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

Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference [1] are in this C-terminal domain. [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. (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 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 is structurally related to the PreATP-grasp domain. The family contains the N-terminus of biotin carboxylase enzymes [1,3], and propionyl-CoA carboxylase A chain [2]. [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]. 25383525. Structure and function of a single-chain, multi-domain. long-chain acyl-CoA carboxylase.. Tran TH, Hsiao YS, Jo J, Chou CY, Dietrich LE, Walz T, Tong L;. Nature. 2015;518:120-124.. [3]. 20443544. Structural impact of human and Escherichia coli biotin carboxyl. carrier proteins on biotin attachment.. Healy S, McDonald MK, Wu X, Yue WW, Kochan G, Oppermann U,. Gravel RA;. Biochemistry. 2010;49:4687-4694. (from Pfam)

Date:

2024-08-14

acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha is a biotin-dependent carboxylase

Date:

2017-07-03

Catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA

Date:

2021-08-24

This model represents the biotin carboxylase subunit found usually as a component of acetyl-CoA carboxylase. Acetyl-CoA carboxylase is designated EC 6.4.1.2 and this component, biotin carboxylase, has its own designation, EC 6.3.4.14. Homologous domains are found in eukaryotic forms of acetyl-CoA carboxylase and in a number of other carboxylases (e.g. pyruvate carboxylase), but seed members and trusted cutoff are selected so as to exclude these. In some systems, the biotin carboxyl carrier protein and this protein (biotin carboxylase) may be shared by different carboxyltransferases. However, this model is not intended to identify the biotin carboxylase domain of propionyl-coA carboxylase. The model should hit the full length of proteins, except for chloroplast transit peptides in plants. If it hits a domain only of a longer protein, there may be a problem with the identification.

Gene:

accC

Date:

2024-06-21