The Enzyme Database

Displaying entries 101-134 of 134.

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EC 3.1.3.91     
Accepted name: 7-methylguanosine nucleotidase
Reaction: (1) N7-methyl-GMP + H2O = N7-methyl-guanosine + phosphate
(2) CMP + H2O = cytidine + phosphate
Other name(s): cytosolic nucleotidase III-like; cNIII-like; N7-methylguanylate 5′-phosphatase
Systematic name: N7-methyl-GMP phosphohydrolase
Comments: The enzyme also has low activity with N7-methyl-GDP, producing N7-methyl-GMP. Does not accept AMP or GMP, and has low activity with UMP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Buschmann, J., Moritz, B., Jeske, M., Lilie, H., Schierhorn, A. and Wahle, E. Identification of Drosophila and human 7-methyl GMP-specific nucleotidases. J. Biol. Chem. 288 (2013) 2441–2451. [DOI] [PMID: 23223233]
[EC 3.1.3.91 created 2013]
 
 
EC 3.1.4.59     
Accepted name: cyclic-di-AMP phosphodiesterase
Reaction: cyclic di-3′,5′-adenylate + H2O = 5′-O-phosphonoadenylyl-(3′→5′)-adenosine
For diagram of cyclic di-3′,5′-adenylate biosynthesis and breakdown, click here
Glossary: cyclic di-3′,5′-adenylate = cyclic bis(3′→5′)diadenylate
5′-O-phosphonoadenylyl-(3′→5′)-adenosine = pApA
Other name(s): gdpP (gene name)
Systematic name: cyclic bis(3′→5′)diadenylate 3′-adenylylhydrolase
Comments: The enzyme, described from Gram-positive bacteria, degrades the second messenger cyclic di-3′,5′-adenylate. It is a membrane-bound protein that contains a cytoplasmic facing Per-Arnt-Sim (PAS) domain, a modified GGDEF domain, and a DHH/DHHA1 domain, which confers the phosphodiesterase activity. Activity requires Mn2+ and is inhibited by pApA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Rao, F., See, R.Y., Zhang, D., Toh, D.C., Ji, Q. and Liang, Z.X. YybT is a signaling protein that contains a cyclic dinucleotide phosphodiesterase domain and a GGDEF domain with ATPase activity. J. Biol. Chem. 285 (2010) 473–482. [PMID: 19901023]
2.  Corrigan, R.M., Abbott, J.C., Burhenne, H., Kaever, V. and Grundling, A. c-di-AMP is a new second messenger in Staphylococcus aureus with a role in controlling cell size and envelope stress. PLoS Pathog. 7:e1002217 (2011). [PMID: 21909268]
3.  Griffiths, J.M. and O'Neill, A.J. Loss of function of the gdpP protein leads to joint β-lactam/glycopeptide tolerance in Staphylococcus aureus. Antimicrob. Agents Chemother. 56 (2012) 579–581. [PMID: 21986827]
4.  Bowman, L., Zeden, M.S., Schuster, C.F., Kaever, V. and Grundling, A. New insights into the cyclic di-adenosine monophosphate (c-di-AMP) degradation pathway and the requirement of the cyclic dinucleotide for acid stress resistance in Staphylococcus aureus. J. Biol. Chem. 291 (2016) 26970–26986. [PMID: 27834680]
[EC 3.1.4.59 created 2019]
 
 
EC 3.1.7.2     
Accepted name: guanosine-3′,5′-bis(diphosphate) 3′-diphosphatase
Reaction: guanosine 3′,5′-bis(diphosphate) + H2O = GDP + diphosphate
Glossary: GDP = guanosine 5′-diphosphate
Other name(s): guanosine-3′,5′-bis(diphosphate) 3′-pyrophosphatase; PpGpp-3′-pyrophosphohydrolase; PpGpp phosphohydrolase
Systematic name: guanosine-3′,5′-bis(diphosphate) 3′-diphosphohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 70457-12-4
References:
1.  Heinemeyer, E.-A. and Richter, D. Characterization of the guanosine 5′-triphosphate 3′-diphosphate and guanosine 5′-diphosphate 3′-diphosphate degradation reaction catalyzed by a specific pyrophosphorylase from Escherichia coli. Biochemistry 17 (1978) 5368–5372. [PMID: 365225]
2.  Richter, D., Fehr, S. and Harder, R. The guanosine 3′,5′-bis(diphosphate) (ppGpp) cycle. Comparison of synthesis and degradation of guanosine 3′,5′-bis(diphosphate) in various bacterial systems. Eur. J. Biochem. 99 (1979) 57–64. [DOI] [PMID: 114395]
[EC 3.1.7.2 created 1980]
 
 
EC 3.2.1.42     
Accepted name: GDP-glucosidase
Reaction: GDP-glucose + H2O = D-glucose + GDP
Other name(s): guanosine diphosphoglucosidase; guanosine diphosphate D-glucose glucohydrolase
Systematic name: GDP-glucose glucohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37288-36-1
References:
1.  Sonnino, S., Carinatti, H. and Cabib, E. Guanosine diphosphate D-glucose glucohydrolase. Arch. Biochem. Biophys. 116 (1966) 26–33. [DOI] [PMID: 5963308]
[EC 3.2.1.42 created 1972]
 
 
EC 3.2.1.184     
Accepted name: UDP-N,N′-diacetylbacillosamine 2-epimerase (hydrolysing)
Reaction: UDP-N,N′-diacetylbacillosamine + H2O = UDP + 2,4-diacetamido-2,4,6-trideoxy-D-mannopyranose
For diagram of legionaminic acid biosynthesis, click here, and for mechanism, click here
Glossary: UDP-N,N′-diacetylbacillosamine = UDP-2,4-diacetamido-2,4,6-trideoxy-α-D-glucopyranose
Other name(s): UDP-Bac2Ac4Ac 2-epimerase; NeuC
Systematic name: UDP-N,N′-diacetylbacillosamine hydrolase (2-epimerising)
Comments: Requires Mg2+. Involved in biosynthesis of legionaminic acid, a nonulosonate derivative that is incorporated by some bacteria into assorted virulence-associated cell surface glycoconjugates. The initial product formed by the enzyme from Legionella pneumophila, which incorporates legionaminic acid into the O-antigen moiety of its lipopolysaccharide, is 2,4-diacetamido-2,4,6-trideoxy-α-D-mannopyranose, which rapidly mutarotates to a mixture of anomers [1]. The enzyme from Campylobacter jejuni, which incorporates legionaminic acid into flagellin, prefers GDP-N,N′-diacetylbacillosamine [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Glaze, P.A., Watson, D.C., Young, N.M. and Tanner, M.E. Biosynthesis of CMP-N,N′-diacetyllegionaminic acid from UDP-N,N′-diacetylbacillosamine in Legionella pneumophila. Biochemistry 47 (2008) 3272–3282. [DOI] [PMID: 18275154]
2.  Schoenhofen, I.C., Vinogradov, E., Whitfield, D.M., Brisson, J.R. and Logan, S.M. The CMP-legionaminic acid pathway in Campylobacter: biosynthesis involving novel GDP-linked precursors. Glycobiology 19 (2009) 715–725. [DOI] [PMID: 19282391]
[EC 3.2.1.184 created 2012]
 
