Continued from EC 6.3.1 and EC 6.3.2
EC 6.3.3 Cyclo-Ligases
EC 6.3.4 Other Carbon—Nitrogen Ligases
EC 6.3.5 Carbon—Nitrogen Ligases with Glutamine as Amido-N-Donor
Accepted name: phosphoribosylformylglycinamidine cyclo-ligase
Reaction: ATP + 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine = ADP + phosphate + 5-amino-1-(5-phospho-D-ribosyl)imidazole
For reaction pathway click here.
Other name(s): phosphoribosylaminoimidazole synthetase; AIR synthetase; 5'-aminoimidazole ribonucleotide synthetase
Systematic name: 2-(formamido)-N1-(5-phosphoribosyl)acetamidine cyclo-ligase (ADP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9023-53-4
References:
1. Levenberg, B. and Buchanan, J.M. Properties of the purines. XII. Structure, enzymatic synthesis, and metabolism of 5-aminoimidazole ribotide. J. Biol. Chem. 224 (1957) 1005-1018.
2. Levenberg, B. and Buchanan, J.M. Properties of the purines. XIII. Structure, enzymatic synthesis, and metabolism of (α-N-formyl)-glycinamidine ribotide. J. Biol. Chem. 224 (1957) 1018-1027.
Accepted name: 5-formyltetrahydrofolate cyclo-ligase
Reaction: ATP + 5-formyltetrahydrofolate = ADP + phosphate + 5,10-methenyltetrahydrofolate
For diagram of reaction click here (another example).
Other name(s): 5,10-methenyltetrahydrofolate synthetase; formyltetrahydrofolic cyclodehydrase; 5-formyltetrahydrofolate cyclodehydrase
Systematic name: 5-formyltetrahydrofolate cyclo-ligase (ADP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37318-64-2
References:
1. Greenberg, D.M., Wynston, L.K. and Nagabhushanan, A. Further studies on N5-formyltetrahydrofolic acid cyclodehydrase. Biochemistry 4 (1965) 1872-1878.
Accepted name: dethiobiotin synthase
Reaction: ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin
Other name(s): desthiobiotin synthase
Systematic name: 7,8-diaminononanoate:carbon-dioxide cyclo-ligase (ADP-forming)
Comments: CTP has half the activity of ATP.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37259-75-9
References:
1. Krell, K. and Eisenberg, M.A. The purification and properties of dethiobiotin synthetase. J. Biol. Chem. 245 (1970) 6558-6566. [PMID: 4921568]
2. Yang, H.-C., Tani, Y. and Ogata, K. Synthesis of biotin vitamers from biotin diaminocarboxylic acid or 7,8-diaminopelargonic acid by a purified enzyme of Pseudomonas graveolens. Agric. Biol. Chem. 34 (1970) 1748-1750.
Accepted name: (carboxyethyl)arginine β-lactam-synthase
Reaction: ATP + L-N2-(2-carboxyethyl)arginine = AMP + diphosphate + deoxyamidinoproclavaminate
For diagram click here.
Systematic name: L-N2-(2-carboxyethyl)arginine cyclo-ligase (AMP-forming)
Comments: Forms part of the pathway for the biosythesis of the β-lactamase inhibitor clavulanate in Streptomyces clavuligerus. It has been proposed [3] that L-N2-(2-carboxyethyl)arginine is first converted into an acyl-AMP by reaction with ATP and loss of diphosphate, and that the β-lactam ring is then formed by the intramolecular attack of the β-nitrogen on the activated carboxy group.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Zhou, J., Kelly, W.L., Bachmann, B.O., Gunsior, M., Townsend, C.A. and Solomon, E.I. Spectroscopic studies of substrate interactions with clavaminate synthase 2, a multifunctional α-KG-dependent non-heme iron enzyme: Correlation with mechanisms and reactivities. J. Am. Chem. Soc. 123 (2001) 7388-7398.
2. Townsend, C.A. New reactions in clavulanic acid biosynthesis. Curr. Opin. Chem. Biol. 6 (2002) 583-589. [PMID: 12413541]
3. Bachmann, B.O., Li, R. and Townsend, C.A. β-Lactam synthetase: a new biosynthetic enzyme. Proc. Natl. Acad. Sci. USA 95 (1998) 9082-9086. [PMID: 9689037]
Accepted name: GMP synthase
Reaction: ATP + XMP + NH3 = AMP + diphosphate + GMP
For diagram click here.
Glossary: XMP = xanthosine 5'-phosphate
Other name(s): xanthosine-5'-phosphate—ammonia ligase; guanylate synthetase; XMP aminase; xanthosine 5'-monophosphate aminase
Systematic name: xanthosine-5'-phosphate:ammonia ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9023-55-6
References:
1. Moyed, H.S. and Magasanik, B. Enzymes essential for the biosynthesis of nucleic acid guanine; xanthosine 5'-phosphate aminase of Aerobacter aerogenes. J. Biol. Chem. 226 (1957) 351-363.
Accepted name: CTP synthase
Reaction: ATP + UTP + NH3 = ADP + phosphate + CTP
Other name(s): UTP—ammonia ligase; cytidine triphosphate synthetase; uridine triphosphate aminase; cytidine 5'-triphosphate synthetase
Systematic name: UTP:ammonia ligase (ADP-forming)
Comments: Glutamine can replace NH3.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9023-56-7
References:
1. Lieberman, I. Enzymatic amination of uridine triphosphate to cytidine triphosphate. J. Biol. Chem. 222 (1956) 765-775.
