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

Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. [1]. 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 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:

2024-08-14

This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site [1]. [1]. 10526357. Structure classification-based assessment of CASP3 predictions. for the fold recognition targets.. Murzin AG;. Proteins 1999;37:88-103. (from Pfam)

Date:

2024-08-14

Carbamoyl-phosphate synthase (CPSase) catalyzes the first committed step in pyrimidine, arginine, and urea biosynthesis. In general, it is a glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II in eukaryotes. An exception is the mammalian mitochondrial urea-cycle form, CPSase I, in which the glutamine amidotransferase domain active site Cys on the small subunit has been lost, and the enzyme is ammonia-dependent. In both CPSase I and the closely related, glutamine-dependent CPSase III (allosterically activated by acetyl-glutamate) demonstrated in some other vertebrates, the small and large chain regions are fused in a single polypeptide chain. This HMM represents the large chain of glutamine-hydrolysing carbamoyl-phosphate synthases, or the corresponding regions of larger, multifunctional proteins, as found in all domains of life, and CPSase I forms are considered exceptions within the family. In several thermophilic species (Methanobacterium thermoautotrophicum, Methanococcus jannaschii, Aquifex aeolicus), the large subunit appears split, at different points, into two separate genes.

Gene:

carB

Date:

2021-04-27

carbamoyl-phosphate synthase (glutamine-hydrolyzing) large subunit is a component of carbamoylphosphate synthetase (CPS), which catalyzes the formation of carbamoylphosphate from C02, ATP, and ammonia or glutamine, for pyrimidine biosynthesis, arginine biosynthesis, or the urea cycle

Date:

2021-09-27

Gene:

carB

Date:

2024-05-02

Date:

2020-10-26