Protein Family Models

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:

2024-08-14

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:

2024-08-14

This family represents the N-terminal region of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4 which is thought to be involved in substrate binding [2]. 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]. This domain is structurally related to the PreATP-grasp domain. [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:

2024-08-14

Catalyzes the formation of D-alanyl-D-alanine from two D-alanines in peptidoglycan synthesis

Date:

2021-08-30

This model describes D-Ala--D-Ala ligase, an enzyme that makes a required precursor of the bacterial cell wall. It also describes some closely related proteins responsible for resistance to glycopeptide antibiotics such as vancomycin. The mechanism of glyopeptide antibiotic resistance involves the production of D-alanine-D-lactate (VanA and VanB families) or D-alanine-D-serine (VanC). The seed alignment contains only chromosomally encoded D-ala--D-ala ligases, but a number of antibiotic resistance proteins score above the trusted cutoff of this model.

Date:

2024-05-30