2. Long, C.W., Levitzki, A., Houston, L.L and Koshland, D.E., Jr. Subunit structures and interactions of CTP synthetase. Fed. Proc. 28 (1969) 342 only.
Accepted name: formate—tetrahydrofolate ligase
Reaction: ATP + formate + tetrahydrofolate = ADP + phosphate + 10-formyltetrahydrofolate
For diagram of reaction click here (another example).
Other name(s): formyltetrahydrofolate synthetase; 10-formyltetrahydrofolate synthetase; tetrahydrofolic formylase; tetrahydrofolate formylase
Systematic name: formate:tetrahydrofolate ligase (ADP-forming)
Comments: In eukaryotes occurs as a trifunctional enzyme also having methylenetetrahydrofolate dehydrogenase (NADP+) (EC 1.5.1.5) and methenyltetrahydrofolate cyclohydrolase (EC 3.5.4.9) activity.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9023-66-9
References:
1. Jaenicke, L. and Brode, E. Untersuchungen über Einkohlenstoffkörper. I. Die Tetrahydrofolatformylase aus Taubenleber. Rinigung und Mechanismus. Biochem. Z. 334 (1961) 108-132.
2. Long, C.W., Levitzki, A., Houston, L.L and Koshland, D.E., Jr. Subunit structures and interactions of CTP synthetase. Fed. Proc. 28 (1969) 342 only.
3. Rabinowitz, J.C. and Pricer, W.E. Formyltetrahydrofolate synthetase. I. Isolation and crystallization of the enzyme. J. Biol. Chem. 237 (1962) 2898-2902.
4. Whiteley, H.R., Osborn, M.J. and Huennekens, F.M. Purification and properties of the formate-activating enzyme from Micrococcus aerogenes. J. Biol. Chem. 234 (1959) 1538-1543.
Accepted name: adenylosuccinate synthase
Reaction: GTP + IMP + L-aspartate = GDP + phosphate + N6-(1,2-dicarboxyethyl)-AMP
For diagram 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.
2. Lieberman, I. Enzymatic synthesis of adenosine-5'-phosphate from inosine-5'-phosphate. J. Biol. Chem. 223 (1956) 327-339.
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.
Accepted name: argininosuccinate synthase
Reaction: ATP + L-citrulline + L-aspartate = AMP + diphosphate + 2-(Nω-L-arginino)succinate
For diagram click here.
Other name(s): citrulline—aspartate ligase; argininosuccinate synthetase; arginine succinate synthetase; argininosuccinic acid synthetase; arginosuccinate synthetase
Systematic name: L-citrulline:L-aspartate ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9023-58-9
References:
1. Ratner, S. Urea synthesis and metabolism of arginine and citrulline. Adv. Enzymol. Relat. Subj. Biochem. 15 (1954) 319-387.
2. Schuegraf, A., Ratner, S. and Warner, R.C. Free energy changes of the argininosuccinate synthetase reaction and of the hydrolysis of the inner pyrophosphate bond of adenosine triphosphate. J. Biol. Chem. 235 (1960) 3597-3602.
Accepted name: urea carboxylase
Reaction: ATP + urea + HCO3- = ADP + phosphate + urea-1-carboxylate
Glossary: allophanate = urea-1-carboxylate
Other name(s): urease (ATP-hydrolysing); urea carboxylase (hydrolysing); ATP—urea amidolyase; urea amido-lyase; UALase; UCA
Systematic name: urea:carbon-dioxide ligase (ADP-forming)
Comments: A biotinyl-protein. The yeast enzyme (but not that from green algae) also catalyses the reaction of EC 3.5.1.54 allophanate hydrolase, thus bringing about the hydrolysis of urea to CO2 and NH3. Previously also listed as EC 3.5.1.45. The enzyme from the prokaryotic bacterium Oleomonas sagaranensis can also use acetamide and formamide as substrates [4].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9058-98-4
References:
1. Roon, R.J. and Levenberg, B. ATP-Urea amidolyase (ADP) (Candida utilis). Methods Enzymol. 17A (1970) 317-324.
2. Roon, R.J. and Levenberg, B. Urea amidolyase. I. Properties of the enzyme from Candida utilis. J. Biol. Chem. 247 (1972) 4107-4113. [PMID: 4556303]
3. Sumrada, R.A. and Cooper, T.G. Urea carboxylase and allophanate hydrolase are components of a multifunctional protein in yeast. J. Biol. Chem. 257 (1982) 9119-9127. [PMID: 6124544]
4. Kanamori, T., Kanou, N., Atomi, H. and Imanaka, T. Enzymatic characterization of a prokaryotic urea carboxylase. J. Bacteriol. 186 (2004) 2532-2539. [PMID: 15090492]
Accepted name: ribose-5-phosphate—ammonia ligase
Reaction: ATP + ribose 5-phosphate + NH3 = ADP + phosphate + 5-phosphoribosylamine
For diagram of reaction click here.