 
EC 3.6.1.6     
Accepted name: nucleoside diphosphate phosphatase
Reaction: a nucleoside diphosphate + H2O = a nucleoside phosphate + phosphate
Other name(s): nucleoside-diphosphatase; thiaminpyrophosphatase; UDPase; inosine diphosphatase; adenosine diphosphatase; IDPase; ADPase; adenosinepyrophosphatase; guanosine diphosphatase; guanosine 5′-diphosphatase; inosine 5′-diphosphatase; uridine diphosphatase; uridine 5′-diphosphatase; type B nucleoside diphosphatase; GDPase; CDPase; nucleoside 5′-diphosphatase; type L nucleoside diphosphatase; NDPase; nucleoside diphosphate phosphohydrolase
Systematic name: nucleoside-diphosphate phosphohydrolase
Comments: The enzyme, which appears to be limited to metazoa, acts on multiple nucleoside diphosphates as well as on D-ribose 5-diphosphate. Specificity depends on species and isoform.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9027-69-4
References:
1.  Gibson, D.M., Ayengar, P. and Sanadi, D.R. A phosphatase specific for nucleoside diphosphates. Biochim. Biophys. Acta 16 (1955) 536–538. [DOI] [PMID: 14389272]
2.  Horecker, B.L., Hurwitz, J. and Heppel, L.A. The synthesis of ribose 5-pyrophosphate and ribose 5-triphosphate. J. Am. Chem. Soc. 79 (1957) 701–702.
3.  Yeung, G., Mulero, J.J., McGowan, D.W., Bajwa, S.S. and Ford, J.E. CD39L2, a gene encoding a human nucleoside diphosphatase, predominantly expressed in the heart. Biochemistry 39 (2000) 12916–12923. [DOI] [PMID: 11041856]
4.  Failer, B.U., Braun, N. and Zimmermann, H. Cloning, expression, and functional characterization of a Ca(2+)-dependent endoplasmic reticulum nucleoside diphosphatase. J. Biol. Chem. 277 (2002) 36978–36986. [DOI] [PMID: 12167635]
5.  Uccelletti, D., O'Callaghan, C., Berninsone, P., Zemtseva, I., Abeijon, C. and Hirschberg, C.B. ire-1-dependent transcriptional up-regulation of a lumenal uridine diphosphatase from Caenorhabditis elegans. J. Biol. Chem. 279 (2004) 27390–27398. [DOI] [PMID: 15102851]
[EC 3.6.1.6 created 1961]
 
 
EC 3.6.1.42     
Accepted name: guanosine-diphosphatase
Reaction: GDP + H2O = GMP + phosphate
Other name(s): GDPase
Systematic name: GDP phosphohydrolase
Comments: Also acts on UDP but not on other nucleoside diphosphates and triphosphates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 98037-56-0
References:
1.  Raychaudhuri, P., Ghosh, S. and Maitra, U. Purification and characterization of a guanosine diphosphatase activity from calf liver microsomal salt wash proteins. J. Biol. Chem. 260 (1985) 8306–8311. [PMID: 2989286]
[EC 3.6.1.42 created 1989]
 
 
EC 3.6.1.58     
Accepted name: 8-oxo-dGDP phosphatase
Reaction: (1) 8-oxo-dGDP + H2O = 8-oxo-dGMP + phosphate
(2) 8-oxo-GDP + H2O = 8-oxo-GMP + phosphate
Glossary: 8-oxo-dGDP = 8-oxo-7,8-dihydro-2′-deoxyguanosine 5′-diphosphate
Other name(s): NUDT5; MTH3 (gene name); NUDT18
Systematic name: 8-oxo-dGDP phosphohydrolase
Comments: The enzyme catalyses the hydrolysis of both 8-oxo-dGDP and 8-oxo-GDP thereby preventing translational errors caused by oxidative damage. The preferred in vivo substrate is not known. The enzyme does not degrade 8-oxo-dGTP and 8-oxo-GTP to the monophosphates (cf. EC 3.6.1.55, 8-oxo-dGTP diphosphatase) [1,2]. Ribonucleotide diphosphates and deoxyribonucleotide diphosphates are hydrolysed with broad specificity. The bifunctional enzyme NUDT5 also hydrolyses ADP-ribose to AMP and D-ribose 5-phosphate (cf. EC 3.6.1.13, ADP-ribose diphosphatase) [4]. The human enzyme NUDT18 also hydrolyses 8-oxo-dADP and 2-hydroxy-dADP, the latter at a slower rate [6].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Ishibashi, T., Hayakawa, H., Ito, R., Miyazawa, M., Yamagata, Y. and Sekiguchi, M. Mammalian enzymes for preventing transcriptional errors caused by oxidative damage. Nucleic Acids Res. 33 (2005) 3779–3784. [DOI] [PMID: 16002790]
2.  Ishibashi, T., Hayakawa, H. and Sekiguchi, M. A novel mechanism for preventing mutations caused by oxidation of guanine nucleotides. EMBO Rep. 4 (2003) 479–483. [DOI] [PMID: 12717453]
3.  Kamiya, H., Hori, M., Arimori, T., Sekiguchi, M., Yamagata, Y. and Harashima, H. NUDT5 hydrolyzes oxidized deoxyribonucleoside diphosphates with broad substrate specificity. DNA Repair (Amst) 8 (2009) 1250–1254. [DOI] [PMID: 19699693]
4.  Ito, R., Sekiguchi, M., Setoyama, D., Nakatsu, Y., Yamagata, Y. and Hayakawa, H. Cleavage of oxidized guanine nucleotide and ADP sugar by human NUDT5 protein. J. Biochem. 149 (2011) 731–738. [DOI] [PMID: 21389046]
5.  Zha, M., Zhong, C., Peng, Y., Hu, H. and Ding, J. Crystal structures of human NUDT5 reveal insights into the structural basis of the substrate specificity. J. Mol. Biol. 364 (2006) 1021–1033. [DOI] [PMID: 17052728]
6.  Takagi, Y., Setoyama, D., Ito, R., Kamiya, H., Yamagata, Y. and Sekiguchi, M. Human MTH3 (NUDT18) protein hydrolyzes oxidized forms of guanosine and deoxyguanosine diphosphates: comparison with MTH1 and MTH2. J. Biol. Chem. 287 (2012) 21541–21549. [DOI] [PMID: 22556419]
[EC 3.6.1.58 created 2012]
 
