Protein Family Models

Formate-dependent phosphoribosylglycinamide formyltransferase (PurT) is involved in de novo purine biosynthesis. PurT belongs to the ATP-grasp superfamily of enzymes and catalyses the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR) [1,2]. This entry represents the C-terminal domain which has a rudiment single hybrid motif consisting of a sandwich of half-barrel shaped beta-sheets [2]. Paper describing PDB structure 1eyz. [1]. 10913290. Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase. Thoden JB, Firestine S, Nixon A, Benkovic SJ, Holden HM;. Biochemistry. 2000;39:8791-8802. Paper describing PDB structure 1kj8. [2]. 11953435. PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site. Thoden JB, Firestine SM, Benkovic SJ, Holden HM;. J Biol Chem. 2002;277:23898-23908. (from Pfam)

Date:

2024-10-16

This domain precedes the ATP-grasp domain in a number of ribonucleotide synthetases [1-5]. Paper describing PDB structure 1b6r. [1]. 10569930. Three-dimensional structure of N5-carboxyaminoimidazole ribonucleotide synthetase: a member of the ATP grasp protein superfamily. Thoden JB, Kappock TJ, Stubbe J, Holden HM;. Biochemistry. 1999;38:15480-15492. Paper describing PDB structure 1eyz. [2]. 10913290. Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase. Thoden JB, Firestine S, Nixon A, Benkovic SJ, Holden HM;. Biochemistry. 2000;39:8791-8802. Paper describing PDB structure 1kj8. [3]. 11953435. PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site. Thoden JB, Firestine SM, Benkovic SJ, Holden HM;. J Biol Chem. 2002;277:23898-23908. Paper describing PDB structure 3eth. [4]. 19053251. Structural analysis of the active site geometry of N5-carboxyaminoimidazole ribonucleotide synthetase from Escherichia coli. Thoden JB, Holden HM, Firestine SM;. Biochemistry. 2008;47:13346-13353. Paper describing PDB structure 3k5h. [5]. 20050602. Structural and functional studies of Aspergillus clavatus N(5)-carboxyaminoimidazole ribonucleotide synthetase . Thoden JB, Holden HM, Paritala H, Firestine SM;. Biochemistry. 2010;49:752-760. (from Pfam)

Date:

2024-10-16

This ATP-grasp domain is found in the ribosomal S6 modification enzyme RimK [1]. [1]. 9416615. A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity. Galperin MY, Koonin EV;. Protein Sci 1997;6:2639-2643. (from Pfam)

Date:

2024-10-16

This family represents the C-terminal, catalytic domain of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF) [3]. [1]. 9054558. D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant. Fan C, Park IS, Walsh CT, Knox JR;. Biochemistry 1997;36:2531-2538. [2]. 10908650. The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA). Roper DI, Huyton T, Vagin A, Dodson G;. Proc Natl Acad Sci U S A 2000;97:8921-8925. [3]. 12499203. Roles of Mycobacterium smegmatis D-alanine:D-alanine ligase and D-alanine racemase in the mechanisms of action of and resistance to the peptidoglycan inhibitor D-cycloserine. Feng Z, Barletta RG;. Antimicrob Agents Chemother 2003;47:283-291. (from Pfam)

Date:

2024-10-16

Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines [2]. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See Pfam:PF00988. The small chain has a GATase domain in the carboxyl terminus. See Pfam:PF00117. The ATP binding domain (this one) has an ATP-grasp fold. [1]. 7915138. Three-dimensional structure of the biotin carboxylase subunit. of acetyl-CoA carboxylase. Waldrop GL, Rayment I, Holden HM;. Biochemistry 1994;33:10249-10256. [2]. 1972379. Mammalian carbamyl phosphate synthetase (CPS). DNA sequence and evolution of the CPS domain of the Syrian hamster multifunctional protein CAD. Simmer JP, Kelly RE, Rinker AG Jr, Scully JL, Evans DR;. Biol Chem 1990;265:10395-10402. [3]. 10089390. The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution. Thoden JB, Raushel FM, Benning MM, Rayment I, Holden HM;. Acta Crystallogr D Biol Crystallogr 1999;55:8-24. (from Pfam)

Date:

2024-10-16

No functional information or experimental verification of function is known in this family. This family appears to be an ATP-grasp domain (Pers. obs. A Bateman). (from Pfam)

Date:

2024-08-14

This family does not contain all known ATP-grasp domain members. This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity. [1]. 9416615. A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity. Galperin MY, Koonin EV;. Protein Sci 1997;6:2639-2643. (from Pfam)

Date:

2024-10-16

Non-folate utilizing enzyme, catalyzes the production of beta-formyl glycinamide ribonucleotide from formate, ATP, and beta-GAR and a side reaction producing acetyl phosphate and ADP from acetate and ATP; involved in de novo purine biosynthesis

Gene:

purT

Date:

2021-07-23

This enzyme is an alternative to PurN (TIGR00639)

Gene:

purT

Date:

2024-05-30