Yamashita, S. and Nishino, T. Novel medium-chain prenyl diphosphate synthase from the thermoacidophilic archaeon Sulfolobus solfataricus. J. Bacteriol. 184 (2002) 615–620. [PMID: 11790729]
2.  Hemmi, H., Noike, M., Nakayama, T. and Nishino, T. Change of product specificity of hexaprenyl diphosphate synthase from Sulfolobus solfataricus by introducing mimetic mutations. Biochem. Biophys. Res. Commun. 297 (2002) 1096–1101. [PMID: 12372398]
3.  Sun, H.Y., Ko, T.P., Kuo, C.J., Guo, R.T., Chou, C.C., Liang, P.H. and Wang, A.H. Homodimeric hexaprenyl pyrophosphate synthase from the thermoacidophilic crenarchaeon Sulfolobus solfataricus displays asymmetric subunit structures. J. Bacteriol. 187 (2005) 8137–8148. [PMID: 16291686]
[EC 2.5.1.82 created 1984 as EC 2.5.1.33, part transferred 2010 to EC 2.5.1.82]
 
 
EC 2.5.1.83
Accepted name: hexaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
Reaction: (2E,6E)-farnesyl diphosphate + 3 isopentenyl diphosphate = 3 diphosphate + all-trans-hexaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): HexPS (ambiguous); hexaprenyl pyrophosphate synthetase (ambiguous); hexaprenyl diphosphate synthase (ambiguous)
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 3 isopentenyl units)
Comments: The enzyme prefers farnesyl diphosphate to geranylgeranyl diphosphate as an allylic substrate and does not show activity for geranyl diphosphate and dimethylallyl diphosphate [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Fujii, H., Koyama, T. and Ogura, K. Hexaprenyl pyrophosphate synthetase from Micrococcus luteus B-P 26. Separation of two essential components. J. Biol. Chem. 257 (1982) 14610–14612. [PMID: 7174655]
2.  Shimizu, N., Koyama, T. and Ogura, K. Molecular cloning, expression, and characterization of the genes encoding the two essential protein components of Micrococcus luteus B-P 26 hexaprenyl diphosphate synthase. J. Bacteriol. 180 (1998) 1578–1581. [PMID: 9515931]
3.  Nagaki, M., Kimura, K., Kimura, H., Maki, Y., Goto, E., Nishino, T. and Koyama, T. Artificial substrates of medium-chain elongating enzymes, hexaprenyl- and heptaprenyl diphosphate synthases. Bioorg. Med. Chem. Lett. 11 (2001) 2157–2159. [PMID: 11514159]
[EC 2.5.1.83 created 1984 as EC 2.5.1.33, part transferred 2010 to EC 2.5.1.83]
 
 
EC 2.5.1.84
Accepted name: all-trans-nonaprenyl-diphosphate synthase [geranyl-diphosphate specific]
Reaction: geranyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + all-trans-nonaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Glossary: solanesyl diphosphate = all-trans-nonaprenyl diphosphate
Other name(s): nonaprenyl diphosphate synthase (ambiguous); solanesyl diphosphate synthase (ambiguous); SolPP synthase (ambiguous); SPP-synthase (ambiguous); SPP synthase (ambiguous); solanesyl-diphosphate synthase (ambiguous); OsSPS2
Systematic name: geranyl-diphosphate:isopentenyl-diphosphate transtransferase (adding 7 isopentenyl units)
Comments: (2E,6E)-Farnesyl diphosphate and geranylgeranyl diphosphate are less effective as substrates than geranyl diphosphate. The enzyme is involved in the synthesis of the side chain of menaquinone-9 [1]. In Oryza sativa the enzyme SPS2 is involved in providing solanesyl diphosphate for plastoquinone-9 formation [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sagami, H., Ogura, K. and Seto, S. Solanesyl pyrophosphate synthetase from Micrococcus lysodeikticus. Biochemistry 16 (1977) 4616–4622. [PMID: 911777]
2.  Fujii, H., Sagami, H., Koyama, T., Ogura, K., Seto, S., Baba, T. and Allen, C.M. Variable product specificity of solanesyl pyrophosphate synthetase. Biochem. Biophys. Res. Commun. 96 (1980) 1648–1653. [PMID: 7447947]
3.  Ohara, K., Sasaki, K. and Yazaki, K. Two solanesyl diphosphate synthases with different subcellular localizations and their respective physiological roles in Oryza sativa. J. Exp. Bot. 61 (2010) 2683–2692. [PMID: 20421194]
4.  Ohnuma, S., Koyama, T. and Ogura, K. Purification of solanesyl-diphosphate synthase from Micrococcus luteus. A new class of prenyltransferase. J. Biol. Chem. 266 (1991) 23706–23713. [PMID: 1748647]
5.  Gotoh, T., Koyama, T. and Ogura, K. Farnesyl diphosphate synthase and solanesyl diphosphate synthase reactions of diphosphate-modified allylic analogs: the significance of the diphosphate linkage involved in the allylic substrates for prenyltransferase. J. Biochem. 112 (1992) 20–27. [PMID: 1429508]
6.  Teclebrhan, H., Olsson, J., Swiezewska, E. and Dallner, G. Biosynthesis of the side chain of ubiquinone:trans-prenyltransferase in rat liver microsomes. J. Biol. Chem. 268 (1993) 23081–23086. [PMID: 8226825]
[EC 2.5.1.84 created 1972 as EC 2.5.1.11, part transferred 2010 to EC 2.5.1.84]
 