 
EC 3.6.1.59     
Accepted name: 5′-(N7-methyl 5′-triphosphoguanosine)-[mRNA] diphosphatase
Reaction: a 5′-(N7-methyl 5′-triphosphoguanosine)-[mRNA] + H2O = N7-methylguanosine 5′-phosphate + a 5′-diphospho-[mRNA]
Other name(s): DcpS; m7GpppX pyrophosphatase; m7GpppN m7GMP phosphohydrolase; m7GpppX diphosphatase; m7G5′ppp5’N m7GMP phosphohydrolase
Systematic name: 5′-(N7-methyl 5′-triphosphoguanosine)-[mRNA] N7-methylguanosine 5′-phosphate phosphohydrolase
Comments: The enzyme removes (decaps) the N7-methylguanosine 5-phosphate cap from an mRNA degraded to a maximal length of 10 nucleotides [3,6]. Decapping is an important process in the control of eukaryotic mRNA degradation. The enzyme functions to clear the cell of cap structure following decay of the RNA body [2]. The nematode enzyme can also decap triply methylated substrates, 5′-(N2,N2,N7-trimethyl 5′-triphosphoguanosine)-[mRNA] [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Malys, N. and McCarthy, J.E. Dcs2, a novel stress-induced modulator of m7GpppX pyrophosphatase activity that locates to P bodies. J. Mol. Biol. 363 (2006) 370–382. [DOI] [PMID: 16963086]
2.  Liu, S.W., Rajagopal, V., Patel, S.S. and Kiledjian, M. Mechanistic and kinetic analysis of the DcpS scavenger decapping enzyme. J. Biol. Chem. 283 (2008) 16427–16436. [DOI] [PMID: 18441014]
3.  Liu, H., Rodgers, N.D., Jiao, X. and Kiledjian, M. The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. EMBO J. 21 (2002) 4699–4708. [DOI] [PMID: 12198172]
4.  van Dijk, E., Le Hir, H. and Seraphin, B. DcpS can act in the 5′-3′ mRNA decay pathway in addition to the 3′-5′ pathway. Proc. Natl. Acad. Sci. USA 100 (2003) 12081–12086. [DOI] [PMID: 14523240]
5.  Chen, N., Walsh, M.A., Liu, Y., Parker, R. and Song, H. Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping. J. Mol. Biol. 347 (2005) 707–718. [DOI] [PMID: 15769464]
6.  Cohen, L.S., Mikhli, C., Friedman, C., Jankowska-Anyszka, M., Stepinski, J., Darzynkiewicz, E. and Davis, R.E. Nematode m7GpppG and m3(2,2,7)GpppG decapping: activities in Ascaris embryos and characterization of C. elegans scavenger DcpS. RNA 10 (2004) 1609–1624. [DOI] [PMID: 15383679]
7.  Wypijewska, A., Bojarska, E., Lukaszewicz, M., Stepinski, J., Jemielity, J., Davis, R.E. and Darzynkiewicz, E. 7-Methylguanosine diphosphate (m7GDP) is not hydrolyzed but strongly bound by decapping scavenger (DcpS) enzymes and potently inhibits their activity. Biochemistry 51 (2012) 8003–8013. [DOI] [PMID: 22985415]
[EC 3.6.1.59 created 2012, modified 2013]
 
 
EC 3.6.1.62     
Accepted name: 5′-(N7-methylguanosine 5′-triphospho)-[mRNA] hydrolase
Reaction: a 5′-(N7-methylguanosine 5′-triphospho)-[mRNA] + H2O = N7-methylguanosine 5′-diphosphate + a 5′-phospho-[mRNA]
Glossary: N7-methylguanosine 5′-diphosphate = m7GDP
Other name(s): Dcp2; NUDT16; D10 protein; D9 protein; D10 decapping enzyme; decapping enzyme; m7GpppN-mRNA hydrolase; m7GpppN-mRNA m7GDP phosphohydrolase
Systematic name: 5′-(N7-methylguanosine 5′-triphospho)-[mRNA] N7-methylguanosine-5′-diphosphate phosphohydrolase
Comments: Decapping of mRNA is a critical step in eukaryotic mRNA turnover. The enzyme is unable to cleave a free cap structure (m7GpppG) [3]. The enzyme from Vaccinia virus is synergistically activated in the presence of Mg2+ and Mn2+ [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Xu, J., Yang, J.Y., Niu, Q.W. and Chua, N.H. Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for postembryonic development. Plant Cell 18 (2006) 3386–3398. [DOI] [PMID: 17158604]
2.  Lu, G., Zhang, J., Li, Y., Li, Z., Zhang, N., Xu, X., Wang, T., Guan, Z., Gao, G.F. and Yan, J. hNUDT16: a universal decapping enzyme for small nucleolar RNA and cytoplasmic mRNA. Protein Cell 2 (2011) 64–73. [DOI] [PMID: 21337011]
3.  van Dijk, E., Cougot, N., Meyer, S., Babajko, S., Wahle, E. and Seraphin, B. Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J. 21 (2002) 6915–6924. [DOI] [PMID: 12486012]
4.  Parrish, S., Resch, W. and Moss, B. Vaccinia virus D10 protein has mRNA decapping activity, providing a mechanism for control of host and viral gene expression. Proc. Natl. Acad. Sci. USA 104 (2007) 2139–2144. [DOI] [PMID: 17283339]
5.  Souliere, M.F., Perreault, J.P. and Bisaillon, M. Characterization of the vaccinia virus D10 decapping enzyme provides evidence for a two-metal-ion mechanism. Biochem. J. 420 (2009) 27–35. [DOI] [PMID: 19210265]
6.  Parrish, S. and Moss, B. Characterization of a second vaccinia virus mRNA-decapping enzyme conserved in poxviruses. J. Virol. 81 (2007) 12973–12978. [DOI] [PMID: 17881455]
7.  Song, M.G., Li, Y. and Kiledjian, M. Multiple mRNA decapping enzymes in mammalian cells. Mol. Cell 40 (2010) 423–432. [DOI] [PMID: 21070968]
[EC 3.6.1.62 created 2012, modified 2013]
 
 
EC 3.6.1.64     
Accepted name: inosine diphosphate phosphatase
Reaction: (1) IDP + H2O = IMP + phosphate
(2) dIDP + H2O = dIMP + phosphate
Other name(s): (deoxy)inosine diphosphatase; NUDT16
Systematic name: inosine diphosphate phosphatase
Comments: The human enzyme also hydrolyses GDP and dGDP, and to a lesser extent ITP, dITP and XTP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Iyama, T., Abolhassani, N., Tsuchimoto, D., Nonaka, M. and Nakabeppu, Y. NUDT16 is a (deoxy)inosine diphosphatase, and its deficiency induces accumulation of single-strand breaks in nuclear DNA and growth arrest. Nucleic Acids Res. 38 (2010) 4834–4843. [DOI] [PMID: 20385596]
[EC 3.6.1.64 created 2013]
 
 
EC 3.6.1.69     
Accepted name: 8-oxo-(d)GTP phosphatase
Reaction: (1) 8-oxo-GTP + H2O = 8-oxo-GDP + phosphate
(2) 8-oxo-dGTP + H2O = 8-oxo-dGDP + phosphate
Glossary: 8-oxo-dGTP = 2′-deoxy-7,8-dihydro-8-oxoguanosine 5′-triphosphate
Other name(s): mutT1 (gene name)
Systematic name: 8-oxo-dGTP diphosphohydrolase
Comments: The enzyme, characterized from the bacterium Mycobacterium tuberculosis, catalyses the hydrolysis of both 8-oxo-GTP and 8-oxo-dGTP, thereby preventing transcriptional and translational errors caused by oxidative damage. The enzyme is highly specific. Unlike EC 3.6.1.55, 8-oxo-dGTP diphosphatase, it removes only a single phosphate group. The nucleoside diphosphate products are hydrolysed further by EC 3.6.1.58, 8-oxo-dGDP phosphatase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Patil, A.G., Sang, P.B., Govindan, A. and Varshney, U. Mycobacterium tuberculosis MutT1 (Rv2985) and ADPRase (Rv1700) proteins constitute a two-stage mechanism of 8-oxo-dGTP and 8-oxo-GTP detoxification and adenosine to cytidine mutation avoidance. J. Biol. Chem. 288 (2013) 11252–11262. [PMID: 23463507]
[EC 3.6.1.69 created 2019]
 
