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, Ron Caspi, Ture Damhus, Shinya Fushinobu, Julia Hauenstein, Antje Jäde, Ingrid Keseler, Masaaki Kotera, Andrew McDonald, Gerry Moss, 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 To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.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 1.3.1.82 (-)-isopiperitenone reductase
*EC 1.4.3.16 L-aspartate oxidase
EC 1.13.12.15 3,4-dihydroxyphenylalanine oxidative deaminase
EC 1.14.19.5 acyl-CoA 11-(Z)-desaturase
EC 1.14.19.6 acyl-CoA (9+3)-desaturase
EC 2.1.3.11 N-succinylornithine carbamoyltransferase
*EC 2.3.1.94 6-deoxyerythronolide-B synthase
EC 2.5.1.72 quinolinate synthase
EC 3.1.3.78 phosphatidylinositol-4,5-bisphosphate 4-phosphatase
EC 3.2.2.26 futalosine hydrolase
*EC 3.5.1.77 N-carbamoyl-D-amino-acid hydrolase
*EC 3.5.1.87 N-carbamoyl-L-amino-acid hydrolase
EC 3.6.1.53 Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase
EC 4.1.2.43 3-hexulose-6-phosphate synthase
*EC 4.2.1.92 hydroperoxide dehydratase
EC 5.1.99.5 hydantoin racemase
EC 5.3.1.27 6-phospho-3-hexuloisomerase

EC 1.3.1.82
Accepted name: (-)-isopiperitenone reductase
Reaction: (+)-cis-isopulegone + NADP+ = (-)-isopiperitenone + NADPH + H+
Systematic name: (+)-cis-isopulegone:NADP+ oxidoreductase
Comments: The reaction occurs in the opposite direction to that shown above. The enzyme participates in the menthol-biosynthesis pathway of Mentha plants. (+)-Pulegone, (+)-cis-isopulegone and (-)-menthone are not substrates. The enzyme has a preference for NADPH as the reductant, with NADH being a poor substitute [2]. The enzyme is highly regioselective for the reduction of the endocyclic 1,2-double bond, and is stereoselective, producing only the 1R-configured product. It is a member of the short-chain dehydrogenase/reductase superfamily.
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Croteau, R. and Venkatachalam, K.V. Metabolism of monoterpenes: demonstration that (+)-cis-isopulegone, not piperitenone, is the key intermediate in the conversion of (-)-isopiperitenone to (+)-pulegone in peppermint (Mentha piperita). Arch. Biochem. Biophys. 249 (1986) 306–315. [DOI] [PMID: 3755881]
2.  Ringer, K.L., McConkey, M.E., Davis, E.M., Rushing, G.W. and Croteau, R. Monoterpene double-bond reductases of the (-)-menthol biosynthetic pathway: isolation and characterization of cDNAs encoding (-)-isopiperitenone reductase and (+)-pulegone reductase of peppermint. Arch. Biochem. Biophys. 418 (2003) 80–92. [DOI] [PMID: 13679086]
[EC 1.3.1.82 created 2008]
 
 
*EC 1.4.3.16
Accepted name: L-aspartate oxidase
Reaction: L-aspartate + O2 = iminosuccinate + H2O2
For diagram of quinolinate biosynthesis, click here
Other name(s): NadB; Laspo; AO
Systematic name: L-aspartate:oxygen oxidoreductase
Comments: A flavoprotein (FAD). L-Aspartate oxidase catalyses the first step in the de novo biosynthesis of NAD+ in some bacteria. O2 can be replaced by fumarate as electron acceptor, yielding succinate [5]. The ability of the enzyme to use both O2 and fumarate in cofactor reoxidation enables it to function under both aerobic and anaerobic conditions [5]. Iminosuccinate can either be hydrolysed to form oxaloacetate and NH3 or can be used by EC 2.5.1.72, quinolinate synthase, in the production of quinolinate. The enzyme is a member of the succinate dehydrogenase/fumarate-reductase family of enzymes [5].
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 69106-47-4
References:
1.  Nasu, S., Wicks, F.D. and Gholson, R.K. L-Aspartate oxidase, a newly discovered enzyme of Escherichia coli, is the B protein of quinolinate synthetase. J. Biol. Chem. 257 (1982) 626–632. [PMID: 7033218]
2.  Mortarino, M., Negri, A., Tedeschi, G., Simonic, T., Duga, S., Gassen, H.G. and Ronchi, S. L-Aspartate oxidase from Escherichia coli. I. Characterization of coenzyme binding and product inhibition. Eur. J. Biochem. 239 (1996) 418–426. [DOI] [PMID: 8706749]
3.  Tedeschi, G., Negri, A., Mortarino, M., Ceciliani, F., Simonic, T., Faotto, L. and Ronchi, S. L-Aspartate oxidase from Escherichia coli. II. Interaction with C4 dicarboxylic acids and identification of a novel L-aspartate: fumarate oxidoreductase activity. Eur. J. Biochem. 239 (1996) 427–433. [DOI] [PMID: 8706750]
4.  Mattevi, A., Tedeschi, G., Bacchella, L., Coda, A., Negri, A. and Ronchi, S. Structure of L-aspartate oxidase: implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family. Structure 7 (1999) 745–756. [DOI] [PMID: 10425677]
5.  Bossi, R.T., Negri, A., Tedeschi, G. and Mattevi, A. Structure of FAD-bound L-aspartate oxidase: insight into substrate specificity and catalysis. Biochemistry 41 (2002) 3018–3024. [DOI] [PMID: 11863440]
6.  Katoh, A., Uenohara, K., Akita, M. and Hashimoto, T. Early steps in the biosynthesis of NAD in Arabidopsis start with aspartate and occur in the plastid. Plant Physiol. 141 (2006) 851–857. [DOI] [PMID: 16698895]
[EC 1.4.3.16 created 1984, modified 2008]
 