Other name(s): 5-phosphoribosylamine synthetase; ribose 5-phosphate aminotransferase; ammonia-ribose 5-phosphate aminotransferase
Systematic name: ribose-5-phosphate:ammonia ligase (ADP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9082-52-4
References:
1. Reem, G.H. Enzymatic synthesis of 5'-phosphoribosylamine from ribose 5-phosphate and ammonia, an alternate first step in purine biosynthesis. J. Biol. Chem. 243 (1968) 5695-5701. [PMID: 5699059]
Accepted name: imidazoleacetate—phosphoribosyldiphosphate ligase
Reaction: ATP + imidazole-4-acetate + 5-phosphoribosyl diphosphate = ADP + phosphate + 1-(5-phosphoribosyl)imidazole-4-acetate + diphosphate
Other name(s): 5-phosphoribosylimidazoleacetate synthetase
Systematic name: imidazoleacetate:5-phosphoribosyl-diphosphate ligase (ADP- and diphosphate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37318-65-3
References:
1. Crowley, G.M. The enzymatic synthesis of 5'-phosphoribosylimidazoleacetic acid. J. Biol. Chem. 239 (1964) 2593-2601.
Accepted name: biotin—[methylmalonyl-CoA-carboxytransferase] ligase
Reaction: ATP + biotin + apo-[methylmalonyl-CoA:pyruvate carboxytransferase] = AMP + diphosphate + [methylmalonyl-CoA:pyruvate carboxytransferase]
Other name(s): biotin-[methylmalonyl-CoA-carboxyltransferase] synthetase; biotin-methylmalonyl coenzyme A carboxyltransferase synthetase; biotin-transcarboxylase synthetase; methylmalonyl coenzyme A holotranscarboxylase synthetase; biotin—[methylmalonyl-CoA-carboxyltransferase] ligase; biotin:apo[methylmalonyl-CoA:pyruvate carboxyltransferase] ligase (AMP-forming)
Systematic name: biotin:apo[methylmalonyl-CoA:pyruvate carboxytransferase] ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37318-66-4
References:
1. Lane, M.D., Young, D.L. and Lynen, F. The enzymatic synthesis of holotranscarboxylase from apotranscarboxylase and (+)-biotin. I. Purification of the apoenzyme and synthetase; characteristics of the reaction. J. Biol. Chem. 239 (1964) 2858-2864.
Accepted name: biotin—[propionyl-CoA-carboxylase (ATP-hydrolysing)] ligase
Reaction: ATP + biotin + apo-[propionyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP + diphosphate + [propionyl-CoA:carbon-dioxide ligase (ADP-forming)]
Other name(s): biotin-[propionyl-CoA-carboxylase (ATP-hydrolysing)] synthetase; biotin-propionyl coenzyme A carboxylase synthetase; propionyl coenzyme A holocarboxylase synthetase
Systematic name: biotin:apo-[propanoyl-CoA:carbon-dioxide ligase (ADP-forming)] ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37318-67-5
References:
1. Siegel, L., Foote, J.L. and Coon, M.J. The enzymatic synthesis of propionyl coenzyme A holocarboxylase from d-biotinyl 5'-adenylate and the apocarboxylase. J. Biol. Chem. 240 (1965) 1025-1031.
Accepted name: biotin—[methylcrotonoyl-CoA-carboxylase] ligase
Reaction: ATP + biotin + apo-[3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP + diphosphate + [3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)]
Other name(s): biotin-[methylcrotonoyl-CoA-carboxylase] synthetase; biotin-β-methylcrotonyl coenzyme A carboxylase synthetase; β-methylcrotonyl coenzyme A holocarboxylase synthetase; holocarboxylase-synthetase
Systematic name: biotin:apo-[3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)] ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37318-68-6
References:
1. Höpner, T. and Knappe, J. Einbau von Biotin in β-methylcrotonyl-CoA-carboxylase urch Holocarboxylase-synthetase. Biochem. Z. 342 (1965) 190-206. [PMID: 5867144]
Accepted name: glutamate—methylamine ligase
Reaction: ATP + L-glutamate + methylamine = ADP + phosphate + N5-methyl-L-glutamine
Other name(s): γ-glutamylmethylamide synthetase
Systematic name: L-glutamate:methylamine ligase (ADP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 37318-69-7
References:
1. Kung, H.-F. and Wagner, C. γ-Glutamylmethylamide. A new intermediate in the metabolism of methylamine. J. Biol. Chem. 244 (1969) 4136-4140. [PMID: 5800436]
Accepted name: phosphoribosylamine—glycine ligase
Reaction: ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N1-(5-phospho-D-ribosyl)glycinamide
For reaction pathway click here.
Other name(s): phosphoribosylglycinamide synthetase; glycinamide ribonucleotide synthetase; phosphoribosylglycineamide synthetase; glycineamide ribonucleotide synthetase; 2-amino-N-ribosylacetamide 5'-phosphate kinosynthase; 5'-phosphoribosylglycinamide synthetase; GAR
Systematic name: 5-phospho-D-ribosylamine:glycine ligase (ADP-forming)
Comments: Formerly EC 6.3.1.3.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9032-01-3
References:
1. Goldthwait, D.A., Peabody, R.A. and Greenberg, G.R. On the mechanism of synthesis of glycinamide ribotide and its formyl derivative. J. Biol. Chem. 221 (1956) 569-577.