 
EC 3.6.5.1     
Accepted name: heterotrimeric G-protein GTPase
Reaction: GTP + H2O = GDP + phosphate
Systematic name: GTP phosphohydrolase (signalling)
Comments: This group comprises GTP-hydrolysing systems, where GTP and GDP alternate in binding. This group includes stimulatory and inhibitory G-proteins such as Gs, Gi, Go and Golf, targetting adenylate cyclase and/or K+ and Ca2+ channels; Gq stimulating phospholipase C; transducin activating cGMP phosphodiesterase; gustducin activating cAMP phosphodiesterase. Golf is instrumental in odour perception, transducin in vision and gustducin in taste recognition. At least 16 different α subunits (39-52 kDa), 5 β subunits (36 kDa) and 12 γ subunits (6-9 kDa) are known.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Neer, E.J. Heterotrimeric G proteins: organizers of transmembrane signals. Cell 80 (1995) 249–259. [DOI] [PMID: 7834744]
2.  Sprang, S.R. G protein mechanisms: insights from structural analysis. Annu. Rev. Biochem. 66 (1997) 639–678. [DOI] [PMID: 9242920]
3.  Bondarenko, V.A., Deasi, M., Dua, S., Yamazaki, M., Amin, R.H., Yousif, K.K., Kinumi, T., Ohashi, M., Komori, N., Matsumoto, H., Jackson, K.W., Hayashi, F., Usukura, J., Lipikin, V.M. and Yamazaki, A. Residues within the polycationic region of cGMP phosphodiesterase γ subunit crucial for the interaction with transducin α subunit. Identification by endogenous ADP-ribosylation and site-directed mutagenesis. J. Biol. Chem. 272 (1997) 15856–15864. [DOI] [PMID: 9188484]
4.  Ming, D., Ruiz-Avila, L. and Margolskee, R.F. Characterization and solubilization of bitter-responsive receptors that couple to gustducin. Proc. Natl. Acad. Sci. USA 95 (1998) 8933–8938. [DOI] [PMID: 9671782]
[EC 3.6.5.1 created 2000 as EC 3.6.1.46, transferred 2003 to EC 3.6.5.1]
 
 
EC 3.6.5.2     
Accepted name: small monomeric GTPase
Reaction: GTP + H2O = GDP + phosphate
Systematic name: GTP phosphohydrolase (cell-regulating)
Comments: A family of about 50 enzymes with a molecular mass of 21 kDa that are distantly related to the α-subunit of heterotrimeric G-protein GTPase (EC 3.6.5.1). They are involved in cell-growth regulation (Ras subfamily), membrane vesicle traffic and uncoating (Rab and ARF subfamilies), nuclear protein import (Ran subfamily) and organization of the cytoskeleton (Rho and Rac subfamilies).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Bourne, H.R., Sanders, D.A. and McCormick, F. The GTPase superfamily: conserved structure and molecular mechanisms. Nature 349 (1991) 117–127. [DOI] [PMID: 1898771]
2.  Hall, A. Small GTP-binding proteins and the regulation of actin cytoskeleton. Annu. Rev. Cell Biol. 10 (1994) 31–54. [DOI] [PMID: 7888179]
3.  Geyer, M. and Wittinghofer, A. GEFs, GAPs, GDIs and effectors: taking a closer (3D) look at the regulation of Ras-related GTP-binding proteins. Curr. Opin. Struct. Biol. 7 (1997) 786–792. [DOI] [PMID: 9434896]
4.  Vitale, N., Moss, J. and Vaughan, M. Molecular characterization of the GTPase-activating domain of ADP-ribosylation factor domain protein 1 (ARD1). J. Biol. Chem. 273 (1998) 2553–2560. [DOI] [PMID: 9446556]
[EC 3.6.5.2 created 2000 as EC 3.6.1.47, transferred 2003 to EC 3.6.5.2]
 
 
EC 3.6.5.3     
Accepted name: protein-synthesizing GTPase
Reaction: GTP + H2O = GDP + phosphate
Other name(s): elongation factor (EF); initiation factor (IF); peptide-release or termination factor
Systematic name: GTP phosphohydrolase (mRNA-translation-assisting)
Comments: This enzyme comprises a family of proteins involved in prokaryotic as well as eukaryotic protein synthesis. In the initiation factor complex, it is IF-2b (98 kDa) that binds GTP and subsequently hydrolyses it in prokaryotes. In eukaryotes, it is eIF-2 (150 kDa) that binds GTP. In the elongation phase, the GTP-hydrolysing proteins are the EF-Tu polypeptide of the prokaryotic transfer factor (43 kDa), the eukaryotic elongation factor EF-1α (53 kDa), the prokaryotic EF-G (77 kDa), the eukaryotic EF-2 (70-110 kDa) and the signal recognition particle that play a role in endoplasmic reticulum protein synthesis (325 kDa). EF-Tu and EF-1α catalyse binding of aminoacyl-tRNA to the ribosomal A-site, while EF-G and EF-2 catalyse the translocation of peptidyl-tRNA from the A-site to the P-site. GTPase activity is also involved in polypeptide release from the ribosome with the aid of the pRFs and eRFs.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Kurzchalia, T.V., Bommer, U.A., Babkina, G.T. and Karpova, G.G. GTP interacts with the γ-subunit of eukaryotic initiation factor EIF-2. FEBS Lett. 175 (1984) 313–316. [DOI] [PMID: 6566615]
2.  Kisselev, L.L. and Frolova, L.Yu. Termination of translation in eukaryotes. Biochem. Cell Biol. 73 (1995) 1079–1086. [PMID: 8722024]
3.  Rodnina, M.V., Savelsberg, A., Katunin, V.I. and Wintermeyer, W. Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. Nature 385 (1997) 37–41. [DOI] [PMID: 8985244]
4.  Freistroffer, D.V., Pavlov, M.Y., MacDougall, J., Buckingham, R.H. and Ehrenberg, M. Release factor RF3 in E. coli accelerates the dissociation of release factors RF1 and RF2 from the ribosome in a GTP-dependent manner. EMBO J. 16 (1997) 4126–4133. [DOI] [PMID: 9233821]
5.  Krab, I.M. and Parmeggiani, A. EF-Tu, a GTPase odyssey. Biochim. Biophys. Acta 1443 (1998) 1–22. [DOI] [PMID: 9838020]
[EC 3.6.5.3 created 2000 as EC 3.6.1.48, transferred 2003 to EC 3.6.5.3]
 
 
EC 3.6.5.4     
Accepted name: signal-recognition-particle GTPase
Reaction: GTP + H2O = GDP + phosphate
Systematic name: GTP phosphohydrolase (protein-synthesis-assisting)
Comments: Activity is associated with the signal-recognition particle (a protein- and RNA-containing structure involved in endoplasmic-reticulum-associated protein synthesis).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Connolly, T. and Gilmore, R. The signal recognition particle receptor mediates the GTP-dependent displacement of SRP from the signal sequence of the nascent polypeptide. Cell 57 (1989) 599–610. [DOI] [PMID: 2541918]
2.  Connolly, T., Rapiejko, P.J. and Gilmore, R. Requirement of GTP hydrolysis for dissociation of the signal recognition particle from its receptor. Science 252 (1991) 1171–1173. [DOI] [PMID: 1851576]
3.  Miller, J.D., Wilhelm, H., Gierasch, L., Gilmore, R. and Walter, P. GTP binding and hydrolysis by the signal recognition particle during initiation of protein translocation. Nature 366 (1993) 351–354. [DOI] [PMID: 8247130]
4.  Freymann, D.M., Keenan, R.J., Stroud, R.M. and Walter, P. Structure of the conserved GTPase domain of the signal recognition particle. Nature 385 (1997) 361–364. [DOI] [PMID: 9002524]
[EC 3.6.5.4 created 2000 as EC 3.6.1.49, transferred 2003 to EC 3.6.5.4]
 
