The Enzyme Database

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EC 2.7.7.6     
Accepted name: DNA-directed RNA polymerase
Reaction: nucleoside triphosphate + RNAn = diphosphate + RNAn+1
Other name(s): RNA polymerase; RNA nucleotidyltransferase (DNA-directed); RNA polymerase I; RNA polymerase II; RNA polymerase III; C RNA formation factors; deoxyribonucleic acid-dependent ribonucleic acid polymerase; DNA-dependent ribonucleate nucleotidyltransferase; DNA-dependent RNA nucleotidyltransferase; DNA-dependent RNA polymerase; ribonucleate nucleotidyltransferase; ribonucleate polymerase; C ribonucleic acid formation factors; ribonucleic acid nucleotidyltransferase; ribonucleic acid polymerase; ribonucleic acid transcriptase; ribonucleic polymerase; ribonucleic transcriptase; RNA nucleotidyltransferase; RNA transcriptase; transcriptase; RNA nucleotidyltransferase I
Systematic name: nucleoside-triphosphate:RNA nucleotidyltransferase (DNA-directed)
Comments: Catalyses DNA-template-directed extension of the 3′- end of an RNA strand by one nucleotide at a time. Can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to α-amanitin, and the type of RNA synthesized. See also EC 2.7.7.19 (polynucleotide adenylyltransferase) and EC 2.7.7.48 (RNA-directed RNA polymerase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9014-24-8
References:
1.  Krakow, J.S. and Ochoa, S. RNA polymerase from Azotobacter vinelandii. Methods Enzymol. 6 (1963) 11–17.
2.  Mans, R.J. and Walter, T.J. Transfer RNA-primed oligoadenylate synthesis in maize seedlings. II. Primer, substrate and metal specificities and size of product. Biochim. Biophys. Acta 247 (1971) 113–121. [DOI] [PMID: 4946277]
3.  Roeder, R.G. In: Losick, R. and Chamberlin, M. (Eds), RNA Polymerase, Cold Spring Harbor Laboratory, 1976, p. 285.
4.  Sheldon, R., Jurale, C. and Kates, J. Detection of polyadenylic acid sequences in viral and eukaryotic RNA(poly(U)-cellulose columns-poly(U) filters-fiberglass-HeLa cells-bacteriophage T4). Proc. Natl. Acad. Sci. USA 69 (1972) 417–421. [DOI] [PMID: 4501121]
5.  Weaver, R.F., Blatti, S.P. and Rutter, W.J. Molecular structures of DNA-dependent RNA polymerases (II) from calf thymus and rat liver. Proc. Natl. Acad. Sci. USA 68 (1971) 2994–2999. [DOI] [PMID: 5289245]
[EC 2.7.7.6 created 1961, modified 1981, modified 1982, modified 1989]
 
 
EC 2.7.7.60     
Accepted name: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Reaction: CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol
For diagram of non-mevalonate terpenoid biosynthesis, click here
Other name(s): MEP cytidylyltransferase
Systematic name: CTP:2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Comments: The enzyme from Escherichia coli requires Mg2+ or Mn2+. ATP or UTP can replace CTP, but both are less effective. GTP and TTP are not substrates. Forms part of an alternative nonmevalonate pathway for terpenoid biosynthesis (for diagram, click here).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 251990-59-7
References:
1.  Rohdich, F., Wungsintaweekul, J., Fellermeier, M., Sagner, S., Herz, S., Kis, K., Eisenreich, W., Bacher, A. and Zenk, M.H. Cytidine 5′-triphosphate-dependent biosynthesis of isoprenoids: YgbP protein of Escherichia coli catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erithritol. Proc. Natl Acad. Sci. USA 96 (1999) 11758–11763. [DOI] [PMID: 10518523]
2.  Kuzuyama, T., Takagi, M., Kaneda, K., Dairi, T. and Seto, H. Formation of 4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol from 2-C-methyl-D-erythritol 4-phosphate by 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, a new enzyme in the nonmevalonate pathway. Tetrahedron Lett. 41 (2000) 703–706.
[EC 2.7.7.60 created 2001]
 