 
EC 1.13.12.15
Accepted name: 3,4-dihydroxyphenylalanine oxidative deaminase
Reaction: 2 L-dopa + O2 = 2 3,4-dihydroxyphenylpyruvate + 2 NH3
Glossary: L-dopa = 3,4-dihydroxy-L-phenylalanine
Other name(s): 3,4-dihydroxy-L-phenylalanine: oxidative deaminase; oxidative deaminase; DOPA oxidative deaminase; DOPAODA
Systematic name: 3,4-dihydroxy-L-phenylalanine:oxygen oxidoreductase (deaminating)
Comments: This enzyme is one of the three enzymes involved in L-dopa (3,4-dihydroxy-L-phenylalanine) catabolism in the non-oxygenic phototrophic bacterium Rubrivivax benzoatilyticus OU5 (and not Rhodobacter sphaeroides OU5 as had been thought [1]), the other two being EC 4.3.1.22 (dihydroxyphenylalanine reductive deaminase) and EC 2.6.1.49 (3,4-dihydroxyphenylalanine transaminase). In addition to L-dopa, the enzyme can also use L-tyrosine, L-phenylalanine, L-tryptophan and glutamate as substrate, but more slowly. The enzyme is inhibited by NADH and 2-oxoglutarate.
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Ranjith, N.K., Ramana, Ch.V. and Sasikala, Ch. Purification and characterization of 3,4-dihydroxyphenylalanine oxidative deaminase from Rhodobacter sphaeroides OU5. Can. J. Microbiol. 54 (2008) 829–834. [DOI] [PMID: 18923551]
[EC 1.13.12.15 created 2008]
 
 
EC 1.14.19.5
Accepted name: acyl-CoA 11-(Z)-desaturase
Reaction: an acyl-CoA + 2 ferrocytochrome b5 + O2 + 2 H+ = an (11Z)-enoyl-CoA + 2 ferricytochrome b5 + 2 H2O
Other name(s): Δ11 desaturase; fatty acid Δ11-desaturase; TpDESN; Cro-PG; Δ11 fatty acid desaturase; Z/E11-desaturase; Δ11-palmitoyl-CoA desaturase; acyl-CoA,hydrogen donor:oxygen Δ11-oxidoreductase; Δ11-fatty-acid desaturase
Systematic name: acyl-CoA,ferrocytochrome b5:oxygen oxidoreductase (11,12 cis-dehydrogenating)
Comments: The enzyme introduces a cis double bond at position C-11 of saturated fatty acyl-CoAs. In moths the enzyme participates in the biosynthesis of their sex pheromones. The enzyme from the marine microalga Thalassiosira pseudonana is specific for palmitoyl-CoA (16:0) [4], that from the leafroller moth Choristoneura rosaceana desaturates myristoyl-CoA (14:0) [5], while that from the moth Spodoptera littoralis accepts both substrates [1]. The enzyme contains three histidine boxes that are conserved in all desaturases [2]. It is membrane-bound, and contains a cytochrome b5-like domain at the N-terminus that serves as the electron donor for the active site of the desaturase.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Martinez, T., Fabrias, G. and Camps, F. Sex pheromone biosynthetic pathway in Spodoptera littoralis and its activation by a neurohormone. J. Biol. Chem. 265 (1990) 1381–1387. [PMID: 2295634]
2.  Rodriguez, F., Hallahan, D.L., Pickett, J.A. and Camps, F. Characterization of the Δ11-palmitoyl-CoA-desaturase from Spodoptera littoralis (Lepidoptera:Noctuidae). Insect Biochem. Mol. Biol. 22 (1992) 143–148.
3.  Navarro, I., Font, I., Fabrias, G. and Camps, F. Stereospecificity of the (E)- and (Z)-11 myristoyl desaturases in the biosynthesis of Spodoptera littoralis sex pheromone. J. Am. Chem. Soc. 119 (1997) 11335–11336.
4.  Tonon, T., Harvey, D., Qing, R., Li, Y., Larson, T.R. and Graham, I.A. Identification of a fatty acid Δ11-desaturase from the microalga Thalassiosira pseudonana. FEBS Lett. 563 (2004) 28–34. [DOI] [PMID: 15063718]
5.  Hao, G., O'Connor, M., Liu, W. and Roelofs, W.L. Characterization of Z/E11- and Z9-desaturases from the obliquebanded leafroller moth, Choristoneura rosaceana. J. Insect Sci. 2:26 (2002) 1–7. [PMID: 15455060]
[EC 1.14.19.5 created 2008 (EC 1.14.99.32 created 2000, incorporated 2015), modified 2015]
 