 
EC 2.5.1.85
Accepted name: all-trans-nonaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific]
Reaction: geranylgeranyl diphosphate + 5 isopentenyl diphosphate = 5 diphosphate + all-trans-nonaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Glossary: solanesyl diphosphate = all-trans-nonaprenyll diphosphate
Other name(s): nonaprenyl diphosphate synthase (ambiguous); solanesyl diphosphate synthase (ambiguous); At-SPS2; At-SPS1; SPS1; SPS2
Systematic name: geranylgeranyl-diphosphate:isopentenyl-diphosphate transtransferase (adding 5 isopentenyl units)
Comments: Geranylgeranyl diphosphate is preferred over farnesyl diphosphate as allylic substrate [1]. The plant Arabidopsis thaliana has two different enzymes that catalyse this reaction. SPS1 contributes to the biosynthesis of the ubiquinone side-chain while SPS2 supplies the precursor of the plastoquinone side-chains [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Hirooka, K., Bamba, T., Fukusaki, E. and Kobayashi, A. Cloning and kinetic characterization of Arabidopsis thaliana solanesyl diphosphate synthase. Biochem. J. 370 (2003) 679–686. [PMID: 12437513]
2.  Hirooka, K., Izumi, Y., An, C.I., Nakazawa, Y., Fukusaki, E. and Kobayashi, A. Functional analysis of two solanesyl diphosphate synthases from Arabidopsis thaliana. Biosci. Biotechnol. Biochem. 69 (2005) 592–601. [PMID: 15784989]
3.  Jun, L., Saiki, R., Tatsumi, K., Nakagawa, T. and Kawamukai, M. Identification and subcellular localization of two solanesyl diphosphate synthases from Arabidopsis thaliana. Plant Cell Physiol. 45 (2004) 1882–1888. [PMID: 15653808]
[EC 2.5.1.85 created 1972 as EC 2.5.1.11, part transferred 2010 to EC 2.5.1.85]
 
 
EC 2.5.1.86
Accepted name: trans,polycis-decaprenyl diphosphate synthase
Reaction: (2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + trans,octacis-decaprenyl diphosphate
For diagram of trans,polycis-polyprenol diphosphate biosynthesis, click here
Other name(s): Rv2361c; (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate synthase
Systematic name: (2Z,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesylcistransferase (adding 7 isopentenyl units)
Comments: The enzyme is involved in the biosynthesis of decaprenyl phosphate, which plays a central role in the biosynthesis of essential mycobacterial cell wall components, such as the mycolyl-arabinogalactan-peptidoglycan complex and lipoarabinomannan [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kaur, D., Brennan, P.J. and Crick, D.C. Decaprenyl diphosphate synthesis in Mycobacterium tuberculosis. J. Bacteriol. 186 (2004) 7564–7570. [PMID: 15516568]
2.  Wang, W., Dong, C., McNeil, M., Kaur, D., Mahapatra, S., Crick, D.C. and Naismith, J.H. The structural basis of chain length control in Rv1086. J. Mol. Biol. 381 (2008) 129–140. [PMID: 18597781]
3.  Crick, D.C., Schulbach, M.C., Zink, E.E., Macchia, M., Barontini, S., Besra, G.S. and Brennan, P.J. Polyprenyl phosphate biosynthesis in Mycobacterium tuberculosis and Mycobacterium smegmatis. J. Bacteriol. 182 (2000) 5771–5778. [PMID: 11004176]
[EC 2.5.1.86 created 2010]
 