2. Hartman, S.C. and Buchanan, J.M. Biosynthesis of the purines. XXII. 2-Amino-N-ribosylacetamide-5'-phosphate kinosynthase. J. Biol. Chem. 233 (1958) 456-461.
Accepted name: biotin carboxylase
Reaction: ATP + biotin-carboxyl-carrier protein + CO2 = ADP + phosphate + carboxybiotin-carboxyl-carrier protein
Other name(s): biotin carboxylase (component of acetyl CoA carboxylase)
Systematic name: biotin-carboxyl-carrier-protein:carbon-dioxide ligase (ADP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9075-71-2
References:
1. Dimroth, P., Guchhait, R.B., Stoll, E. and Lane, M.D. Enzymatic carboxylation of biotin: molecular and catalytic properties of a component enzyme of acetyl CoA carboxylase. Proc. Natl. Acad. Sci. USA 67 (1970) 1353-1360. [PMID: 4922289]
Accepted name: biotin—[acetyl-CoA-carboxylase] ligase
Reaction: ATP + biotin + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
Other name(s): biotin-[acetyl-CoA carboxylase] synthetase; biotin-[acetyl coenzyme A carboxylase] synthetase; acetyl coenzyme A holocarboxylase synthetase; acetyl CoA holocarboxylase synthetase; biotin:apocarboxylase ligase; Biotin holoenzyme synthetase; HCS
Systematic name: biotin:apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)] ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37340-95-7
References:
1. Landman, A.D. and Dakshinamurti, K. Acetyl-Coenzyme A carboxylase. Role of the prosthetic group in enzyme polymerization. Biochem. J. 145 (1975) 545-548. [PMID: 239688]
Accepted name: carbamoyl-phosphate synthase (ammonia)
Reaction: 2 ATP +NH3 + CO2 + H2O = 2 ADP + phosphate + carbamoyl phosphate
For diagram click here.
Other name(s): carbon-dioxide—ammonia ligase; carbamoylphosphate synthase; carbamylphosphate synthetase; carbamoylphosphate synthase (ammonia); carbamoylphosphate synthetase; carbamylphosphate synthetase I
Systematic name: carbon-dioxide:ammonia ligase (ADP-forming, carbamate-phosphorylating)
Comments: Formerly EC 2.7.2.5.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9026-23-7
References:
1. Fahien, L.A. and Cohen, P.P. A kinetic study of carbamyl phosphate synthetase. J. Biol. Chem. 239 (1964) 1925-1934.
2. Jones, M.E. and Spector, L. The pathway of carbonate in the biosynthesis of carbamyl phosphate. J. Biol. Chem. 235 (1960) 2897-2901.
3. Marshall, M., Metzenberg, R.L. and Cohen, P.P. Purification of carbamyl phosphate synthetase from frog liver. J. Biol. Chem. 233 (1958) 102-105.
4. Marshall, M., Metzenberg, R.L. and Cohen, P.P. Physical and kinetic properties of carbamyl phosphate synthetase from frog liver. J. Biol. Chem. 236 (1961) 2229-2237.
Accepted name: formate—dihydrofolate ligase
Reaction: ATP + formate + dihydrofolate = ADP + phosphate + 10-formyldihydrofolate
Other name(s): formyltransferase, dihydrofolate; dihydrofolate formyltransferase; formyl dihydrofolate synthase
Systematic name: formate:dihydrofolate ligase (ADP-forming)
Comments: Not identical with EC 6.3.4.3 (formate—tetrahydrofolate ligase).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 123303-25-3
References:
1. Drake, J.C., Baram, J. and Allegra, C.J. Isolation and characterization of a novel dihydrofolate formylating enzyme from human MCF-7 breast cancer cells. Biochem. Pharmacol. 39 (1990) 615-618. [PMID: 2306274]
Accepted name: 5-(carboxyamino)imidazole ribonucleotide synthase
Reaction: ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- = ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
For diagram, click here
Other name(s): N5-CAIR synthetase; N5-carboxyaminoimidazole ribonucleotide synthetase; PurK
Systematic name: 5-amino-1-(5-phospho-D-ribosyl)imidazole:carbon-dioxide ligase (ADP-forming)
Comments: In Escherichia coli, this enzyme, along with EC 5.4.99.18, 5-(carboxyamino)imidazole ribonucleotide mutase, is required to carry out the single reaction catalysed by EC 4.1.1.21, phosphoribosylaminoimidazole carboxylase, in vertebrates. Belongs to the ATP grasp protein superfamily [3]. Carboxyphosphate is the putative acyl phosphate intermediate. Involved in the late stages of purine biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 255379-40-9
References:
1. Meyer, E., Leonard, N.J., Bhat, B., Stubbe, J. and Smith, J.M. Purification and characterization of the purE, purK, and purC gene products: identification of a previously unrecognized energy requirement in the purine biosynthetic pathway. Biochemistry 31 (1992) 5022-5032. [PMID: 1534690]