 
EC 1.14.19.6
Accepted name: acyl-CoA (9+3)-desaturase
Reaction: (1) oleoyl-CoA + 2 ferrocytochrome b5 + O2 + 2 H+ = linoleoyl-CoA + 2 ferricytochrome b5 + 2 H2O
(2) palmitoleoyl-CoA + 2 ferrocytochrome b5 + O2 + 2 H+ = (9Z,12Z)-hexadeca-9,12-dienoyl-CoA + 2 ferricytochrome b5 + 2 H2O
Glossary: oleoyl-CoA = cis-octadec-9-enoyl-CoA = (9Z)-octadec-9-enoyl-CoA = 18:1 cis-9 = 18:1(n-9)
linoleoyl-CoA = cis,cis-octadeca-9,12-dienoyl-CoA = (9Z,12Z)-octadeca-9,12-dienoyl-CoA = 18:2(n-6)
palmitoleoyl-CoA = (9Z)-hexadec-9-enoyl-CoA
Other name(s): oleoyl-CoA 12-desaturase; Δ12 fatty acid desaturase; Δ12(ω6)-desaturase; oleoyl-CoA Δ12 desaturase; Δ12 desaturase; Δ12-desaturase; Δ12-fatty-acid desaturase; acyl-CoA,hydrogen donor:oxygen Δ12-oxidoreductase
Systematic name: acyl-CoA,ferrocytochrome b5:oxygen oxidoreductase (12,13 cis-dehydrogenating)
Comments: This microsomal enzyme introduces a cis double bond at position 12 of fatty-acyl-CoAs that contain a cis double bond at position 9. When acting on 19:1Δ10 fatty acyl-CoA the enzyme from the pathogenic protozoan Trypanosoma brucei introduces the new double bond at position 13, indicating that the new double bond is introduced three carbons from the existing cis double bond, towards the methyl-end of the fatty acid. Requires cytochrome b5 as the electron donor [4].
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Borgeson, C.E., de Renobales, M. and Blomquist, G.J. Characterization of the Δ12 desaturase in the American cockroach, Periplaneta americana: the nature of the substrate. Biochim. Biophys. Acta 1047 (1990) 135–140. [DOI] [PMID: 2248971]
2.  Lomascolo, A., Dubreucq, E. and Galzy, P. Study of the Δ12-desaturase system of Lipomyces starkeyi. Lipids 31 (1996) 253–259. [DOI] [PMID: 8900454]
3.  Tocher, D.R., Leaver, M.J. and Hodgson, P.A. Recent advances in the biochemistry and molecular biology of fatty acyl desaturases. Prog. Lipid Res. 37 (1998) 73–117. [DOI] [PMID: 9829122]
4.  Petrini, G.A., Altabe, S.G. and Uttaro, A.D. Trypanosoma brucei oleate desaturase may use a cytochrome b5-like domain in another desaturase as an electron donor. Eur. J. Biochem. 271 (2004) 1079–1086. [PMID: 15009186]
[EC 1.14.19.6 created 2008, modified 2015]
 
 
EC 2.1.3.11
Accepted name: N-succinylornithine carbamoyltransferase
Reaction: carbamoyl phosphate + N2-succinyl-L-ornithine = phosphate + N-succinyl-L-citrulline
Glossary: N-acetyl-L-citrulline = N5-acetylcarbamoyl-L-ornithine
Other name(s): succinylornithine transcarbamylase; N-succinyl-L-ornithine transcarbamylase; SOTCase
Systematic name: carbamoyl phosphate:N2-succinyl-L-ornithine carbamoyltransferase
Comments: This enzyme is specific for N-succinyl-L-ornithine and cannot use either L-ornithine (see EC 2.1.3.3, ornithine carbamoyltransferase) or N-acetyl-L-ornithine (see EC 2.1.3.9, N-acetylornithine carbamoyltransferase) as substrate. However, a single amino-acid substitution (Pro90 → Glu90) is sufficient to switch the enzyme to one that uses N-acetyl-L-ornithine as substrate. It is essential for de novo arginine biosynthesis in the obligate anaerobe Bacteroides fragilis, suggesting that this organism uses an alternative pathway for synthesizing arginine.
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Shi, D., Morizono, H., Cabrera-Luque, J., Yu, X., Roth, L., Malamy, M.H., Allewell, N.M. and Tuchman, M. Structure and catalytic mechanism of a novel N-succinyl-L-ornithine transcarbamylase in arginine biosynthesis of Bacteroides fragilis. J. Biol. Chem. 281 (2006) 20623–20631. [DOI] [PMID: 16704984]
2.  Shi, D., Yu, X., Cabrera-Luque, J., Chen, T.Y., Roth, L., Morizono, H., Allewell, N.M. and Tuchman, M. A single mutation in the active site swaps the substrate specificity of N-acetyl-L-ornithine transcarbamylase and N-succinyl-L-ornithine transcarbamylase. Protein Sci. 16 (2007) 1689–1699. [DOI] [PMID: 17600144]
[EC 2.1.3.11 created 2008]
 
 
*EC 2.3.1.94
Accepted name: 6-deoxyerythronolide-B synthase
Reaction: propanoyl-CoA + 6 (2S)-methylmalonyl-CoA + 6 NADPH + 6 H+ = 6-deoxyerythronolide B + 7 CoA + 6 CO2 + H2O + 6 NADP+
For diagram of reaction, click here
Other name(s): erythronolide condensing enzyme; malonyl-CoA:propionyl-CoA malonyltransferase (cyclizing); erythronolide synthase; malonyl-CoA:propanoyl-CoA malonyltransferase (cyclizing); deoxyerythronolide B synthase; 6-deoxyerythronolide B synthase; DEBS
Systematic name: propanoyl-CoA:(2S)-methylmalonyl-CoA malonyltransferase (cyclizing)
Comments: The product, 6-deoxyerythronolide B, contains a 14-membered lactone ring and is an intermediate in the biosynthesis of erythromycin antibiotics. Biosynthesis of 6-deoxyerythronolide B requires 28 active sites that are precisely arranged along three large polypeptides, denoted DEBS1, -2 and -3 [6]. The polyketide product is synthesized by the processive action of a loading didomain, six extension modules and a terminal thioesterase domain [5]. Each extension module contains a minimum of a ketosynthase (KS), an acyltransferase (AT) and an acyl-carrier protein (ACP). The KS domain both accepts the growing polyketide chain from the previous module and catalyses the subsequent decarboxylative condensation between this substrate and an ACP-bound methylmalonyl extender unit, introduce by the AT domain. This combined effort gives rise to a new polyketide intermediate that has been extended by two carbon atoms [5].
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 87683-77-0
References:
1.  Omura, S. and Nakagawa, A. Biosynthesis of 16-membered macrolide antibiotics. Antibiotics 4 (1981) 175–192.
2.  Roberts, G. and Leadley, P.F. Use of [3H]tetrahydrocerulenin to assay condensing enzyme activity in Streptomyces erythreus. Biochem. Soc. Trans. 12 (1984) 642–643.
3.  Pfeifer, B.A., Admiraal, S.J., Gramajo, H., Cane, D.E. and Khosla, C. Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli. Science 291 (2001) 1790–1792. [DOI] [PMID: 11230695]
4.  Tsai, S.C., Miercke, L.J., Krucinski, J., Gokhale, R., Chen, J.C., Foster, P.G., Cane, D.E., Khosla, C. and Stroud, R.M. Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel. Proc. Natl. Acad. Sci. USA 98 (2001) 14808–14813. [DOI] [PMID: 11752428]
5.  Khosla, C., Tang, Y., Chen, A.Y., Schnarr, N.A. and Cane, D.E. Structure and mechanism of the 6-deoxyerythronolide B synthase. Annu. Rev. Biochem. 76 (2007) 195–221. [DOI] [PMID: 17328673]
[EC 2.3.1.94 created 1989, modified 2008]
 