 
EC 2.5.1.87
Accepted name: ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific]
Reaction: (2E,6E)-farnesyl diphosphate + n isopentenyl diphosphate = n diphosphate + ditrans,polycis-polyprenyl diphosphate (n = 10–55)
For diagram of di- and tritrans,polycis-polyprenol biosynthesis, click here
Other name(s): RER2; Rer2p; Rer2p Z-prenyltransferase; Srt1p; Srt2p Z-prenyltransferase; ACPT; dehydrodolichyl diphosphate synthase 1
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 10–55 isopentenyl units)
Comments: The enzyme is involved in biosynthesis of dolichol (a long-chain polyprenol) with a saturated α-isoprene unit, which serves as a glycosyl carrier in protein glycosylation [1]. The yeast Saccharomyces cerevisiae has two different enzymes that catalyse this reaction. Rer2p synthesizes a well-defined family of polyprenols of 13–18 isoprene residues with dominating C80 (16 isoprene residues) extending to C120, while Srt1p synthesizes mainly polyprenol with 22 isoprene subunits. Largest Srt1p products reach C290 [2]. The enzyme from Arabidopsis thaliana catalyses the formation of polyprenyl diphosphates with predominant carbon number C120 [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sato, M., Fujisaki, S., Sato, K., Nishimura, Y. and Nakano, A. Yeast Saccharomyces cerevisiae has two cis-prenyltransferases with different properties and localizations. Implication for their distinct physiological roles in dolichol synthesis. Genes Cells 6 (2001) 495–506. [PMID: 11442630]
2.  Poznanski, J. and Szkopinska, A. Precise bacterial polyprenol length control fails in Saccharomyces cerevisiae. Biopolymers 86 (2007) 155–164. [PMID: 17345630]
3.  Sato, M., Sato, K., Nishikawa, S., Hirata, A., Kato, J. and Nakano, A. The yeast RER2 gene, identified by endoplasmic reticulum protein localization mutations, encodes cis-prenyltransferase, a key enzyme in dolichol synthesis. Mol. Cell Biol. 19 (1999) 471–483. [PMID: 9858571]
4.  Oh, S.K., Han, K.H., Ryu, S.B. and Kang, H. Molecular cloning, expression, and functional analysis of a cis-prenyltransferase from Arabidopsis thaliana. Implications in rubber biosynthesis. J. Biol. Chem. 275 (2000) 18482–18488. [PMID: 10764783]
5.  Cunillera, N., Arro, M., Fores, O., Manzano, D. and Ferrer, A. Characterization of dehydrodolichyl diphosphate synthase of Arabidopsis thaliana, a key enzyme in dolichol biosynthesis. FEBS Lett. 477 (2000) 170–174. [PMID: 10908715]
[EC 2.5.1.87 created 2010]
 
 
EC 2.5.1.88
Accepted name: trans,polycis-polyprenyl diphosphate synthase [(2Z,6E)-farnesyl diphosphate specific]
Reaction: (2Z,6E)-farnesyl diphosphate + n isopentenyl diphosphate = n diphosphate + trans,polycis-polyprenyl diphosphate (n = 9–11)
For diagram of trans-polycis-polyprenol diphosphate biosynthesis, click here
Systematic name: (2Z,6E)-farnesyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 9–11 isopentenyl units)
Comments: Highest activity with (2Z,6E)-farnesyl diphosphate as allylic substrate. Broad product specificity with the major product being dodecaprenyl diphosphate. Synthesizes even C70 prenyl diphosphate as the maximum chain-length product [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ambo, T., Noike, M., Kurokawa, H. and Koyama, T. Cloning and functional analysis of cis-prenyltransferase from Thermobifida fusca. J. Biosci. Bioeng. 107 (2009) 620–622. [PMID: 19447338]
[EC 2.5.1.88 created 2010]
 
 
EC 2.5.1.89
Accepted name: tritrans,polycis-undecaprenyl-diphosphate synthase [geranylgeranyl-diphosphate specific]
Reaction: geranylgeranyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + tritrans,heptacis-undecaprenyl diphosphate
For diagram of di- and tritrans,polycis-polyprenol biosynthesis, click here
Systematic name: geranylgeranyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 7 isopentenyl units)
Comments: This enzyme is involved in the biosynthesis of the glycosyl carrier lipid in some archaebacteria. Unlike EC 2.5.1.31, its counterpart in most bacteria, it prefers geranylgeranyl diphosphate to farnesyl diphosphate as the allylic substrate, resulting in production of a tritrans,polycis variant of undecaprenyl diphosphate [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Hemmi, H., Yamashita, S., Shimoyama, T., Nakayama, T. and Nishino, T. Cloning, expression, and characterization of cis-polyprenyl diphosphate synthase from the thermoacidophilic archaeon Sulfolobus acidocaldarius. J. Bacteriol. 183 (2001) 401–404. [PMID: 11114943]
[EC 2.5.1.89 created 2010, modified 2011]
 
 
EC 2.5.1.90
Accepted name: all-trans-octaprenyl-diphosphate synthase
Reaction: (2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate = 5 diphosphate + all-trans-octaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Glossary: all-trans-octaprenyl diphosphate = OPP
Other name(s): octaprenyl-diphosphate synthase; octaprenyl pyrophosphate synthetase; polyprenylpyrophosphate synthetase; terpenoidallyltransferase; terpenyl pyrophosphate synthetase; trans-heptaprenyltranstransferase; trans-prenyltransferase
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 5 isopentenyl units)
Comments: This enzyme catalyses the condensation reactions resulting in the formation of all-trans-octaprenyl diphosphate, the isoprenoid side chain of ubiquinone-8 and menaquinone-8. The enzyme adds five isopentenyl diphosphate molecules sequentially to farnesyl diphosphate with trans stereochemistry
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Fujisaki, S., Nishino, T. and Katsuki, H. Isoprenoid synthesis in Escherichia coli. Separation and partial purification of four enzymes involved in the synthesis. J. Biochem. 99 (1986) 1327–1337. [PMID: 3519603]
2.  Asai, K., Fujisaki, S., Nishimura, Y., Nishino, T., Okada, K., Nakagawa, T., Kawamukai, M. and Matsuda, H. The identification of Escherichia coli ispB (cel) gene encoding the octaprenyl diphosphate synthase. Biochem. Biophys. Res. Commun. 202 (1994) 340–345. [PMID: 8037730]
[EC 2.5.1.90 created 2010]
 