 
EC 3.6.5.5     
Accepted name: dynamin GTPase
Reaction: GTP + H2O = GDP + phosphate
Systematic name: GTP phosphohydrolase (vesicle-releasing)
Comments: An enzyme with a molecular mass of about 100 kDa that is involved in endocytosis and is instrumental in pinching off membrane vesicles.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Warnock, D.E. and Schmid, S.L. Dynamin GTPase, a force-generating molecular switch. Bioessays 18 (1996) 885–893. [DOI] [PMID: 8939066]
2.  McClure, S.J. and Robinson, P.J. Dynamin, endocytosis and intracellular signalling. Mol. Membr. Biol. 13 (1996) 189–215. [PMID: 9116759]
3.  Oh, P., McIntosh, D.P. and Schnitzer, J.E. Dynamin at the neck of caveolae mediates their budding to form transport vesicles by GTP-driven fission from the plasma membrane of endothelium. J. Cell Biol. 141 (1998) 101–114. [PMID: 9531551]
[EC 3.6.5.5 created 2000 as EC 3.6.1.50, transferred 2003 to EC 3.6.5.5]
 
 
EC 3.6.5.6     
Accepted name: tubulin GTPase
Reaction: GTP + H2O = GDP + phosphate
Systematic name: GTP phosphohydrolase (microtubule-releasing)
Comments: An intrinsic activity of α-tubulin involved in tubulin folding, division plane formation in prokaryotic cells and others.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Yu, X.C. and Margolin, W. Ca2+-mediated GTP-dependent dynamic assembly of bacetrial cell division protein FtsZ into asters and polymer networks in vitro. EMBO J. 16 (1997) 5455–5463. [DOI] [PMID: 9312004]
2.  Tian, G., Bhamidipati, A., Cowan, N.J. and Lewis, S.A. Tubulin folding cofactors as GTPase-activating proteins. GTP hydrolysis and the assembly of the α/β-tubulin heterodimer. J. Biol. Chem. 274 (1999) 24054–24058. [DOI] [PMID: 10446175]
3.  Roychowdhury, S., Panda, D., Wilson, L. and Rasenick, M.M. G protein α subunits activate tubulin GTPase and modulate microtubule polymerization dynamics. J. Biol. Chem. 274 (1999) 13485–13490. [DOI] [PMID: 10224115]
[EC 3.6.5.6 created 2000 as EC 3.6.1.51, transferred 2003 to EC 3.6.5.6]
 
 
EC 4.1.1.32     
Accepted name: phosphoenolpyruvate carboxykinase (GTP)
Reaction: GTP + oxaloacetate = GDP + phosphoenolpyruvate + CO2
Other name(s): phosphoenolpyruvate carboxylase (ambiguous); phosphopyruvate carboxylase (ambiguous); phosphopyruvate (guanosine triphosphate) carboxykinase; phosphoenolpyruvic carboxykinase (GTP); phosphopyruvate carboxylase (GTP); phosphoenolpyruvic carboxylase (GTP); phosphoenolpyruvic carboxykinase (ambiguous); phosphoenolpyruvate carboxykinase (ambiguous); PEP carboxylase (ambiguous); GTP:oxaloacetate carboxy-lyase (transphosphorylating)
Systematic name: GTP:oxaloacetate carboxy-lyase (adding GTP; phosphoenolpyruvate-forming)
Comments: ITP can act as phosphate donor.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9013-08-5
References:
1.  Change, H.-C. and Lane, M.D. The enzymatic carboxylation of phosphoenolpyruvate. II. Purification and properties of liver mitochondrial phosphoenolpyruvate carboxykinase. J. Biol. Chem. 241 (1966) 2413–2420. [PMID: 5911620]
2.  Kurahashi, K., Pennington, R.J. and Utter, M.J. Nucleotide specificity of oxalacetic carboxylase. J. Biol. Chem. 226 (1957) 1059–1075. [PMID: 13438893]
[EC 4.1.1.32 created 1961]
 
 
EC 4.2.1.47     
Accepted name: GDP-mannose 4,6-dehydratase
Reaction: GDP-α-D-mannose = GDP-4-dehydro-α-D-rhamnose + H2O
For diagram of gdp-l-fucose and GDP-mannose biosynthesis, click here
Glossary: GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose
Other name(s): guanosine 5′-diphosphate-D-mannose oxidoreductase; guanosine diphosphomannose oxidoreductase; guanosine diphosphomannose 4,6-dehydratase; GDP-D-mannose dehydratase; GDP-D-mannose 4,6-dehydratase; Gmd; GDP-mannose 4,6-hydro-lyase; GDP-mannose 4,6-hydro-lyase (GDP-4-dehydro-6-deoxy-D-mannose-forming)
Systematic name: GDP-α-D-mannose 4,6-hydro-lyase (GDP-4-dehydro-α-D-rhamnose-forming)
Comments: The bacterial enzyme requires bound NAD+. This enzyme forms the first step in the biosynthesis of GDP-α-D-rhamnose and GDP-β-L-fucose. In Aneurinibacillus thermoaerophilus L420-91T, this enzyme acts as a bifunctional enzyme, catalysing the above reaction as well as the reaction catalysed by EC 1.1.1.281, GDP-4-dehydro-6-deoxy-D-mannose reductase [5]. Belongs to the short-chain dehydrogenase/reductase enzyme family, having homologous structures and a conserved catalytic triad of Lys, Tyr and Ser/Thr residues [6].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37211-59-9
References:
1.  Elbein, A.D. and Heath, E.C. The biosynthesis of cell wall lipopolysaccharide in Escherichia coli. II. Guanosine diphosphate 4-keto-6-deoxy-D-mannose, an intermediate in the biosynthesis of guanosine diphosphate colitose. J. Biol. Chem. 240 (1965) 1926–1931. [PMID: 14299611]
2.  Liao, T.-H. and Barber, G.A. Purification of guanosine 5′-diphosphate D-mannose oxidoreductase from Phaseolus vulgaris. Biochim. Biophys. Acta 276 (1972) 85–93. [DOI] [PMID: 5047712]
3.  Melo, A., Elliott, H. and Glaser, L. The mechanism of 6-deoxyhexose synthesis. I. Intramolecular hydrogen transfer catalyzed by deoxythymidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 243 (1968) 1467–1474. [PMID: 4869560]
4.  Sullivan, F.X., Kumar, R., Kriz, R., Stahl, M., Xu, G.Y., Rouse, J., Chang, X.J., Boodhoo, A., Potvin, B. and Cumming, D.A. Molecular cloning of human GDP-mannose 4,6-dehydratase and reconstitution of GDP-fucose biosynthesis in vitro. J. Biol. Chem. 273 (1988) 8193–8202. [DOI] [PMID: 9525924]
5.  Kneidinger, B., Graninger, M., Adam, G., Puchberger, M., Kosma, P., Zayni, S. and Messner, P. Identification of two GDP-6-deoxy-D-lyxo-4-hexulose reductases synthesizing GDP-D-rhamnose in Aneurinibacillus thermoaerophilus L420-91T. J. Biol. Chem. 276 (2001) 5577–5583. [DOI] [PMID: 11096116]
6.  Mulichak, A.M., Bonin, C.P., Reiter, W.D. and Garavito, R.M. Structure of the MUR1 GDP-mannose 4,6-dehydratase from Arabidopsis thaliana: implications for ligand binding and specificity. Biochemistry 41 (2000) 15578–15589. [DOI] [PMID: 12501186]
[EC 4.2.1.47 created 1972, modified 2004]
 