2. Mueller, E.J., Meyer, E., Rudolph, J., Davisson, V.J. and Stubbe, J. N5-Carboxyaminoimidazole ribonucleotide: evidence for a new intermediate and two new enzymatic activities in the de novo purine biosynthetic pathway of Escherichia coli. Biochemistry 33 (1994) 2269-2278. [PMID: 8117684]
3. Thoden, J.B., Kappock, T.J., Stubbe, J. and Holden, H.M. Three-dimensional structure of N5-carboxyaminoimidazole ribonucleotide synthetase: a member of the ATP grasp protein superfamily. Biochemistry 38 (1999) 15480-15492. [PMID: 10569930]
Accepted name: tRNAIle-lysidine synthase
Reaction: [tRNAIle2]-cytidine34 + L-lysine + ATP = [tRNAIle2]-lysidine34 + AMP + diphosphate + H2O
Glossary: lysidine = N6-(4-amino-1-β-D-ribofuranosylpyrimidin-2-ylidene)-L-lysine
Other name(s): TilS; mesJ (gene name); yacA (gene name); isoleucine-specific transfer ribonucleate lysidine synthetase; tRNAIle-lysidine synthetase
Systematic name: L-lysine:[tRNAIle2]-cytidine34 ligase (AMP-forming)
Comments: The bacterial enzyme modifies the wobble base of the CAU anticodon of tRNAIle at the oxo group in position 2 of cytidine34. This modification determines both codon and amino acid specificities of tRNAIle.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Ikeuchi, Y., Soma, A., Ote, T., Kato, J., Sekine, Y. and Suzuki, T. molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition. Mol. Cell 19 (2005) 235-246. [PMID: 16039592]
2. Salowe, S.P., Wiltsie, J., Hawkins, J.C. and Sonatore, L.M. The catalytic flexibility of tRNAIle-lysidine synthetase can generate alternative tRNA substrates for isoleucyl-tRNA synthetase. J. Biol. Chem. 284 (2009) 9656-9662. [PMID: 19233850]
3. Nakanishi, K., Fukai, S., Ikeuchi, Y., Soma, A., Sekine, Y., Suzuki, T. and Nureki, O. Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain. Proc. Natl. Acad. Sci. USA 102 (2005) 7487-7492. [PMID: 15894617]
4. Soma, A., Ikeuchi, Y., Kanemasa, S., Kobayashi, K., Ogasawara, N., Ote, T., Kato, J., Watanabe, K., Sekine, Y. and Suzuki, T. An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol. Cell 12 (2003) 689-698. [PMID: 14527414]
5. Nakanishi, K., Bonnefond, L., Kimura, S., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase. Nature 461 (2009) 1144-1148. [PMID: 19847269]
Accepted name: 7-cyano-7-deazaguanine synthase
Reaction: 7-carboxy-7-carbaguanine + NH3 + ATP = 7-cyano-7-carbaguanine + ADP + phosphate + H2O
For diagram of reaction click here.
Glossary: preQ0 = 7-cyano-7-carbaguanine = 7-cyano-7-deazaguanine
7-carboxy-7-carbaguanine = 7-carboxy-7-deazaguanine
Other name(s): preQ0 synthase; 7-cyano-7-carbaguanine synthase; queC (gene name)
Systematic name: 7-carboxy-7-carbaguanine:ammonia ligase (ADP-forming)
Comments: Binds Zn2+. The reaction is part of the biosynthesis pathway of queuosine.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. McCarty, R.M., Somogyi, A., Lin, G., Jacobsen, N.E. and Bandarian, V. The deazapurine biosynthetic pathway revealed: in vitro enzymatic synthesis of preQ0 from guanosine 5'-triphosphate in four steps. Biochemistry 48 (2009) 3847-3852. [PMID: 19354300]
2. Cicmil, N. and Huang, R.H. Crystal structure of QueC from Bacillus subtilis: an enzyme involved in preQ1 biosynthesis. Proteins 72 (2008) 1084-1088. [PMID: 18491386]
Accepted name: NAD+ synthase (glutamine-hydrolysing)
Reaction: ATP + deamido-NAD+ + L-glutamine + H2O = AMP + diphosphate + NAD+ + L-glutamate
For diagram of reaction click here
Other name(s): NAD synthetase (glutamine-hydrolysing); nicotinamide adenine dinucleotide synthetase (glutamine); desamidonicotinamide adenine dinucleotide amidotransferase; DPN synthetase
Systematic name: deamido-NAD+:L-glutamine amido-ligase (AMP-forming)
Comments: NH3 can act instead of glutamine (cf. EC 6.3.1.5 NAD+ synthase).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37318-70-0
References:
1. Imsande, J. Pathway of diphosphopyridine nucleotide biosynthesis in Escherichia coli. J. Biol. Chem. 236 (1961) 1494-1497.
2. Imsande, J. and Handler, P. Biosynthesis of diphosphopyridine nucleotide. III. Nicotinic acid mononucleotide pyrophosphorylase. J. Biol. Chem. 236 (1961) 525-530.
Accepted name: GMP synthase (glutamine-hydrolysing)
Reaction: ATP + XMP + L-glutamine + H2O = AMP + diphosphate + GMP + L-glutamate
For diagram click here.