 
EC 2.5.1.72
Accepted name: quinolinate synthase
Reaction: glycerone phosphate + iminosuccinate = pyridine-2,3-dicarboxylate + 2 H2O + phosphate
For diagram of quinolinate biosynthesis, click here
Glossary: quinolinate = pyridine-2,3-dicarboxylate
glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): NadA; QS; quinolinate synthetase
Systematic name: glycerone phosphate:iminosuccinate alkyltransferase (cyclizing)
Comments: An iron-sulfur protein that requires a [4Fe-4S] cluster for activity [1]. Quinolinate synthase catalyses the second step in the de novo biosynthesis of NAD+ from aspartate in some bacteria, with EC 1.4.3.16 (L-aspartate oxidase) catalysing the first step and EC 2.4.2.19 [nicotinate-nucleotide diphosphorylase (carboxylating)] the third step. In Escherichia coli, two of the residues that are involved in the [4Fe-4S] cluster binding appear to undergo reversible disulfide-bond formation that regulates the activity of the enzyme [5].
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Ollagnier-de Choudens, S., Loiseau, L., Sanakis, Y., Barras, F. and Fontecave, M. Quinolinate synthetase, an iron-sulfur enzyme in NAD biosynthesis. FEBS Lett. 579 (2005) 3737–3743. [DOI] [PMID: 15967443]
2.  Katoh, A., Uenohara, K., Akita, M. and Hashimoto, T. Early steps in the biosynthesis of NAD in Arabidopsis start with aspartate and occur in the plastid. Plant Physiol. 141 (2006) 851–857. [DOI] [PMID: 16698895]
3.  Sakuraba, H., Tsuge, H., Yoneda, K., Katunuma, N. and Ohshima, T. Crystal structure of the NAD biosynthetic enzyme quinolinate synthase. J. Biol. Chem. 280 (2005) 26645–26648. [DOI] [PMID: 15937336]
4.  Rousset, C., Fontecave, M. and Ollagnier de Choudens, S. The [4Fe-4S] cluster of quinolinate synthase from Escherichia coli: Investigation of cluster ligands. FEBS Lett. 582 (2008) 2937–2944. [DOI] [PMID: 18674537]
5.  Saunders, A.H. and Booker, S.J. Regulation of the activity of Escherichia coli quinolinate synthase by reversible disulfide-bond formation. Biochemistry 47 (2008) 8467–8469. [DOI] [PMID: 18651751]
[EC 2.5.1.72 created 2008]
 
 
EC 3.1.3.78
Accepted name: phosphatidylinositol-4,5-bisphosphate 4-phosphatase
Reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate
Glossary: 1-phosphatidyl-1D-myo-inositol 3-phosphate = PtdIns3P
1-phosphatidyl-1D-myo-inositol 4-phosphate = PtdIns4P
1-phosphatidyl-1D-myo-inositol 5-phosphate = PtdIns5P
1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate = PtdIns(3,4)P2
1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate = PtdIns(3,5)P2
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate = PtdIns(4,5)P2
1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate = PtdIns(3,4,5)P3
Other name(s): phosphatidylinositol-4,5-bisphosphate 4-phosphatase I; phosphatidylinositol-4,5-bisphosphate 4-phosphatase II; type I PtdIns-4,5-P2 4-Ptase; type II PtdIns-4,5-P2 4-Ptase; IpgD; PtdIns-4,5-P2 4-phosphatase type I; PtdIns-4,5-P2 4-phosphatase type II; type I phosphatidylinositol-4,5-bisphosphate 4-phosphatase; type 1 4-phosphatase
Systematic name: 1-phosphatidyl-1D-myo-inositol-4,5-bisphosphate 4-phosphohydrolase
Comments: Two pathways exist in mammalian cells to degrade 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate [PtdIns(4,5)P2] [2]. One is catalysed by this enzyme and the other by EC 3.1.3.36, phosphoinositide 5-phosphatase, where the product is PtdIns4P. The enzyme from human is specific for PtdIns(4,5)P2 as substrate, as it cannot use PtdIns(3,4,5)P3, PtdIns(3,4)P2, PtdIns(3,5)P2, PtdIns5P, PtdIns4P or PtdIns3P [2]. In humans, the enzyme is localized to late endosomal/lysosomal membranes [2]. It can control nuclear levels of PtdIns5P and thereby control p53-dependent apoptosis [3].
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Niebuhr, K., Giuriato, S., Pedron, T., Philpott, D.J., Gaits, F., Sable, J., Sheetz, M.P., Parsot, C., Sansonetti, P.J. and Payrastre, B. Conversion of PtdIns(4,5)P2 into PtdIns(5)P by the S. flexneri effector IpgD reorganizes host cell morphology. EMBO J. 21 (2002) 5069–5078. [DOI] [PMID: 12356723]
2.  Ungewickell, A., Hugge, C., Kisseleva, M., Chang, S.C., Zou, J., Feng, Y., Galyov, E.E., Wilson, M. and Majerus, P.W. The identification and characterization of two phosphatidylinositol-4,5-bisphosphate 4-phosphatases. Proc. Natl. Acad. Sci. USA 102 (2005) 18854–18859. [DOI] [PMID: 16365287]
3.  Zou, J., Marjanovic, J., Kisseleva, M.V., Wilson, M. and Majerus, P.W. Type I phosphatidylinositol-4,5-bisphosphate 4-phosphatase regulates stress-induced apoptosis. Proc. Natl. Acad. Sci. USA 104 (2007) 16834–16839. [DOI] [PMID: 17940011]
4.  Mason, D., Mallo, G.V., Terebiznik, M.R., Payrastre, B., Finlay, B.B., Brumell, J.H., Rameh, L. and Grinstein, S. Alteration of epithelial structure and function associated with PtdIns(4,5)P2 degradation by a bacterial phosphatase. J. Gen. Physiol. 129 (2007) 267–283. [DOI] [PMID: 17389247]
[EC 3.1.3.78 created 2008]
 