 
EC 2.7.7.61     
Accepted name: citrate lyase holo-[acyl-carrier protein] synthase
Reaction: 2′-(5-triphosphoribosyl)-3′-dephospho-CoA + apo-[citrate (pro-3S)-lyase] = diphosphate + holo-[citrate (pro-3S)-lyase]
For diagram of reaction, click here
Other name(s): 2′-(5′′-phosphoribosyl)-3′-dephospho-CoA transferase; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate lyase; CitX; holo-ACP synthase (ambiguous); 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate lyase adenylyltransferase; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate lyase 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA transferase; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate-lyase adenylyltransferase; holo-citrate lyase synthase (incorrect); 2′-(5-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate-lyase 2′-(5-phosphoribosyl)-3′-dephospho-CoA-transferase
Systematic name: 2′-(5-triphosphoribosyl)-3′-dephospho-CoA:apo-[citrate (pro-3S)-lyase] 2′-(5-phosphoribosyl)-3′-dephospho-CoA-transferase
Comments: The γ-subunit of EC 4.1.3.6, citrate (pro-3S) lyase, serves as an acyl-carrier protein (ACP) and contains the prosthetic group 2′-(5-triphosphoribosyl)-3′-dephospho-CoA [1,3]. Synthesis and attachment of the prosthetic group requires the concerted action of this enzyme and EC 2.4.2.52, triphosphoribosyl-dephospho-CoA synthase [1]. In the enzyme from Escherichia coli, the prosthetic group is attached to serine-14 of the ACP via a phosphodiester bond.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 312492-44-7
References:
1.  Schneider, K., Dimroth, P. and Bott, M. Biosynthesis of the prosthetic group of citrate lyase. Biochemistry 39 (2000) 9438–9450. [DOI] [PMID: 10924139]
2.  Schneider, K., Dimroth, P. and Bott, M. Identification of triphosphoribosyl-dephospho-CoA as precursor of the citrate lyase prosthetic group. FEBS Lett. 483 (2000) 165–168. [DOI] [PMID: 11042274]
3.  Schneider, K., Kästner, C.N., Meyer, M., Wessel, M., Dimroth, P. and Bott, M. Identification of a gene cluster in Klebsiella pneumoniae which includes citX, a gene required for biosynthesis of the citrate lyase prosthetic group. J. Bacteriol. 184 (2002) 2439–2446. [DOI] [PMID: 11948157]
[EC 2.7.7.61 created 2002, modified 2008]
 