Glossary: XMP = xanthosine 5'-phosphate
Other name(s): GMP synthetase (glutamine-hydrolysing); guanylate synthetase (glutamine-hydrolyzing); guanosine monophosphate synthetase (glutamine-hydrolyzing); xanthosine 5'-phosphate amidotransferase; guanosine 5'-monophosphate synthetase
Systematic name: xanthosine-5'-phosphate:L-glutamine amido-ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37318-71-1
References:
1. Abrams, R. and Bentley, M. Biosynthesis of nucleic acid purines. III. Guanosine 5'-phosphate formation from xanthosine 5'-phosphate and L-glutamine. Arch. Biochem. Biophys. 79 (1959) 91-110.
2. Lagerkvist, U. Biosynthesis of guanosine 5'-phosphate. II. Amination of xanthosine 5'-phosphate by purified enzyme from pigeon liver. J. Biol. Chem. 233 (1958) 143-149.
Accepted name: phosphoribosylformylglycinamidine synthase
Reaction: ATP + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide + L-glutamine + H2O = ADP + phosphate + 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine + L-glutamate
For reaction pathway click here.
Other name(s): phosphoribosylformylglycinamidine synthetase; formylglycinamide ribonucloetide amidotransferase; phosphoribosylformylglycineamidine synthetase; FGAM synthetase; FGAR amidotransferase
Systematic name: N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide:L-glutamine amido-ligase (ADP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9032-84-2
References:
1. Melnick, I. and Buchanan, J.M. Biosynthesis of the purines. I. Conversion of (α-N-formyl)glycinamide ribotide to (α-N-formyl)glycinamidine ribotide; purification and requirements of the enzyme system. J. Biol. Chem. 225 (1957) 157-162.
Accepted name: asparagine synthase (glutamine-hydrolysing)
Reaction: ATP + L-aspartate + L-glutamine + H2O = AMP + diphosphate + L-asparagine + L-glutamate (overall reaction)
(1a) L-glutamine + H2O = L-glutamate + NH3
(1b) ATP + L-aspartate + NH3 = AMP + diphosphate + L-asparagine
Other name(s): asparagine synthetase (glutamine-hydrolysing); glutamine-dependent asparagine synthetase; asparagine synthetase B; AS; AS-B
Systematic name: L-aspartate:L-glutamine amido-ligase (AMP-forming)
Comments: The enzyme from Escherichia coli has two active sites [4] that are connected by an intramolecular ammonia tunnel [6,7]. The enzyme catalyses three distinct chemical reactions: glutamine hydrolysis to yield ammonia takes place in the N-terminal domain. The C-terminal active site mediates both the synthesis of a β-aspartyl-AMP intermediate and its subsequent reaction with ammonia. The ammonia released is channeled to the other active site to yield asparagine [7].
Links to other databases: BRENDA, EXPASY, KEGG, PDB, Metacyc, PDB, CAS registry number: 37318-72-2
References:
1. Patterson, M.K., Jr. and Orr, G.R. Asparagine biosynthesis by the Novikoff hepatoma. Isolation, purification, property, and mechanism studies of the enzyme system. J. Biol. Chem. 243 (1968) 376-380. [PMID: 4295091]
2. Boehlein, S.K., Richards, N.G. and Schuster, S.M. Glutamine-dependent nitrogen transfer in Escherichia coli asparagine synthetase B. Searching for the catalytic triad. J. Biol. Chem. 269 (1994) 7450-7457. [PMID: 7907328]
3. Richards, N.G. and Schuster, S.M. Mechanistic issues in asparagine synthetase catalysis. Adv. Enzymol. Relat. Areas Mol. Biol. 72 (1998) 145-198. [PMID: 9559053]
4. Larsen, T.M., Boehlein, S.K., Schuster, S.M., Richards, N.G., Thoden, J.B., Holden, H.M. and Rayment, I. Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product. Biochemistry 38 (1999) 16146-16157. [PMID: 10587437]
5. Huang, X., Holden, H.M. and Raushel, F.M. Channeling of substrates and intermediates in enzyme-catalyzed reactions. Annu. Rev. Biochem. 70 (2001) 149-180. [PMID: 11395405]
6. Tesson, A.R., Soper, T.S., Ciustea, M. and Richards, N.G. Revisiting the steady state kinetic mechanism of glutamine-dependent asparagine synthetase from Escherichia coli. Arch. Biochem. Biophys. 413 (2003) 23-31. [PMID: 12706338]
Accepted name: carbamoyl-phosphate synthase (glutamine-hydrolysing)
Reaction: 2 ATP + L-glutamine + HCO3- + H2O = 2 ADP + phosphate + L-glutamate + carbamoyl phosphate
(1) L-glutamine + H2O = L-glutamate + NH3
(2) 2 ATP + HCO3- = 2 ADP + phosphate + carbamoyl phosphate
For diagram of reaction click here.