 
EC 2.5.1.91
Accepted name: all-trans-decaprenyl-diphosphate synthase
Reaction: (2E,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + all-trans-decaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): decaprenyl-diphosphate synthase; decaprenyl pyrophosphate synthetase; polyprenylpyrophosphate synthetase; terpenoidallyltransferase; terpenyl pyrophosphate synthetase; trans-prenyltransferase
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 7 isopentenyl units)
Comments: This enzyme catalyses the condensation reactions resulting in the formation of all-trans-decaprenyl diphosphate, the isoprenoid side chain of ubiquinone-10 and menaquinone-10. The enzyme adds seven isopentenyl diphosphate molecules sequentially to farnesyl diphosphate with trans stereochemistry.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Saiki, R., Nagata, A., Kainou, T., Matsuda, H. and Kawamukai, M. Characterization of solanesyl and decaprenyl diphosphate synthases in mice and humans. FEBS J. 272 (2005) 5606–5622. [PMID: 16262699]
[EC 2.5.1.91 created 2010]
 
 
EC 2.5.1.92
Accepted name: (2Z,6Z)-farnesyl diphosphate synthase
Reaction: dimethylallyl diphosphate + 2 isopentenyl diphosphate = 2 diphosphate + (2Z,6Z)-farnesyl diphosphate
For diagram of all-cis-polyprenyl diphosphate, click here
Other name(s): cis,cis-farnesyl diphosphate synthase; Z,Z-FPP synthase; zFPS; Z,Z-farnesyl pyrophosphate synthase
Systematic name: dimethylallyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 2 isopentenyl units)
Comments: This enzyme, originally characterized from wild tomato, specifically forms (2Z,6Z)-farnesyl diphosphate via neryl diphosphate and isopentenyl diphosphate. In wild tomato it is involved in the biosynthesis of several sesquiterpenes. See also EC 2.5.1.68 [(2Z,6E)-farnesyl diphosphate synthase] and EC 2.5.1.10 [(2E,6E)-farnesyl diphosphate synthase].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sallaud, C., Rontein, D., Onillon, S., Jabes, F., Duffe, P., Giacalone, C., Thoraval, S., Escoffier, C., Herbette, G., Leonhardt, N., Causse, M. and Tissier, A. A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites. Plant Cell 21 (2009) 301–317. [PMID: 19155349]
[EC 2.5.1.92 created 2010, modified 2011]
 
 
EC 2.7.7.69
Accepted name: GDP-L-galactose phosphorylase
Reaction: GDP-β-L-galactose + phosphate = β-L-galactose 1-phosphate + GDP
Other name(s): VTC2; VTC5
Systematic name: GDP:α-L-galactose 1-phosphate guanylyltransferase
Comments: The enzyme catalyses a reaction of the Smirnoff-Wheeler pathway, the major route to ascorbate biosynthesis in plants.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Linster, C.L., Gomez, T.A., Christensen, K.C., Adler, L.N., Young, B.D., Brenner, C. and Clarke, S.G. Arabidopsis VTC2 encodes a GDP-L-galactose phosphorylase, the last unknown enzyme in the Smirnoff-Wheeler pathway to ascorbic acid in plants. J. Biol. Chem. 282 (2007) 18879–18885. [PMID: 17462988]
2.  Linster, C.L., Adler, L.N., Webb, K., Christensen, K.C., Brenner, C. and Clarke, S.G. A second GDP-L-galactose phosphorylase in arabidopsis en route to vitamin C. Covalent intermediate and substrate requirements for the conserved reaction. J. Biol. Chem. 283 (2008) 18483–18492. [PMID: 18463094]
3.  Dowdle, J., Ishikawa, T., Gatzek, S., Rolinski, S. and Smirnoff, N. Two genes in Arabidopsis thaliana encoding GDP-L-galactose phosphorylase are required for ascorbate biosynthesis and seedling viability. Plant J. 52 (2007) 673–689. [PMID: 17877701]
4.  Muller-Moule, P. An expression analysis of the ascorbate biosynthesis enzyme VTC2. Plant Mol. Biol. 68 (2008) 31–41. [PMID: 18516687]
[EC 2.7.7.69 created 2010]
 
 
EC 2.7.8.30
Transferred entry: undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase. Now EC 2.4.2.53, undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
[EC 2.7.8.30 created 2010, modified 2011, deleted 2013]
 