 
EC 4.2.1.168     
Accepted name: GDP-4-dehydro-6-deoxy-α-D-mannose 3-dehydratase
Reaction: GDP-4-dehydro-α-D-rhamnose + L-glutamate = GDP-4-dehydro-3,6-dideoxy-α-D-mannose + 2-oxoglutarate + NH3 (overall reaction)
(1a) GDP-4-dehydro-α-D-rhamnose + L-glutamate = 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol] + 2-oxoglutarate + H2O
(1b) 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol] = 2-GDP-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] (spontaneous)
(1c) GDP-2-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] + H2O = GDP-4-dehydro-3,6-dideoxy-α-D-mannose + NH3 (spontaneous)
For diagram of GDP-colitose biosynthesis, click here
Glossary: GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose
Other name(s): colD (gene name)
Systematic name: GDP-4-dehydro-α-D-rhamnose 3-hydro-lyase
Comments: This enzyme, involved in β-L-colitose biosynthesis, is a unique vitamin-B6-dependent enzyme. In the first step of catalysis, the bound pyridoxal phosphate (PLP) cafactor is transaminated to the pyridoxamine 5′-phosphate (PMP) form of vitamin B6, using L-glutamate as the amino group donor. The PMP cofactor then forms a Schiff base with the sugar substrate and the resulting adduct undergoes a 1,4-dehydration to eliminate the 3-OH group. Hydrolysis of the product from the enzyme restores the PLP cofactor and results in the release of an unstable enamine intermediate. This intermediate tautomerizes to form an imine form, which hydrolyses spontaneously, releasing ammonia and forming the final product.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Alam, J., Beyer, N. and Liu, H.W. Biosynthesis of colitose: expression, purification, and mechanistic characterization of GDP-4-keto-6-deoxy-D-mannose-3-dehydrase (ColD) and GDP-L-colitose synthase (ColC). Biochemistry 43 (2004) 16450–16460. [DOI] [PMID: 15610039]
2.  Cook, P.D. and Holden, H.M. A structural study of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: caught in the act of geminal diamine formation. Biochemistry 46 (2007) 14215–14224. [DOI] [PMID: 17997582]
[EC 4.2.1.168 created 2016]
 
 
EC 4.2.3.36     
Accepted name: terpentetriene synthase
Reaction: terpentedienyl diphosphate = terpentetriene + diphosphate
For diagram of diterpenoid biosynthesis, click here
Other name(s): Cyc2 (ambiguous)
Systematic name: terpentedienyl-diphosphate diphosphate-lyase (terpentetriene-forming)
Comments: Requires Mg2+ for maximal activity but can use Mn2+, Fe2+ or Co2+ to a lesser extent [2]. Following on from EC 5.5.1.15, terpentedienyl-diphosphate synthase, this enzyme completes the transformation of geranylgeranyl diphosphate (GGDP) into terpentetriene, which is a precursor of the diterpenoid antibiotic terpentecin. Farnesyl diphosphate can also act as a substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Dairi, T., Hamano, Y., Kuzuyama, T., Itoh, N., Furihata, K. and Seto, H. Eubacterial diterpene cyclase genes essential for production of the isoprenoid antibiotic terpentecin. J. Bacteriol. 183 (2001) 6085–6094. [DOI] [PMID: 11567009]
2.  Hamano, Y., Kuzuyama, T., Itoh, N., Furihata, K., Seto, H. and Dairi, T. Functional analysis of eubacterial diterpene cyclases responsible for biosynthesis of a diterpene antibiotic, terpentecin. J. Biol. Chem. 277 (2002) 37098–37104. [DOI] [PMID: 12138123]
3.  Eguchi, T., Dekishima, Y., Hamano, Y., Dairi, T., Seto, H. and Kakinuma, K. A new approach for the investigation of isoprenoid biosynthesis featuring pathway switching, deuterium hyperlabeling, and 1H NMR spectroscopy. The reaction mechanism of a novel streptomyces diterpene cyclase. J. Org. Chem. 68 (2003) 5433–5438. [DOI] [PMID: 12839434]
[EC 4.2.3.36 created 2008]
 
 
EC 4.2.3.38     
Accepted name: α-bisabolene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (E)-α-bisabolene + diphosphate
For diagram of bisabolene-derived sesquiterpenoid biosynthesis, click here
Other name(s): bisabolene synthase
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(E)-α-bisabolene-forming]
Comments: This cytosolic sesquiterpenoid synthase requires a divalent cation cofactor (Mg2+ or, to a lesser extent, Mn2+) to neutralize the negative charge of the diphosphate leaving group. While unlikely to encounter geranyl diphosphate (GDP) in vivo as it is localized to plastids, the enzyme can use GDP as a substrate in vitro to produce (+)-(4R)-limonene [cf. EC 4.2.3.20, (R)-limonene synthase]. The enzyme is induced as part of a defense mechanism in the grand fir Abies grandis as a response to stem wounding.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Bohlmann, J., Crock, J., Jetter, R. and Croteau, R. Terpenoid-based defenses in conifers: cDNA cloning, characterization, and functional expression of wound-inducible (E)-α-bisabolene synthase from grand fir (Abies grandis). Proc. Natl. Acad. Sci. USA 95 (1998) 6756–6761. [DOI] [PMID: 9618485]
[EC 4.2.3.38 created 2009]
 
 
EC 4.2.3.191     
Accepted name: cycloaraneosene synthase
Reaction: geranylgeranyl diphosphate = cycloaraneosene + diphosphate
For diagram of biosynthesis of fusicoccane diterpenoids, click here
Glossary: cycloaraneosene = (1R,3aR,9aS,10aR)-1,9a-dimethyl-4-methylene-7-(propan-2-yl)-1,2,3,3a,4,5,6,8,9,9a,10,10a-dodecahydrodicyclopenta[a,d][8]annulene
Other name(s): SdnA
Systematic name: geranylgeranyl-diphosphate diphosphate-lyase (cycloaraneosene-forming)
Comments: Isolated from the fungus Sordaria araneosa. Cycloaraneosene is a precursor of the antibiotic sordarin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kudo, F., Matsuura, Y., Hayashi, T., Fukushima, M. and Eguchi, T. Genome mining of the sordarin biosynthetic gene cluster from Sordaria araneosa Cain ATCC 36386: characterization of cycloaraneosene synthase and GDP-6-deoxyaltrose transferase. J. Antibiot. (Tokyo) 69 (2016) 541–548. [DOI] [PMID: 27072286]
[EC 4.2.3.191 created 2017]
 