Other name(s): carbamoyl-phosphate synthetase (glutamine-hydrolysing); carbamyl phosphate synthetase (glutamine); carbamoylphosphate synthetase II; glutamine-dependent carbamyl phosphate synthetase; carbamoyl phosphate synthetase; CPS; carbon-dioxide:L-glutamine amido-ligase (ADP-forming, carbamate-phosphorylating)
Systematic name: hydrogen-carbonate:L-glutamine amido-ligase (ADP-forming, carbamate-phosphorylating)
Comments: The product carbamoyl phosphate is an intermediate in the biosynthesis of arginine and the pyrimidine nucleotides [4]. The enzyme from Escherichia coli has three separate active sites, which are connected by a molecular tunnel that is almost 100 Å in length [8]. The amidotransferase domain within the small subunit of the enzyme hydrolyses glutamine to ammonia via a thioester intermediate. The ammonia migrates through the interior of the protein, where it reacts with carboxy phosphate to produce the carbamate intermediate. The carboxy-phosphate intermediate is formed by the phosphorylation of bicarbonate by ATP at a site contained within the N-terminal half of the large subunit. The carbamate intermediate is transported through the interior of the protein to a second site within the C-terminal half of the large subunit, where it is phosphorylated by another ATP to yield the final product, carbamoyl phosphate [6].
Links to other databases: BRENDA, EXPASY, KEGG, PDB, Metacyc, PDB, CAS registry number: 37233-48-0
References:
1. Anderson, P.M. and Meister, A. Evidence for an activated form of carbon dioxide in the reaction catalysed by Escherichia coli carbamyl phosphate synthetase. Biochemistry 4 (1965) 2803-2809.
2. Kalman, S.M., Duffield, P.H. and Brzozowski, T. Purification and properties of a bacterial carbamyl phosphate synthetase. J. Biol. Chem. 241 (1966) 1871-1877. [PMID: 5329589]
3. Yip, M.C.M. and Knox, W.E. Glutamine-dependent carbamyl phosphate synthetase. Properties and distribution in normal and neoplastic rat tissues. J. Biol. Chem. 245 (1970) 2199-2204. [PMID: 5442268]
4. Stapleton, M.A., Javid-Majd, F., Harmon, M.F., Hanks, B.A., Grahmann, J.L., Mullins, L.S. and Raushel, F.M. Role of conserved residues within the carboxy phosphate domain of carbamoyl phosphate synthetase. Biochemistry 35 (1996) 14352-14361. [PMID: 8916922]
5. Holden, H.M., Thoden, J.B. and Raushel, F.M. Carbamoyl phosphate synthetase: a tunnel runs through it. Curr. Opin. Struct. Biol. 8 (1998) 679-685. [PMID: 9914247]
6. Raushel, F.M., Thoden, J.B., Reinhart, G.D. and Holden, H.M. Carbamoyl phosphate synthetase: a crooked path from substrates to products. Curr. Opin. Chem. Biol. 2 (1998) 624-632. [PMID: 9818189]
7. Raushel, F.M., Thoden, J.B. and Holden, H.M. The amidotransferase family of enzymes: molecular machines for the production and delivery of ammonia. Biochemistry 38 (1999) 7891-7899. [PMID: 10387030]
8. Thoden, J.B., Huang, X., Raushel, F.M. and Holden, H.M. Carbamoyl-phosphate synthetase. Creation of an escape route for ammonia. J. Biol. Chem. 277 (2002) 39722-39727. [PMID: 12130656]
Accepted name: asparaginyl-tRNA synthase (glutamine-hydrolysing)
Reaction: ATP + aspartyl-tRNAAsn + L-glutamine + H2O = ADP + phosphate + asparaginyl-tRNAAsn + L-glutamate
Other name(s): Asp-AdT; Asp-tRNAAsn amidotransferase; aspartyl-tRNAAsn amidotransferase; Asn-tRNAAsn:L-glutamine amido-ligase (ADP-forming)
Systematic name: aspartyl-tRNAAsn:L-glutamine amido-ligase (ADP-forming)
Comments: This reaction forms part of a two-reaction system for producing asparaginyl-tRNA in Deinococcus radiodurans and other organisms lacking a specific enzyme for asparagine synthesis. In the first step, a non-discriminating ligase (EC 6.1.1.23, aspartate—tRNAAsn ligase) mischarges tRNAAsn with aspartate, leading to the formation of Asp-tRNAAsn. The aspartyl-tRNAAsn is not used in protein synthesis until the present enzyme converts it into asparaginyl-tRNAAsn (aspartyl-tRNAAsp is not a substrate for this reaction). Ammonia or asparagine can substitute for the preferred substrate glutamine.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37211-76-0
References:
1. Min, B., Pelaschier, J.T., Graham, D.E., Tumbula-Hansen, D. and Söll, D. Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation. Proc. Natl. Acad. Sci. USA 99 (2002) 2678-2683. [PMID: 11880622]
2. Curnow, A.W., Tumbula, D.L., Pelaschier, J.T., Min, B. and Söll, D. Glutamyl-tRNAGln amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. Proc. Natl. Acad. Sci. USA 95 (1998) 12838-12843. [PMID: 9789001]
3. Ibba, M. and Söll, D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69 (2000) 617-650. [PMID: 10966471]
Accepted name: glutaminyl-tRNA synthase (glutamine-hydrolysing)
Reaction: ATP + glutamyl-tRNAGln + L-glutamine = ADP + phosphate + glutaminyl-tRNAGln + L-glutamate