 
EC 3.2.2.26
Accepted name: futalosine hydrolase
Reaction: futalosine + H2O = dehypoxanthine futalosine + hypoxanthine
For diagram of the futalosine pathway, click here
Glossary: futalosine = 3-(3-((3S,4R)-3,4-dihydroxy-5-(6-oxo-3H-purin-9(6H)-yl)tetrahydrofuran-2-yl)propanoyl)benzoate
dehypoxanthine futalosine = 7-(3-carboxyphenyl)-D-ribo-7-dehydro-5,6-dideoxyheptose
Other name(s): futalosine nucleosidase; MqnB (ambiguous)
Systematic name: futalosine ribohydrolase
Comments: This enzyme, which is specific for futalosine, catalyses the second step of a novel menaquinone biosynthetic pathway that is found in some prokaryotes.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Hiratsuka, T., Furihata, K., Ishikawa, J., Yamashita, H., Itoh, N., Seto, H. and Dairi, T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321 (2008) 1670–1673. [DOI] [PMID: 18801996]
[EC 3.2.2.26 created 2008]
 
 
*EC 3.5.1.77
Accepted name: N-carbamoyl-D-amino-acid hydrolase
Reaction: an N-carbamoyl-D-amino acid + H2O = a D-amino acid + NH3 + CO2
Other name(s): D-N-carbamoylase; N-carbamoylase (ambiguous); N-carbamoyl-D-amino acid hydrolase
Systematic name: N-carbamoyl-D-amino-acid amidohydrolase
Comments: This enzyme, along with EC 3.5.1.87 (N-carbamoyl-L-amino-acid hydrolase), EC 5.1.99.5 (hydantoin racemase) and hydantoinase, forms part of the reaction cascade known as the "hydantoinase process", which allows the total conversion of D,L-5-monosubstituted hydantoins into optically pure D- or L-amino acids [2]. It has strict stereospecificity for N-carbamoyl-D-amino acids and does not act upon the corresponding L-amino acids or on the N-formyl amino acids, N-carbamoyl-sarcosine, -citrulline, -allantoin and -ureidopropanoate, which are substrates for other amidohydrolases.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 71768-08-6
References:
1.  Ogawa, J., Shimizu, S., Yamada, H. N-Carbamoyl-D-amino acid amidohydrolase from Comamonas sp. E222c; purification and characterization. Eur. J. Biochem. 212 (1993) 685–691. [DOI] [PMID: 8462543]
2.  Altenbuchner, J., Siemann-Herzberg, M. and Syldatk, C. Hydantoinases and related enzymes as biocatalysts for the synthesis of unnatural chiral amino acids. Curr. Opin. Biotechnol. 12 (2001) 559–563. [DOI] [PMID: 11849938]
[EC 3.5.1.77 created 1999, modified 2008]
 