 
EC 2.7.7.62     
Accepted name: adenosylcobinamide-phosphate guanylyltransferase
Reaction: GTP + adenosylcobinamide phosphate = diphosphate + adenosylcobinamide-GDP
For diagram of the enzyme’s role in corrin biosynthesis, click here
Other name(s): CobU; adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; AdoCbi kinase/AdoCbi-phosphate guanylyltransferase
Systematic name: GTP:adenosylcobinamide-phosphate guanylyltransferase
Comments: In Salmonella typhimurium LT2, under anaerobic conditions, CobU (EC 2.7.7.62 and EC 2.7.1.156), CobT (EC 2.4.2.21), CobC (EC 3.1.3.73) and CobS (EC 2.7.8.26) catalyse reactions in the nucleotide loop assembly pathway, which convert adenosylcobinamide (AdoCbi) into adenosylcobalamin (AdoCbl). CobT and CobC are involved in 5,6-dimethylbenzimidazole activation whereby 5,6-dimethylbenzimidazole is converted to its riboside, α-ribazole. The second branch of the nuclotide loop assembly pathway is the cobinamide (Cbi) activation branch where AdoCbi or adenosylcobinamide-phosphate is converted to the activated intermediate AdoCbi-GDP by the bifunctional enzyme Cob U. The final step in adenosylcobalamin biosynthesis is the condensation of AdoCbi-GDP with α-ribazole, which is catalysed by EC 2.7.8.26, cobalamin synthase (CobS), to yield adenosylcobalamin. CobU is a bifunctional enzyme that has both kinase (EC 2.7.1.156) and guanylyltransferase (EC 2.7.7.62) activities. However, both activities are not required at all times.The kinase activity has been proposed to function only when S. typhimurium is assimilating cobinamide whereas the guanylyltransferase activity is required for both assimilation of exogenous cobinamide and for de novo synthesis of adenosylcobalamin [4]. The guanylyltransferase reaction is a two-stage reaction with formation of a CobU-GMP intermediate [1]. Guanylylation takes place at histidine-46.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 169592-55-6
References:
1.  O'Toole, G.A. and Escalante-Semerena, J.C. Purification and characterization of the bifunctional CobU enzyme of Salmonella typhimurium LT2. Evidence for a CobU-GMP intermediate. J. Biol. Chem. 270 (1995) 23560–23569. [DOI] [PMID: 7559521]
2.  Thompson, T.B., Thomas, M.G., Escalante-Semerena, J.C. and Rayment, I. Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase from Salmonella typhimurium determined to 2.3 Å resolution. Biochemistry 37 (1998) 7686–7695. [DOI] [PMID: 9601028]
3.  Thompson, T.B., Thomas, M.G., Escalante-Semerena, J.C. and Rayment, I. Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) complexed with GMP: evidence for a substrate-induced transferase active site. Biochemistry 38 (1999) 12995–13005. [DOI] [PMID: 10529169]
4.  Thomas, M.G., Thompson, T.B., Rayment, I. and Escalante-Semerena, J.C. Analysis of the adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase (CobU) enzyme of Salmonella typhimurium LT2. Identification of residue His-46 as the site of guanylylation. J. Biol. Chem. 275 (2000) 27576–27586. [DOI] [PMID: 10869342]
5.  Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390–412. [PMID: 12195810]
[EC 2.7.7.62 created 2004]
 
 
EC 2.7.7.63      
Transferred entry: lipoate—protein ligase, now EC EC 6.3.1.20, lipoate—protein ligase.
[EC 2.7.7.63 created 2006, deleted 2016]
 
 
EC 2.7.7.64     
Accepted name: UTP-monosaccharide-1-phosphate uridylyltransferase
Reaction: UTP + a monosaccharide 1-phosphate = diphosphate + UDP-monosaccharide
Glossary: UDP-Xyl = UDP-α-D-xylose
UDP-L-Ara = UDP-β-L-arabinopyranose
Other name(s): UDP-sugar pyrophosphorylase; PsUSP
Comments: Requires Mg2+ or Mn2+ for maximal activity. The reaction can occur in either direction and it has been postulated that MgUTP and Mg-diphosphate are the actual substrates [1,2]. The enzyme catalyses the formation of UDP-Glc, UDP-Gal, UDP-GlcA, UDP-L-Ara and UDP-Xyl, showing broad substrate specificity towards monosaccharide 1-phosphates. Mannose 1-phosphate, L-Fucose 1-phosphate and glucose 6-phosphate are not substrates and UTP cannot be replaced by other nucleotide triphosphates [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kotake, T., Yamaguchi, D., Ohzono, H., Hojo, S., Kaneko, S., Ishida, H.K. and Tsumuraya, Y. UDP-sugar pyrophosphorylase with broad substrate specificity toward various monosaccharide 1-phosphates from pea sprouts. J. Biol. Chem. 279 (2004) 45728–45736. [DOI] [PMID: 15326166]
2.  Rudick, V.L. and Weisman, R.A. Uridine diphosphate glucose pyrophosphorylase of Acanthamoeba castellanii. Purification, kinetic, and developmental studies. J. Biol. Chem. 249 (1974) 7832–7840. [PMID: 4430676]
[EC 2.7.7.64 created 2006]
 