Other name(s): Glu-AdT; Glu-tRNAGln amidotransferase; glutamyl-tRNAGln amidotransferase; Glu-tRNAGln:L-glutamine amido-ligase (ADP-forming)
Systematic name: glutamyl-tRNAGln:L-glutamine amido-ligase (ADP-forming)
Comments: In systems lacking discernible glutamine—tRNA ligase (EC 6.1.1.18), glutaminyl-tRNAGln is formed by a two-enzyme system. In the first step, a nondiscriminating ligase (EC 6.1.1.24, glutamate—tRNAGln ligase) mischarges tRNAGln with glutamate, forming glutamyl-tRNAGln. The glutamyl-tRNAGln is not used in protein synthesis until the present enzyme converts it into glutaminyl-tRNAGln (glutamyl-tRNAGlu is not a substrate for this reaction). Ammonia or asparagine can substitute for the preferred substrate glutamine.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 52232-48-1
References:
1. Horiuchi, K.Y., Harpel, M.R., Shen, L., Luo, Y., Rogers, K.C. and Copeland, R.A. Mechanistic studies of reaction coupling in Glu-tRNAGln amidotransferase. Biochemistry 40 (2001) 6450-6457. [PMID: 11371208]
2. Curnow, A.W., Tumbula, D.L., Pelaschier, J.T., Min, B. and Söll, D. Glutamyl-tRNAGln amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. Proc. Natl. Acad. Sci. USA 95 (1998) 12838-12843. [PMID: 9789001]
3. Ibba, M. and Söll, D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69 (2000) 617-650. [PMID: 10966471]
[EC 6.3.5.8 Transferred entry: Now EC 2.6.1.85, aminodeoxychorismate synthase. As ATP is not hydrolysed during the reaction, the classification of the enzyme as a ligase was incorrect. (EC 6.3.5.8 created 2003, deleted 2007)]
Accepted name: hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing)
Reaction: 2 ATP + hydrogenobyrinic acid + 2 L-glutamine + 2 H2O = 2 ADP + 2 phosphate + hydrogenobyrinic acid a,c-diamide + 2 L-glutamate
For diagram click here.
Other name(s): CobB
Systematic name: hydrogenobyrinic-acid:L-glutamine amido-ligase (AMP-forming)
Comments: This step in the aerobic biosynthesis of cobalamin generates hydrogenobyrinic acid a,c-diamide, the substrate required by EC 6.6.1.2, cobaltochelatase, which adds cobalt to the macrocycle.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 132053-22-6
References:
1. Debussche, L., Thibaut, D., Cameron, B., Crouzet, J. and Blanche, F. Purification and characterization of cobyrinic acid a,c-diamide synthase from Pseudomonas denitrificans. J. Bacteriol. 172 (1990) 6239-6244. [PMID: 2172209]
2. 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]
Accepted name: adenosylcobyric acid synthase (glutamine-hydrolysing)
Reaction: 4 ATP + adenosylcobyrinic acid a,c-diamide + 4 L-glutamine + 4 H2O = 4 ADP + 4 phosphate + adenosylcobyric acid + 4 L-glutamate
For diagram click here.
Other name(s): CobQ; cobyric acid synthase; 5'-deoxy-5'-adenosylcobyrinic-acid-a,c-diamide:L-glutamine amido-ligase; Ado-cobyric acid synthase [glutamine hydrolyzing]
Systematic name: adenosylcobyrinic-acid-a,c-diamide:L-glutamine amido-ligase (ADP-forming)
Comments: Requires Mg2+. NH3 can act instead of glutamine. This enzyme catalyses the four-step amidation sequence from cobyrinic acid a,c-diamide to cobyric acid via the formation of cobyrinic acid triamide, tetraamide and pentaamide intermediates.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 137672-90-3
References:
1. Blanche, F., Couder, M., Debussche, L., Thibaut, D., Cameron, B. and Crouzet, J. Biosynthesis of vitamin B12: stepwise amidation of carboxyl groups b, d, e, and g of cobyrinic acid a,c-diamide is catalyzed by one enzyme in Pseudomonas denitrificans. J. Bacteriol. 173 (1991) 6046-6051. [PMID: 1917839]
2. 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]
Accepted name: cobyrinate a,c-diamide synthase
Reaction: 2 ATP + cobyrinate + 2 L-glutamine + 2 H2O = 2 ADP + 2 phosphate + cobyrinate a,c-diamide + 2 L-glutamate
(1a) ATP + cobyrinate + L-glutamine + H2O = ADP + phosphate + cobyrinate c-monamide + L-glutamate
(1b) ATP + cobyrinate c-monamide + L-glutamine + H2O = ADP + phosphate + cobyrinate a,c-diamide + L-glutamate
For diagram click here.
Other name(s): cobyrinic acid a,c-diamide synthetase; CbiA (gene name)
Comments: This enzyme is the first glutamine amidotransferase that participates in the anaerobic (early cobalt insertion) biosynthetic pathway of adenosylcobalamin, and catalyses the ATP-dependent synthesis of cobyrinate a,c-diamide from cobyrinate using either L-glutamine or ammonia as the nitrogen source. It is proposed that the enzyme first catalyses the amidation of the c-carboxylate, and then the intermediate is released into solution and binds to the same catalytic site for the amidation of the a-carboxylate. The Km for ammonia is substantially higher than that for L-glutamine.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Fresquet, V., Williams, L. and Raushel, F.M. Mechanism of cobyrinic acid a,c-diamide synthetase from Salmonella typhimurium LT2. Biochemistry 43 (2004) 10619-10627. [PMID: 15311923]