 
*EC 3.6.1.40
Accepted name: guanosine-5′-triphosphate,3′-diphosphate phosphatase
Reaction: guanosine 5′-triphosphate 3′-diphosphate + H2O = guanosine 3′,5′-bis(diphosphate) + phosphate
Other name(s): pppGpp 5′-phosphohydrolase; guanosine 5′-triphosphate-3′-diphosphate 5′-phosphohydrolase; guanosine pentaphosphatase; guanosine pentaphosphate phosphatase; guanosine 5′-triphosphate 3′-diphosphate 5′-phosphatase; guanosine pentaphosphate phosphohydrolase
Systematic name: guanosine-5′-triphosphate-3′-diphosphate 5′-phosphohydrolase
Comments: Also hydrolyses other guanosine 5′-triphosphate derivatives with at least one unsubstituted phosphate group on the 3′-position, but not GTP, ATP or adenosine 5′-triphosphate 3′-diphosphate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 85130-44-5
References:
1.  Hara, A. and Sy, J. Guanosine 5′-triphosphate, 3′-diphosphate 5′-phosphohydrolase. Purification and substrate specificity. J. Biol. Chem. 258 (1983) 1678–1683. [PMID: 6130093]
[EC 3.6.1.40 created 1986, modified 2010]
 
 
*EC 4.1.99.14
Accepted name: spore photoproduct lyase
Reaction: (5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3′→5′)-thymidylate (in double-helical DNA)
For diagram click here
Other name(s): SAM; SP lyase; SPL; SplB; SplG
Systematic name: spore photoproduct pyrimidine-lyase
Comments: This enzyme is a member of the ’AdoMet radical’ (radical SAM) family. The enzyme binds a [4Fe-4S] cluster. The cluster is coordinated by 3 cysteines and an exchangeable SAM molecule [3]. The 5′-deoxy-adenosine radical formed after electron transfer from the [4Fe-4S] cluster to the S-adenosyl-L-methionine, initiates the repair by abstracting the C-6 hydrogen of the spore photoproduct lesion. During the second part of the repair process the SAM molecule is regenerated [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 37290-70-3
References:
1.  Chandor, A., Berteau, O., Douki, T., Gasparutto, D., Sanakis, Y., Ollagnier-de-Choudens, S., Atta, M. and Fontecave, M. Dinucleotide spore photoproduct, a minimal substrate of the DNA repair spore photoproduct lyase enzyme from Bacillus subtilis. J. Biol. Chem. 281 (2006) 26922–26931. [PMID: 16829676]
2.  Pieck, J.C., Hennecke, U., Pierik, A.J., Friedel, M.G. and Carell, T. Characterization of a new thermophilic spore photoproduct lyase from Geobacillus stearothermophilus (SplG) with defined lesion containing DNA substrates. J. Biol. Chem. 281 (2006) 36317–36326. [PMID: 16968710]
3.  Buis, J.M., Cheek, J., Kalliri, E. and Broderick, J.B. Characterization of an active spore photoproduct lyase, a DNA repair enzyme in the radical S-adenosylmethionine superfamily. J. Biol. Chem. 281 (2006) 25994–26003. [PMID: 16829680]
4.  Mantel, C., Chandor, A., Gasparutto, D., Douki, T., Atta, M., Fontecave, M., Bayle, P.-A., Mouesca, J.-M. and Bardet, M. Combined NMR and DFT studies for the absolute configuration elucidation of the spore photoproduct, a UV-induced DNA lesion. J. Am. Chem. Soc. 130 (2008) 16978–16984. [PMID: 19012397]
5.  Silver, S.C., Chandra, T., Zilinskas, E., Ghose, S., Broderick, W.E. and Broderick, J.B. Complete stereospecific repair of a synthetic dinucleotide spore photoproduct by spore photoproduct lyase. J. Biol. Inorg. Chem. 15 (2010) 943–955. [PMID: 20405152]
[EC 4.1.99.14 created 2009, modified 2010]
 
 
EC 4.1.99.15
Deleted entry: S-specific spore photoproduct lyase. This enzyme was classified on the basis of an incorrect reaction. The activity is covered by EC 4.1.99.14, spore photoproduct lyase
[EC 4.1.99.15 created 2009, deleted 2010]
 