 
EC 2.7.7.65     
Accepted name: diguanylate cyclase
Reaction: 2 GTP = 2 diphosphate + cyclic di-3′,5′-guanylate
For diagram of cyclic di-3′,5′-guanylate biosynthesis and breakdown, click here
Glossary: cyclic di-3′,5′-guanylate = c-di-GMP = c-di-guanylate = cyclic-bis(3′→5′) dimeric GMP
Other name(s): DGC; PleD
Systematic name: GTP:GTP guanylyltransferase (cyclizing)
Comments: A GGDEF-domain-containing protein that requires Mg2+ or Mn2+ for activity. The enzyme can be activated by BeF3, a phosphoryl mimic, which results in dimerization [3]. Dimerization is required but is not sufficient for diguanylate-cyclase activity [3]. Cyclic di-3′,5′-guanylate is an intracellular signalling molecule that controls motility and adhesion in bacterial cells. It was first identified as having a positive allosteric effect on EC 2.4.1.12, cellulose synthase (UDP-forming) [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 146316-82-7
References:
1.  Ryjenkov, D.A., Tarutina, M., Moskvin, O.V. and Gomelsky, M. Cyclic diguanylate is a ubiquitous signaling molecule in bacteria: insights into biochemistry of the GGDEF protein domain. J. Bacteriol. 187 (2005) 1792–1798. [DOI] [PMID: 15716451]
2.  Méndez-Ortiz, M.M., Hyodo, M., Hayakawa, Y. and Membrillo-Hernández, J. Genome-wide transcriptional profile of Escherichia coli in response to high levels of the second messenger 3′,5′-cyclic diguanylic acid. J. Biol. Chem. 281 (2006) 8090–8099. [DOI] [PMID: 16418169]
3.  Paul, R., Abel, S., Wassmann, P., Beck, A., Heerklotz, H. and Jenal, U. Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization. J. Biol. Chem. 282 (2007) 29170–29177. [DOI] [PMID: 17640875]
[EC 2.7.7.65 created 2008]
 
 
EC 2.7.7.66     
Accepted name: malonate decarboxylase holo-[acyl-carrier protein] synthase
Reaction: 2′-(5-triphosphoribosyl)-3′-dephospho-CoA + malonate decarboxylase apo-[acyl-carrier protein] = malonate decarboxylase holo-[acyl-carrier protein] + diphosphate
For diagram of reaction, click here
Other name(s): holo ACP synthase (ambiguous); 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo ACP 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA transferase; MdcG; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-malonate-decarboxylase adenylyltransferase; holo-malonate-decarboxylase synthase (incorrect)
Systematic name: 2′-(5-triphosphoribosyl)-3′-dephospho-CoA:apo-malonate-decarboxylase 2′-(5-phosphoribosyl)-3′-dephospho-CoA-transferase
Comments: The δ subunit of malonate decarboxylase serves as an an acyl-carrier protein (ACP) and contains the prosthetic group 2-(5-triphosphoribosyl)-3-dephospho-CoA. Two reactions are involved in the production of the holo-ACP form of this enzyme. The first reaction is catalysed by EC 2.4.2.52, triphosphoribosyl-dephospho-CoA synthase. The resulting prosthetic group is then attached to the ACP subunit via a phosphodiester linkage to a serine residue, thus forming the holo form of the enzyme, in a manner analogous to that of EC 2.7.7.61, citrate lyase holo-[acyl-carrier protein] synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hoenke, S., Wild, M.R. and Dimroth, P. Biosynthesis of triphosphoribosyl-dephospho-coenzyme A, the precursor of the prosthetic group of malonate decarboxylase. Biochemistry 39 (2000) 13223–13232. [DOI] [PMID: 11052675]
2.  Hoenke, S., Schmid, M. and Dimroth, P. Identification of the active site of phosphoribosyl-dephospho-coenzyme A transferase and relationship of the enzyme to an ancient class of nucleotidyltransferases. Biochemistry 39 (2000) 13233–13240. [DOI] [PMID: 11052676]
[EC 2.7.7.66 created 2008]
 