 
*EC 3.5.1.87
Accepted name: N-carbamoyl-L-amino-acid hydrolase
Reaction: an N-carbamoyl-L-2-amino acid (a 2-ureido carboxylate) + H2O = an L-2-amino acid + NH3 + CO2
Other name(s): N-carbamyl L-amino acid amidohydrolase; N-carbamoyl-L-amino acid amidohydrolase; L-N-carbamoylase; N-carbamoylase (ambiguous)
Systematic name: N-carbamoyl-L-amino-acid amidohydrolase
Comments: This enzyme, along with EC 3.5.1.77 (N-carbamoyl-D-amino-acid hydrolase), EC 5.1.99.5 (hydantoin racemase) and hydantoinase, forms part of the reaction cascade known as the "hydantoinase process", which allows the total conversion of D,L-5-monosubstituted hydantoins into optically pure D- or L-amino acids [3]. The enzyme from Alcaligenes xylosoxidans has broad specificity for carbamoyl-L-amino acids, although it is inactive on the carbamoyl derivatives of glutamate, aspartate, arginine, tyrosine or tryptophan. The enzyme from Sinorhizobium meliloti requires a divalent cation for activity and can hydrolyse N-carbamoyl-L-tryptophan as well as N-carbamoyl L-amino acids with aliphatic substituents [2]. The enzyme is inactive on derivatives of D-amino acids. In addition to N-carbamoyl L-amino acids, the enzyme can also hydrolyse formyl and acetyl derivatives to varying degrees [1,2].
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Ogawa, J., Miyake, H. and Shimizu, S. Purification and characterization of N-carbamoyl-L-amino acid amidohydrolase with broad substrate specificity from Alcaligenes xylosoxidans. Appl. Microbiol. Biotechnol. 43 (1995) 1039–1043. [PMID: 8590654]
2.  Martínez-Rodríguez, S., Clemente-Jiménez, J.M., Rodríguez-Vico, F. and Las Heras-Vázquez, F.J. Molecular cloning and biochemical characterization of L-N-carbamoylase from Sinorhizobium meliloti CECT4114. J. Mol. Microbiol. Biotechnol. 9 (2005) 16–25. [DOI] [PMID: 16254442]
3.  Altenbuchner, J., Siemann-Herzberg, M. and Syldatk, C. Hydantoinases and related enzymes as biocatalysts for the synthesis of unnatural chiral amino acids. Curr. Opin. Biotechnol. 12 (2001) 559–563. [DOI] [PMID: 11849938]
[EC 3.5.1.87 created 2001, modified 2008]
 
 
EC 3.6.1.53
Accepted name: Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase
Reaction: (1) CDP-choline + H2O = CMP + phosphocholine
(2) ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate
Other name(s): Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase; ADPRibase-Mn
Systematic name: CDP-choline phosphohydrolase
Comments: Requires Mn2+. Unlike EC 3.6.1.13, ADP-ribose diphosphatase, it cannot utilize Mg2+. ADP-D-ribose, CDP-choline, CDP-ethanolamine and ADP are substrates for this enzyme but ADP-D-glucose, UDP-D-glucose, CDP-D-glucose, CDP, CMP and AMP are not hydrolysed [2]. The mammalian enzyme hydrolyses cyclic ADP-ribose to 1-(5-phospho-β-D-ribosyl)-AMP with ~100-fold lower efficiency than ADP-D-ribose [3]. In rat, the enzyme is found predominantly in thymus and spleen.
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Canales, J., Pinto, R.M., Costas, M.J., Hernández, M.T., Miró, A., Bernet, D., Fernández, A. and Cameselle, J.C. Rat liver nucleoside diphosphosugar or diphosphoalcohol pyrophosphatases different from nucleotide pyrophosphatase or phosphodiesterase I: substrate specificities of Mg2+-and/or Mn2+-dependent hydrolases acting on ADP-ribose. Biochim. Biophys. Acta 1246 (1995) 167–177. [DOI] [PMID: 7819284]
2.  Canales, J., Fernández, A., Ribeiro, J.M., Cabezas, A., Rodrigues, J.R., Cameselle, J.C. and Costas, M.J. Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase: a novel metallophosphoesterase family preferentially expressed in rodent immune cells. Biochem. J. 413 (2008) 103–113. [DOI] [PMID: 18352857]
3.  Canales, J., Fernandez, A., Rodrigues, J.R., Ferreira, R., Ribeiro, J.M., Cabezas, A., Costas, M.J. and Cameselle, J.C. Hydrolysis of the phosphoanhydride linkage of cyclic ADP-ribose by the Mn(2+)-dependent ADP-ribose/CDP-alcohol pyrophosphatase. FEBS Lett. 583 (2009) 1593–1598. [DOI] [PMID: 19379742]
4.  Rodrigues, J.R., Fernandez, A., Canales, J., Cabezas, A., Ribeiro, J.M., Costas, M.J. and Cameselle, J.C. Characterization of Danio rerio Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase, the structural prototype of the ADPRibase-Mn-like protein family. PLoS One 7:e42249 (2012). [DOI] [PMID: 22848751]
[EC 3.6.1.53 created 2008]
 