 
EC 5.1.3.18     
Accepted name: GDP-mannose 3,5-epimerase
Reaction: (1) GDP-α-D-mannose = GDP-β-L-galactose
(2) GDP-α-D-mannose = GDP-β-L-gulose
Other name(s): GME (gene name); GDP-D-mannose:GDP-L-galactose epimerase; guanosine 5′-diphosphate D-mannose:guanosine 5′-diphosphate L-galactose epimerase
Systematic name: GDP-α-D-mannose 3,5-epimerase
Comments: The enzyme catalyses the formation of the stable intermediate GDP-β-L-gulose as well as GDP-β-L-galactose. The reaction proceeds by C4′ oxidation of GDP-α-D-mannose followed by epimerization of the C5′ position to give GDP-β-L-4-dehydro-gulose. This intermediate is either reduced to give GDP-β-L-gulose or the C3′ position is epimerized to give GDP-β-L-4-dehydro-galactose, followed by C4′ reduction to yield GDP-β-L-galactose. Both products serve as intermediates in two different variants of plant L-ascorbate biosynthesis pathways.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 72162-82-4
References:
1.  Hebda, P.A., Behrman, E.J. and Barber, G.A. The guanosine 5′-diphosphate D-mannose: guanosine 5′-diphosphate L-galactose epimerase of Chlorella pyrenoidosa. Chemical synthesis of guanosine 5′-diphosphate L-galactose and further studies of the enzyme and the reaction it catalyzes. Arch. Biochem. Biophys. 194 (1979) 496–502. [DOI] [PMID: 443816]
2.  Barber, G.A. and Hebda, P.A. GDP-D-mannose: GDP-L-galactose epimerase from Chlorella pyrenoidosa. Methods Enzymol. 83 (1982) 522–525. [PMID: 7098948]
3.  Wolucka, B.A., Persiau, G., Van Doorsselaere, J., Davey, M.W., Demol, H., Vandekerckhove, J., Van Montagu, M., Zabeau, M. and Boerjan, W. Partial purification and identification of GDP-mannose 3",5"-epimerase of Arabidopsis thaliana, a key enzyme of the plant vitamin C pathway. Proc. Natl. Acad. Sci. USA 98 (2001) 14843–14848. [PMID: 11752432]
4.  Major, L.L., Wolucka, B.A. and Naismith, J.H. Structure and function of GDP-mannose-3′,5′-epimerase: an enzyme which performs three chemical reactions at the same active site. J. Am. Chem. Soc. 127 (2005) 18309–18320. [PMID: 16366586]
5.  Watanabe, K., Suzuki, K. and Kitamura, S. Characterization of a GDP-D-mannose 3′′,5′′-epimerase from rice. Phytochemistry 67 (2006) 338–346. [PMID: 16413588]
[EC 5.1.3.18 created 1986, modified 2020]
 
 
EC 5.3.1.8     
Accepted name: mannose-6-phosphate isomerase
Reaction: D-mannose 6-phosphate = D-fructose 6-phosphate
For diagram of GDP-L-fucose and GDP-mannose biosynthesis, click here
Other name(s): phosphomannose isomerase; phosphohexomutase; phosphohexoisomerase; mannose phosphate isomerase; phosphomannoisomerase; D-mannose-6-phosphate ketol-isomerase
Systematic name: D-mannose-6-phosphate aldose-ketose-isomerase
Comments: A zinc protein.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9023-88-5
References:
1.  Bruns, F.H., Noltmann, E. and Willemsen, A. Phosphomannose-isomerase. I. Über die Aktivitätsmessung und die Sulfhydryl-sowie die metallabhängigkeit der Enzymirkung in einigen Tierischen Geweben. Biochem. Z. 330 (1958) 411–420. [PMID: 13596383]
2.  Gracy, R.W. and Noltmann, E.A. Studies on phosphomannose isomerase. II. Characterization as a zinc metalloenzyme. J. Biol. Chem. 243 (1968) 4109–4116. [PMID: 4969968]
3.  Slein, M.W. Phosphomannose isomerase. J. Biol. Chem. 186 (1950) 753–761. [PMID: 14794671]
[EC 5.3.1.8 created 1961, modified 1976]
 
 
EC 5.3.1.28     
Accepted name: D-sedoheptulose-7-phosphate isomerase
Reaction: D-sedoheptulose 7-phosphate = D-glycero-D-manno-heptose 7-phosphate
Other name(s): sedoheptulose-7-phosphate isomerase; phosphoheptose isomerase; gmhA (gene name); lpcA (gene name)
Systematic name: D-glycero-D-manno-heptose 7-phosphate aldose-ketose-isomerase
Comments: In Gram-negative bacteria the enzyme is involved in biosynthesis of ADP-L-glycero-β-D-manno-heptose, which is utilized for assembly of the lipopolysaccharide inner core. In Gram-positive bacteria the enzyme is involved in biosynthesis of GDP-D-glycero-α-D-manno-heptose, which is required for assembly of S-layer glycoprotein.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Kneidinger, B., Marolda, C., Graninger, M., Zamyatina, A., McArthur, F., Kosma, P., Valvano, M.A. and Messner, P. Biosynthesis pathway of ADP-L-glycero-β-D-manno-heptose in Escherichia coli. J. Bacteriol. 184 (2002) 363–369. [DOI] [PMID: 11751812]
2.  Kneidinger, B., Graninger, M., Puchberger, M., Kosma, P. and Messner, P. Biosynthesis of nucleotide-activated D-glycero-D-manno-heptose. J. Biol. Chem. 276 (2001) 20935–20944. [DOI] [PMID: 11279237]
3.  Valvano, M.A., Messner, P. and Kosma, P. Novel pathways for biosynthesis of nucleotide-activated glycero-manno-heptose precursors of bacterial glycoproteins and cell surface polysaccharides. Microbiology 148 (2002) 1979–1989. [DOI] [PMID: 12101286]
4.  Kim, M.S. and Shin, D.H. A preliminary X-ray study of sedoheptulose-7-phosphate isomerase from Burkholderia pseudomallei. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 65 (2009) 1110–1112. [DOI] [PMID: 19923728]
5.  Taylor, P.L., Blakely, K.M., de Leon, G.P., Walker, J.R., McArthur, F., Evdokimova, E., Zhang, K., Valvano, M.A., Wright, G.D. and Junop, M.S. Structure and function of sedoheptulose-7-phosphate isomerase, a critical enzyme for lipopolysaccharide biosynthesis and a target for antibiotic adjuvants. J. Biol. Chem. 283 (2008) 2835–2845. [DOI] [PMID: 18056714]
[EC 5.3.1.28 created 2010]
 
 
EC 5.4.2.8     
Accepted name: phosphomannomutase
Reaction: α-D-mannose 1-phosphate = D-mannose 6-phosphate
For diagram of GDP-L-fucose and GDP-mannose biosynthesis, click here
Other name(s): mannose phosphomutase; phosphomannose mutase; D-mannose 1,6-phosphomutase
Systematic name: α-D-mannose 1,6-phosphomutase
Comments: α-D-Mannose 1,6-bisphosphate or α-D-glucose 1,6-bisphosphate can act as cofactor.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 59536-73-1
References:
1.  Small, D.M. and Matheson, N.K. Phosphomannomutase and phosphoglucomutase in developing Cassia corymbosa seeds. Phytochemistry 18 (1979) 1147–1150.
[EC 5.4.2.8 created 1981 as EC 2.7.5.7, transferred 1984 to EC 5.4.2.8]
 
 
EC 5.5.1.15     
Accepted name: terpentedienyl-diphosphate synthase
Reaction: geranylgeranyl diphosphate = terpentedienyl diphosphate
For diagram of diterpenoid biosynthesis, click here
Glossary: terpentedienyl diphosphate = (2E)-3-methyl-5-[(1R,2R,4aS,8aS)-1,2,4a,5-tetramethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-1-yl]pent-2-en-1-yl diphosphate
Other name(s): terpentedienol diphosphate synthase; Cyc1; clerodadienyl diphosphate synthase; terpentedienyl-diphosphate lyase (decyclizing)
Systematic name: terpentedienyl-diphosphate lyase (ring-opening)
Comments: Requires Mg2+. Contains a DXDD motif, which is a characteristic of diterpene cylases whose reactions are initiated by protonation at the 14,15-double bond of geranylgeranyl diphosphate (GGDP) [2]. The triggering proton is lost at the end of the cyclization reaction [3]. The product of the reaction, terpentedienyl diphosphate, is the substrate for EC 4.2.3.36, terpentetriene synthase and is a precursor of the diterpenoid antibiotic terpentecin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Dairi, T., Hamano, Y., Kuzuyama, T., Itoh, N., Furihata, K. and Seto, H. Eubacterial diterpene cyclase genes essential for production of the isoprenoid antibiotic terpentecin. J. Bacteriol. 183 (2001) 6085–6094. [DOI] [PMID: 11567009]
2.  Hamano, Y., Kuzuyama, T., Itoh, N., Furihata, K., Seto, H. and Dairi, T. Functional analysis of eubacterial diterpene cyclases responsible for biosynthesis of a diterpene antibiotic, terpentecin. J. Biol. Chem. 277 (2002) 37098–37104. [DOI] [PMID: 12138123]
3.  Eguchi, T., Dekishima, Y., Hamano, Y., Dairi, T., Seto, H. and Kakinuma, K. A new approach for the investigation of isoprenoid biosynthesis featuring pathway switching, deuterium hyperlabeling, and 1H NMR spectroscopy. The reaction mechanism of a novel streptomyces diterpene cyclase. J. Org. Chem. 68 (2003) 5433–5438. [DOI] [PMID: 12839434]
[EC 5.5.1.15 created 2008]
 