 
EC 4.2.3.50
Accepted name: (+)-α-santalene synthase [(2Z,6Z)-farnesyl diphosphate cyclizing]
Reaction: (2Z,6Z)-farnesyl diphosphate = (+)-α-santalene + diphosphate
For diagram of santalene and bergamotene biosynthesis, click here
Other name(s): SBS (ambiguous)
Systematic name: (2Z,6Z)-farnesyl diphosphate lyase [cyclizing; (+)-α-santalene-forming]
Comments: The enzyme synthesizes a mixture of sesquiterpenoids from (2Z,6Z)-farnesyl diphosphate. Following dephosphorylation of (2Z,6Z)-farnesyl diphosphate, the (2Z,6Z)-farnesyl carbocation is converted to either the (6R)- or the (6S)-bisabolyl cations depending on the stereochemistry of the 6,1 closure. The (6R)-bisabolyl cation will then lead to the formation of (+)-α-santalene (EC 4.2.3.50), while the (6S)-bisabolyl cation will give rise to (+)-endo-β-bergamotene (see EC 4.2.3.53) as well as (-)-endo-α-bergamotene (see EC 4.2.3.54). Small amounts of (-)-epi-β-santalene are also formed from the (6R)-bisabolyl cation and small amounts of (-)-exo-α-bergamotene are formed from the (6S)-bisabolyl cation [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sallaud, C., Rontein, D., Onillon, S., Jabes, F., Duffe, P., Giacalone, C., Thoraval, S., Escoffier, C., Herbette, G., Leonhardt, N., Causse, M. and Tissier, A. A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites. Plant Cell 21 (2009) 301–317. [PMID: 19155349]
[EC 4.2.3.50 created 2010]
 
 
EC 4.2.3.51
Accepted name: β-phellandrene synthase (neryl-diphosphate-cyclizing)
Reaction: neryl diphosphate = β-phellandrene + diphosphate
Other name(s): phellandrene synthase 1; PHS1; monoterpene synthase PHS1
Systematic name: neryl-diphosphate diphosphate-lyase [cyclizing; β-phellandrene-forming]
Comments: The enzyme from Solanum lycopersicum has very poor affinity with geranyl diphosphate as substrate. Catalyses the formation of the acyclic myrcene and ocimene as major products in addition to β-phellandrene [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Schilmiller, A.L., Schauvinhold, I., Larson, M., Xu, R., Charbonneau, A.L., Schmidt, A., Wilkerson, C., Last, R.L. and Pichersky, E. Monoterpenes in the glandular trichomes of tomato are synthesized from a neryl diphosphate precursor rather than geranyl diphosphate. Proc. Natl. Acad. Sci. USA 106 (2009) 10865–10870. [PMID: 19487664]
[EC 4.2.3.51 created 2010]
 
 
EC 4.2.3.52
Accepted name: (4S)-β-phellandrene synthase (geranyl-diphosphate-cyclizing)
Reaction: geranyl diphosphate = (4S)-β-phellandrene + diphosphate
For diagram of menthane monoterpenoid biosynthesis, click here
Other name(s): phellandrene synthase; (-)-β-phellandrene synthase; (-)-(4S)-β-phellandrene synthase
Systematic name: geranyl-diphosphate diphosphate-lyase [cyclizing; (4S)-β-phellandrene-forming]
Comments: Requires Mn2+. Mg2+ is not effective [1]. Some (-)-α-phellandrene is also formed [3]. The reaction involves a 1,3-hydride shift [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 137010-34-5
References:
1.  Savage, T.J., Hatch, M.W. and Croteau, R. Monoterpene synthases of Pinus contorta and related conifers. A new class of terpenoid cyclase. J. Biol. Chem. 269 (1994) 4012–4020. [PMID: 8307957]
2.  Bohlmann, J., Phillips, M., Ramachandiran, V., Katoh, S. and Croteau, R. cDNA cloning, characterization, and functional expression of four new monoterpene synthase members of the Tpsd gene family from grand fir (Abies grandis). Arch. Biochem. Biophys. 368 (1999) 232–243. [PMID: 10441373]
3.  Wagschal, K., Savage, T.J. and Croteau, R. Isotopically sensitive branching as a tool for evaluating multiple product formation by monoterpene cyclases. Tetrahedron 31 (1991) 5933–5944.
4.  LaFever, R.E. and Croteau, R. Hydride shifts in the biosynthesis of the p-menthane monoterpenes α-terpinene, γ-terpinene, and β-phellandrene. Arch. Biochem. Biophys. 301 (1993) 361–366. [PMID: 8460944]
[EC 4.2.3.52 created 2010]
 
 
EC 4.2.3.53
Accepted name: (+)-endo-β-bergamotene synthase [(2Z,6Z)-farnesyl diphosphate cyclizing]
Reaction: (2Z,6Z)-farnesyl diphosphate = (+)-endo-β-bergamotene + diphosphate
For diagram of santalene and bergamotene biosynthesis, click here
Other name(s): SBS (ambiguous)
Systematic name: (2Z,6Z)-farnesyl diphosphate lyase (cyclizing; (+)-endo-β-bergamotene-forming)
Comments: The enzyme synthesizes a mixture of sesquiterpenoids from (2Z,6Z)-farnesyl diphosphate. Following dephosphorylation of (2Z,6Z)-farnesyl diphosphate, the (2Z,6Z)-farnesyl carbocation is converted to either the (6R)- or the (6S)-bisabolyl cations depending on the stereochemistry of the 6,1 closure. The (6R)-bisabolyl cation will then lead to the formation of (+)-α-santalene (see EC 4.2.3.50), while the (6S)-bisabolyl cation will give rise to (-)-endo-α-bergamotene (see EC 4.2.3.54), as well as (+)-endo-β-bergamotene. Small amounts of (-)-epi-β-santalene are also formed from the (6R)-bisabolyl cation and small amounts of (-)-exo-α-bergamotene are formed from the (6S)-bisabolyl cation [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sallaud, C., Rontein, D., Onillon, S., Jabes, F., Duffe, P., Giacalone, C., Thoraval, S., Escoffier, C., Herbette, G., Leonhardt, N., Causse, M. and Tissier, A. A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites. Plant Cell 21 (2009) 301–317. [PMID: 19155349]
[EC 4.2.3.53 created 2010]
 