 
EC 2.7.7.67     
Accepted name: CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol synthase
Reaction: CTP + 2,3-bis-(O-geranylgeranyl)-sn-glycerol 1-phosphate = diphosphate + CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol
For diagram of archaetidylserine biosynthesis, click here
Glossary: 2,3-bis-(O-geranylgeranyl)-sn-glycerol 1-phosphate = 2,3-bis-(O-geranylgeranyl)-glycerophosphate ether = unsaturated archaetidic acid
CDP-unsaturated archaeol = CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol
Other name(s): carS (gene name); CDP-2,3-di-O-geranylgeranyl-sn-glycerol synthase; CTP:2,3-GG-GP ether cytidylyltransferase; CTP:2,3-di-O-geranylgeranyl-sn-glycero-1-phosphate cytidyltransferase; CDP-2,3-bis-O-(geranylgeranyl)-sn-glycerol synthase; CTP:2,3-bis-O-(geranylgeranyl)-sn-glycero-1-phosphate cytidylyltransferase; CDP-unsaturated archaeol synthase; CDP-archaeol synthase (incorrect)
Systematic name: CTP:2,3-bis-(O-geranylgeranyl)-sn-glycerol 1-phosphate cytidylyltransferase
Comments: This enzyme catalyses one of the steps in the biosynthesis of polar lipids in archaea, which are characterized by having an sn-glycerol 1-phosphate backbone rather than an sn-glycerol 3-phosphate backbone as is found in bacteria and eukaryotes [1]. The enzyme requires Mg2+ and K+ for maximal activity [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 329791-09-5
References:
1.  Morii, H., Nishihara, M. and Koga, Y. CTP:2,3-di-O-geranylgeranyl-sn-glycero-1-phosphate cytidyltransferase in the methanogenic archaeon Methanothermobacter thermoautotrophicus. J. Biol. Chem. 275 (2000) 36568–36574. [DOI] [PMID: 10960477]
2.  Morii, H. and Koga, Y. CDP-2,3-di-O-geranylgeranyl-sn-glycerol:L-serine O-archaetidyltransferase (archaetidylserine synthase) in the methanogenic archaeon Methanothermobacter thermautotrophicus. J. Bacteriol. 185 (2003) 1181–1189. [DOI] [PMID: 12562787]
3.  Jain, S., Caforio, A., Fodran, P., Lolkema, J.S., Minnaard, A.J. and Driessen, A.J. Identification of CDP-archaeol synthase, a missing link of ether lipid biosynthesis in Archaea. Chem. Biol. 21 (2014) 1392–1401. [DOI] [PMID: 25219966]
[EC 2.7.7.67 created 2009, modified 2014]
 
 
EC 2.7.7.68     
Accepted name: 2-phospho-L-lactate guanylyltransferase
Reaction: (2S)-2-phospholactate + GTP = (2S)-lactyl-2-diphospho-5′-guanosine + diphosphate
For diagram of coenzyme F420 biosynthesis, click here
Glossary: (2S)-2-phospholactate = (2S)-2-(phosphonooxy)propanoate
Other name(s): CofC; MJ0887
Systematic name: GTP:2-phospho-L-lactate guanylyltransferase
Comments: This enzyme is involved in the biosynthesis of coenzyme F420, a redox-active cofactor found in all methanogenic archaea, as well as some eubacteria.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Grochowski, L.L., Xu, H. and White, R.H. Identification and characterization of the 2-phospho-L-lactate guanylyltransferase involved in coenzyme F420 biosynthesis. Biochemistry 47 (2008) 3033–3037. [DOI] [PMID: 18260642]
[EC 2.7.7.68 created 2010]
 
 
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, KEGG, MetaCyc
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. [DOI] [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. [DOI] [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. [DOI] [PMID: 17877701]
4.  Muller-Moule, P. An expression analysis of the ascorbate biosynthesis enzyme VTC2. Plant Mol. Biol. 68 (2008) 31–41. [DOI] [PMID: 18516687]
[EC 2.7.7.69 created 2010]
 
 


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