 
EC 4.1.2.43
Accepted name: 3-hexulose-6-phosphate synthase
Reaction: D-arabino-hex-3-ulose 6-phosphate = D-ribulose 5-phosphate + formaldehyde
For diagram of reaction, click here
Other name(s): D-arabino-3-hexulose 6-phosphate formaldehyde-lyase; 3-hexulosephosphate synthase; 3-hexulose phosphate synthase; HPS
Systematic name: D-arabino-hex-3-ulose-6-phosphate formaldehyde-lyase (D-ribulose-5-phosphate-forming)
Comments: Requires Mg2+ or Mn2+ for maximal activity [1]. The enzyme is specific for D-ribulose 5-phosphate as substrate as ribose 5-phosphate, xylulose 5-phosphate, allulose 6-phosphate and fructose 6-phosphate cannot act as substrate. In addition to formaldehyde, the enzyme can also use glycolaldehyde and methylglyoxal [7]. This enzyme, along with EC 5.3.1.27, 6-phospho-3-hexuloisomerase, plays a key role in the ribulose-monophosphate cycle of formaldehyde fixation, which is present in many microorganisms that are capable of utilizing C1-compounds [1]. The hyperthermophilic and anaerobic archaeon Pyrococcus horikoshii OT3 constitutively produces a bifunctional enzyme that sequentially catalyses the reactions of this enzyme and EC 5.3.1.27, 6-phospho-3-hexuloisomerase [6]. This enzyme is a member of the orotidine 5′-monophosphate decarboxylase (OMPDC) suprafamily [5].
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Ferenci, T., Strøm, T. and Quayle, J.R. Purification and properties of 3-hexulose phosphate synthase and phospho-3-hexuloisomerase from Methylococcus capsulatus. Biochem. J. 144 (1974) 477–486. [PMID: 4219834]
2.  Kato, N., Ohashi, H., Tani, Y. and Ogata, K. 3-Hexulosephosphate synthase from Methylomonas aminofaciens 77a. Purification, properties and kinetics. Biochim. Biophys. Acta 523 (1978) 236–244. [DOI] [PMID: 564713]
3.  Yanase, H., Ikeyama, K., Mitsui, R., Ra, S., Kita, K., Sakai, Y. and Kato, N. Cloning and sequence analysis of the gene encoding 3-hexulose-6-phosphate synthase from the methylotrophic bacterium, Methylomonas aminofaciens 77a, and its expression in Escherichia coli. FEMS Microbiol. Lett. 135 (1996) 201–205. [PMID: 8595859]
4.  Yurimoto, H., Kato, N. and Sakai, Y. Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism. Chem. Rec. 5 (2005) 367–375. [DOI] [PMID: 16278835]
5.  Kato, N., Yurimoto, H. and Thauer, R.K. The physiological role of the ribulose monophosphate pathway in bacteria and archaea. Biosci. Biotechnol. Biochem. 70 (2006) 10–21. [DOI] [PMID: 16428816]
6.  Orita, I., Yurimoto, H., Hirai, R., Kawarabayasi, Y., Sakai, Y. and Kato, N. The archaeon Pyrococcus horikoshii possesses a bifunctional enzyme for formaldehyde fixation via the ribulose monophosphate pathway. J. Bacteriol. 187 (2005) 3636–3642. [DOI] [PMID: 15901685]
7.  Kato, N., Miyamoto, N., Shimao, M. and Sakazawa, C. 3-Hexulose phosphate pynthase from a new facultative methylotroph, Mycobacterium gastri MB19. Agric. Biol. Chem. 52 (1988) 2659–2661.
[EC 4.1.2.43 created 2008]
 
 
*EC 4.2.1.92
Accepted name: hydroperoxide dehydratase
Reaction: (9Z,11E,15Z)-(13S)-hydroperoxyoctadeca-9,11,15-trienoate = (9Z,15Z)-(13S)-12,13-epoxyoctadeca-9,11,15-trienoate + H2O
Glossary: 13-hydroperoxylinolenoate = (9Z,11E,15Z)-(13S)-hydroperoxyoctadeca-9,11,15-trienoate
Other name(s): hydroperoxide isomerase; linoleate hydroperoxide isomerase; linoleic acid hydroperoxide isomerase; HPI; (9Z,11E,14Z)-(13S)-hydroperoxyoctadeca-9,11,14-trienoate 12,13-hydro-lyase; (9Z,11E,14Z)-(13S)-hydroperoxyoctadeca-9,11,14-trienoate 12,13-hydro-lyase [(9Z)-(13S)-12,13-epoxyoctadeca-9,11-dienoate-forming]; allene oxide synthase; AOS
Systematic name: (9Z,11E,15Z)-(13S)-hydroperoxyoctadeca-9,11,15-trienoate 12,13-hydro-lyase [(9Z,15Z)-(13S)-12,13-epoxyoctadeca-9,11,15-trienoate-forming]
Comments: Acts on a number of unsaturated fatty-acid hydroperoxides, forming the corresponding allene oxides. The product of the above reaction is unstable and is acted upon by EC 5.3.99.6, allene-oxide cyclase, to form the cyclopentenone derivative (15Z)-12-oxophyto-10,15-dienoate (OPDA), which is the first cyclic and biologically active metabolite in the jasmonate biosynthesis pathway [3]. The enzyme from many plants belongs to the CYP-74 family of P-450 monooxygenases [4].
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Esselman, W.J. and Clagett, C.O. Products of linoleic hydroperoxide-decomposing enzyme of alfalfa seed. J. Lipid Res. 15 (1974) 173–178. [PMID: 4208994]
2.  Hamberg, M. Mechanism of corn hydroperoxide isomerase - detection of 12,13(S)-oxido-9(Z),11-octadecadienoic acid. Biochim. Biophys. Acta 920 (1987) 76–84.
3.  Hamberg, M. Biosynthesis of 12-oxo-10,15(Z)-phytodienoic acid: identification of an allene oxide cyclase. Biochem. Biophys. Res. Commun. 156 (1988) 543–550. [DOI] [PMID: 3178850]
4.  Laudert, D., Pfannschmidt, U., Lottspeich, F., Holländer-Czytko, H. and Weiler, E.W. Cloning, molecular and functional characterization of Arabidopsis thaliana allene oxide synthase (CYP 74), the first enzyme of the octadecanoid pathway to jasmonates. Plant Mol. Biol. 31 (1996) 323–335. [PMID: 8756596]
[EC 4.2.1.92 created 1992, modified 2008]
 