 
EC 4.2.3.54
Accepted name: (-)-endo-α-bergamotene synthase [(2Z,6Z)-farnesyl diphosphate cyclizing]
Reaction: (2Z,6Z)-farnesyl diphosphate = (-)-endo-α-bergamotene + diphosphate
For diagram of santalene and bergamotene biosynthesis, click here
Other name(s): SBS (ambiguous)
Systematic name: (2Z,6Z)-farnesyl diphosphate lyase [cyclizing; (-)-endo-α-bergamotene-forming]
Comments: The enzyme synthesizes a mixture of sesquiterpenoids from (2Z,6Z)-farnesyl diphosphate. Following dephosphorylation of (2Z,6Z)-farnesyl diphosphate, the (2Z,6Z)-farnesyl carbocation is converted to either the (6R)- or the (6S)-bisabolyl cations depending on the stereochemistry of the 6,1 closure. The (6R)-bisabolyl cation will then lead to the formation of (+)-α-santalene (see EC 4.2.3.50), while the (6S)-bisabolyl cation will give rise to (+)-endo-β-bergamotene (EC 4.2.3.53) as well as (-)-endo-α-bergamotene. Small amounts of (-)-epi-β-santalene are also formed from the (6R)-bisabolyl cation and small amounts of (-)-exo-α-bergamotene are formed from the (6S)-bisabolyl cation [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sallaud, C., Rontein, D., Onillon, S., Jabes, F., Duffe, P., Giacalone, C., Thoraval, S., Escoffier, C., Herbette, G., Leonhardt, N., Causse, M. and Tissier, A. A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites. Plant Cell 21 (2009) 301–317. [PMID: 19155349]
[EC 4.2.3.54 created 2010]
 
 
EC 6.1.2 acid—alcohol ligases (ester synthases)
 
EC 6.1.2.1
Accepted name: D-alanine—(R)-lactate ligase
Reaction: D-alanine + (R)-lactate + ATP = D-alanyl-(R)-lactate + ADP + phosphate
Glossary: (R)-lactate = D-lactate
D-alanyl-(R)-lactate = D-alanyl-D-lactate = (2R)-2-(D-alanyloxy)propanoic acid = (R)-2-((R)-2-aminopropanoyloxy)propanoic acid
Other name(s): VanA; VanB; VanD
Systematic name: D-alanine:(R)-lactate ligase (ADP-forming)
Comments: The product of this enzyme, the depsipeptide D-alanyl-(R)-lactate, can be incorporated into the peptidoglycan pentapeptide instead of the usual D-alanyl-D-alanine dipeptide, which is formed by EC 6.3.2.4, D-alanine—D-alanine ligase. The resulting peptidoglycan does not bind the glycopeptide antibiotics vancomycin and teicoplanin, conferring resistance on the bacteria.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Bugg, T.D., Wright, G.D., Dutka-Malen, S., Arthur, M., Courvalin, P. and Walsh, C.T. Molecular basis for vancomycin resistance in Enterococcus faecium BM4147: biosynthesis of a depsipeptide peptidoglycan precursor by vancomycin resistance proteins VanH and VanA. Biochemistry 30 (1991) 10408–10415. [PMID: 1931965]
2.  Meziane-Cherif, D., Badet-Denisot, M.A., Evers, S., Courvalin, P. and Badet, B. Purification and characterization of the VanB ligase associated with type B vancomycin resistance in Enterococcus faecalis V583. FEBS Lett. 354 (1994) 140–142. [PMID: 7957913]
3.  Perichon, B., Reynolds, P. and Courvalin, P. VanD-type glycopeptide-resistant Enterococcus faecium BM4339. Antimicrob. Agents Chemother. 41 (1997) 2016–2018. [PMID: 9303405]
[EC 6.1.2.1 created 2010]
 