 
EC 6.2.1.4     
Accepted name: succinate—CoA ligase (GDP-forming)
Reaction: GTP + succinate + CoA = GDP + phosphate + succinyl-CoA
For diagram of the citric-acid cycle, click here
Other name(s): succinyl-CoA synthetase (GDP-forming); succinyl coenzyme A synthetase (guanosine diphosphate-forming); succinate thiokinase (ambiguous); succinic thiokinase (ambiguous); succinyl coenzyme A synthetase (ambiguous); succinate-phosphorylating enzyme (ambiguous); P-enzyme; SCS (ambiguous); G-STK; succinyl coenzyme A synthetase (GDP-forming); succinyl CoA synthetase (ambiguous)
Systematic name: succinate:CoA ligase (GDP-forming)
Comments: Itaconate can act instead of succinate, and ITP instead of GTP.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9014-36-2
References:
1.  Hager, L.P. Succinyl CoA synthetase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 6, Academic Press, New York, 1962, pp. 387–399.
2.  Kaufman, S., Gilvarg, C., Cori, O. and Ochoa, S. Enzymatic oxidation of α-ketoglutarate and coupled phosphorylation. J. Biol. Chem. 203 (1953) 869–888. [PMID: 13084656]
3.  Mazumder, R., Sanadi, D.R. and Rodwell, W.V. Purification and properties of hog kidney succinic thiokinase. J. Biol. Chem. 235 (1960) 2546–2550. [PMID: 13768680]
4.  Sanadi, D.R., Gibson, D.M. and Ayengar, P. Guanosine triphosphate, the primary product of phosphorylation coupled to the breakdown of succinyl coenzyme A. Biochim. Biophys. Acta 14 (1954) 434–436. [DOI] [PMID: 13181903]
[EC 6.2.1.4 created 1961]
 
 
EC 6.2.1.10     
Accepted name: carboxylic acid—CoA ligase (GDP-forming)
Reaction: GTP + a carboxylate + CoA = GDP + phosphate + acyl-CoA
Other name(s): acyl-CoA synthetase (GDP-forming); acyl coenzyme A synthetase (guanosine diphosphate forming)
Systematic name: carboxylic acid:CoA ligase (GDP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37318-59-5
References:
1.  Rossi, C.R. and Gibson, D.M. Activation of fatty acids by a guanosine triphosphate-specific thiokinase from liver mitochondria. J. Biol. Chem. 239 (1964) 1694–1699. [PMID: 14213337]
[EC 6.2.1.10 created 1972, modified 2011]
 
 
EC 6.3.2.31     
Accepted name: coenzyme F420-0:L-glutamate ligase
Reaction: GTP + coenzyme F420-0 + L-glutamate = GDP + phosphate + coenzyme F420-1
For diagram of coenzyme F420 biosynthesis, click here
Glossary: coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): CofE-AF; MJ0768; CofE
Systematic name: L-glutamate:coenzyme F420-0 ligase (GDP-forming)
Comments: This protein catalyses the successive addition of two glutamate residues to factor F420 (coenzyme F420) by two distinct and independent reactions. In the reaction described here the enzyme attaches a glutamate via its α-amine group to F420-0. In the second reaction (EC 6.3.2.34, coenzyme F420-1:γ-L-glutamate ligase) it catalyses the addition of a second L-glutamate residue to the γ-carboxyl of the first glutamate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Li, H., Graupner, M., Xu, H. and White, R.H. CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii. Biochemistry 42 (2003) 9771–9778. [DOI] [PMID: 12911320]
2.  Nocek, B., Evdokimova, E., Proudfoot, M., Kudritska, M., Grochowski, L.L., White, R.H., Savchenko, A., Yakunin, A.F., Edwards, A. and Joachimiak, A. Structure of an amide bond forming F420:γ-glutamyl ligase from Archaeoglobus fulgidus — a member of a new family of non-ribosomal peptide synthases. J. Mol. Biol. 372 (2007) 456–469. [DOI] [PMID: 17669425]
[EC 6.3.2.31 created 2010]
 
 
EC 6.3.2.34     
Accepted name: coenzyme F420-1:γ-L-glutamate ligase
Reaction: GTP + coenzyme F420-1 + L-glutamate = GDP + phosphate + coenzyme γ-F420-2
For diagram of coenzyme F420 biosynthesis, click here
Glossary: coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): F420:γ-glutamyl ligase; CofE-AF; MJ0768; CofE
Systematic name: L-glutamate:coenzyme F420-1 ligase (GDP-forming)
Comments: This protein catalyses the successive addition of two glutamate residues to factor 420 (coenzyme F420) by two distinct and independent reactions. In the first reaction (EC 6.3.2.31, coenzyme F420-0:L-glutamate ligase) the enzyme attaches a glutamate via its α-amine group to F420-0. In the second reaction, which is described here, the enzyme catalyses the addition of a second L-glutamate residue to the γ-carboxyl of the first glutamate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Li, H., Graupner, M., Xu, H. and White, R.H. CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii. Biochemistry 42 (2003) 9771–9778. [DOI] [PMID: 12911320]
2.  Nocek, B., Evdokimova, E., Proudfoot, M., Kudritska, M., Grochowski, L.L., White, R.H., Savchenko, A., Yakunin, A.F., Edwards, A. and Joachimiak, A. Structure of an amide bond forming F420:γ-glutamyl ligase from Archaeoglobus fulgidus — a member of a new family of non-ribosomal peptide synthases. J. Mol. Biol. 372 (2007) 456–469. [DOI] [PMID: 17669425]
[EC 6.3.2.34 created 2010, modified 2023]
 
 
EC 6.3.4.4     
Accepted name: adenylosuccinate synthase
Reaction: GTP + IMP + L-aspartate = GDP + phosphate + N6-(1,2-dicarboxyethyl)-AMP
For diagram of AMP and GMP biosynthesis, click here
Other name(s): IMP—aspartate ligase; adenylosuccinate synthetase; succinoadenylic kinosynthetase; succino-AMP synthetase
Systematic name: IMP:L-aspartate ligase (GDP-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9023-57-8
References:
1.  Davey, C.L. Synthesis of adenylosuccinic acid in preparations of mammalian skeletal muscle. Nature 183 (1959) 995–996. [PMID: 13644270]
2.  Lieberman, I. Enzymatic synthesis of adenosine-5′-phosphate from inosine-5′-phosphate. J. Biol. Chem. 223 (1956) 327–339. [PMID: 13376602]
3.  Yefimochkina, E.F. and Braunstein, A.E. The amination of inosinic acid to adenylic acid in muscle extracts. Arch. Biochem. Biophys. 83 (1959) 350–352. [DOI] [PMID: 13662023]
[EC 6.3.4.4 created 1961]
 
 


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