 
EC 5.1.99.5
Accepted name: hydantoin racemase
Reaction: D-5-monosubstituted hydantoin = L-5-monosubstituted hydantoin
Glossary: hydantoin = imidazolidine-2,4-dione
Other name(s): 5′-monosubstituted-hydantoin racemase; HyuA; HyuE
Systematic name: D-5-monosubstituted-hydantoin racemase
Comments: This enzyme, along with N-carbamoylase (EC 3.5.1.77 and EC 3.5.1.87) and hydantoinase, forms part of the reaction cascade known as the "hydantoinase process", which allows the total conversion of D,L-5-monosubstituted hydantoins into optically pure D- or L-amino acids [7]. The enzyme from Pseudomonas sp. (HyuE) has a preference for hydantoins with aliphatic substituents, e.g. D- and L-5-[2-(methylsulfanyl)ethyl]hydantoin, whereas that from Arthrobacter aurescens shows highest activity with arylalkyl substituents, especially 5-benzylhydantoin, at the 5-position [2]. In the enzyme from Sinorhizobium meliloti, Cys76 is responsible for recognition and proton retrieval of D-isomers, while Cys181 is responsible for L-isomer recognition and racemization [6].
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Watabe, K., Ishikawa, T., Mukohara, Y. and Nakamura, H. Purification and characterization of the hydantoin racemase of Pseudomonas sp. strain NS671 expressed in Escherichia coli. J. Bacteriol. 174 (1992) 7989–7995. [DOI] [PMID: 1459947]
2.  Wiese, A., Pietzsch, M., Syldatk, C., Mattes, R. and Altenbuchner, J. Hydantoin racemase from Arthrobacter aurescens DSM 3747: heterologous expression, purification and characterization. J. Biotechnol. 80 (2000) 217–230. [DOI] [PMID: 10949312]
3.  Martínez-Rodríguez, S., Las Heras-Vázquez, F.J., Mingorance-Cazorla, L., Clemente-Jiménez, J.M. and Rodríguez-Vico, F. Molecular cloning, purification, and biochemical characterization of hydantoin racemase from the legume symbiont Sinorhizobium meliloti CECT 4114. Appl. Environ. Microbiol. 70 (2004) 625–630. [DOI] [PMID: 14711700]
4.  Martínez-Rodríguez, S., Las Heras-Vázquez, F.J., Clemente-Jiménez, J.M. and Rodríguez-Vico, F. Biochemical characterization of a novel hydantoin racemase from Agrobacterium tumefaciens C58. Biochimie 86 (2004) 77–81. [DOI] [PMID: 15016445]
5.  Suzuki, S., Onishi, N. and Yokozeki, K. Purification and characterization of hydantoin racemase from Microbacterium liquefaciens AJ 3912. Biosci. Biotechnol. Biochem. 69 (2005) 530–536. [DOI] [PMID: 15784981]
6.  Martínez-Rodríguez, S., Andújar-Sánchez, M., Neira, J.L., Clemente-Jiménez, J.M., Jara-Pérez, V., Rodríguez-Vico, F. and Las Heras-Vázquez, F.J. Site-directed mutagenesis indicates an important role of cysteines 76 and 181 in the catalysis of hydantoin racemase from Sinorhizobium meliloti. Protein Sci. 15 (2006) 2729–2738. [DOI] [PMID: 17132860]
7.  Altenbuchner, J., Siemann-Herzberg, M. and Syldatk, C. Hydantoinases and related enzymes as biocatalysts for the synthesis of unnatural chiral amino acids. Curr. Opin. Biotechnol. 12 (2001) 559–563. [DOI] [PMID: 11849938]
[EC 5.1.99.5 created 2008]
 
 
EC 5.3.1.27
Accepted name: 6-phospho-3-hexuloisomerase
Reaction: D-arabino-hex-3-ulose 6-phosphate = D-fructose 6-phosphate
For diagram of reaction, click here
Other name(s): 3-hexulose-6-phosphate isomerase; phospho-3-hexuloisomerase; PHI; 6-phospho-3-hexulose isomerase; YckF
Systematic name: D-arabino-hex-3-ulose-6-phosphate isomerase
Comments: This enzyme, along with EC 4.1.2.43, 3-hexulose-6-phosphate synthase, plays a key role in the ribulose-monophosphate cycle of formaldehyde fixation, which is present in many microorganisms that are capable of utilizing C1-compounds [1]. The hyperthermophilic and anaerobic archaeon Pyrococcus horikoshii OT3 constitutively produces a bifunctional enzyme that sequentially catalyses the reactions of EC 4.1.2.43 (3-hexulose-6-phosphate synthase) and this enzyme [4].
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Ferenci, T., Strøm, T. and Quayle, J.R. Purification and properties of 3-hexulose phosphate synthase and phospho-3-hexuloisomerase from Methylococcus capsulatus. Biochem. J. 144 (1974) 477–486. [PMID: 4219834]
2.  Yurimoto, H., Kato, N. and Sakai, Y. Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism. Chem. Rec. 5 (2005) 367–375. [DOI] [PMID: 16278835]
3.  Kato, N., Yurimoto, H. and Thauer, R.K. The physiological role of the ribulose monophosphate pathway in bacteria and archaea. Biosci. Biotechnol. Biochem. 70 (2006) 10–21. [DOI] [PMID: 16428816]
4.  Orita, I., Yurimoto, H., Hirai, R., Kawarabayasi, Y., Sakai, Y. and Kato, N. The archaeon Pyrococcus horikoshii possesses a bifunctional enzyme for formaldehyde fixation via the ribulose monophosphate pathway. J. Bacteriol. 187 (2005) 3636–3642. [DOI] [PMID: 15901685]
5.  Martinez-Cruz, L.A., Dreyer, M.K., Boisvert, D.C., Yokota, H., Martinez-Chantar, M.L., Kim, R. and Kim, S.H. Crystal structure of MJ1247 protein from M. jannaschii at 2.0 Å resolution infers a molecular function of 3-hexulose-6-phosphate isomerase. Structure 10 (2002) 195–204. [DOI] [PMID: 11839305]
6.  Taylor, E.J., Charnock, S.J., Colby, J., Davies, G.J. and Black, G.W. Cloning, purification and characterization of the 6-phospho-3-hexulose isomerase YckF from Bacillus subtilis. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 1138–1140. [PMID: 11468398]
[EC 5.3.1.27 created 2008]
 
 


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