 
*EC 6.3.2.13
Accepted name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—2,6-diaminopimelate ligase
Reaction: ATP + UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate + meso-2,6-diaminoheptanedioate = ADP + phosphate + UDP-N-acetyl-α-D-muramoyl-L-alanyl-γ-D-glutamyl-meso-2,6-diaminoheptanedioate
For diagram of peptidoglycan biosynthesis (part 1), click here
Other name(s): MurE synthetase [ambiguous]; UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso-2,6-diamino-heptanedioate ligase (ADP-forming); UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate synthetase; UDP-N-acetylmuramoylalanyl-D-glutamate—2,6-diaminopimelate ligase; UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso-2,6-diaminoheptanedioate γ-ligase (ADP-forming)
Systematic name: UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate:meso-2,6-diaminoheptanedioate γ-ligase (ADP-forming)
Comments: Involved in the synthesis of a cell-wall peptide in bacteria. This enzyme adds diaminopimelate in Gram-negative organisms and in some Gram-positive organisms; in others EC 6.3.2.7 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—L-lysine ligase) adds lysine instead. It is the amino group of the L-centre of the diaminopimelate that is acylated.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 9075-09-6
References:
1.  Mizuno, Y. and Ito, E. Purification and properties of uridine diphosphate N-acetylmuramyl-L-alanyl-D-glutamate:meso-2,6-diaminopimelate ligase. J. Biol. Chem. 243 (1968) 2665–2672. [PMID: 4967958]
2.  van Heijenoort, J. Recent advances in the formation of the bacterial peptidoglycan monomer unit. Nat. Prod. Rep. 18 (2001) 503–519. [PMID: 11699883]
[EC 6.3.2.13 created 1972, modified 2002, modified 2010]
 
 
EC 6.3.2.35
Accepted name: D-alanine—D-serine ligase
Reaction: D-alanine + D-serine + ATP = D-alanyl-D-serine + ADP + phosphate
Other name(s): VanC; VanE; VanG
Systematic name: D-alanine:D-serine ligase (ADP-forming)
Comments: The product of this enzyme, D-alanyl-D-serine, can be incorporated into the peptidoglycan pentapeptide instead of the usual D-alanyl-D-alanine dipeptide, which is formed by EC 6.3.2.4, D-alanine—D-alanine ligase. The resulting peptidoglycan does not bind the glycopeptide antibiotics vancomycin and teicoplanin, conferring resistance on the bacteria.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Dutka-Malen, S., Molinas, C., Arthur, M. and Courvalin, P. Sequence of the vanC gene of Enterococcus gallinarum BM4174 encoding a D-alanine:D-alanine ligase-related protein necessary for vancomycin resistance. Gene 112 (1992) 53–58. [PMID: 1551598]
2.  Park, I.S., Lin, C.H. and Walsh, C.T. Bacterial resistance to vancomycin: overproduction, purification, and characterization of VanC2 from Enterococcus casseliflavus as a D-Ala-D-Ser ligase. Proc. Natl. Acad. Sci. USA 94 (1997) 10040–10044. [PMID: 9294159]
3.  Fines, M., Perichon, B., Reynolds, P., Sahm, D.F. and Courvalin, P. VanE, a new type of acquired glycopeptide resistance in Enterococcus faecalis BM4405. Antimicrob. Agents Chemother. 43 (1999) 2161–2164. [PMID: 10471558]
4.  Depardieu, F., Bonora, M.G., Reynolds, P.E. and Courvalin, P. The vanG glycopeptide resistance operon from Enterococcus faecalis revisited. Mol. Microbiol. 50 (2003) 931–948. [PMID: 14617152]
5.  Watanabe, S., Kobayashi, N., Quinones, D., Hayakawa, S., Nagashima, S., Uehara, N. and Watanabe, N. Genetic diversity of the low-level vancomycin resistance gene vanC-2/vanC-3 and identification of a novel vanC subtype (vanC-4) in Enterococcus casseliflavus. Microb. Drug Resist. 15 (2009) 1–9. [PMID: 19216682]
[EC 6.3.2.35 created 2010]
 
 
EC 6.3.5.11
Accepted name: cobyrinate a,c-diamide synthase
Reaction: 2 ATP + cobyrinate + 2 L-glutamine + 2 H2O = 2 ADP + 2 phosphate + cobyrinate a,c-diamide + 2 L-glutamate (overall reaction)
(1a) ATP + cobyrinate + L-glutamine + H2O = ADP + phosphate + cobyrinate c-monamide + L-glutamate
(1b) ATP + cobyrinate c-monamide + L-glutamine + H2O = ADP + phosphate + cobyrinate a,c-diamide + L-glutamate
For diagram of anaerobic corrin biosynthesis (part 2), click here
Other name(s): cobyrinic acid a,c-diamide synthetase; CbiA
Comments: This enzyme is the first glutamine amidotransferase that participates in the anaerobic (early cobalt insertion) biosynthetic pathway of adenosylcobalamin, and catalyses the ATP-dependent synthesis of cobyrinate a,c-diamide from cobyrinate using either L-glutamine or ammonia as the nitrogen source. It is proposed that the enzyme first catalyses the amidation of the c-carboxylate, and then the intermediate is released into solution and binds to the same catalytic site for the amidation of the a-carboxylate. The Km for ammonia is substantially higher than that for L-glutamine.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Fresquet, V., Williams, L. and Raushel, F.M. Mechanism of cobyrinic acid a,c-diamide synthetase from Salmonella typhimurium LT2. Biochemistry 43 (2004) 10619–10627. [PMID: 15311923]
[EC 6.3.5.11 created 2010]
 
 


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