Protein Family Models

This HMM hits multiple proteins of peptidoglycan (murein) biosynthesis, such as MurC, MurD, MurE, and MurF of Escherichia coli.

Date:

2024-08-14

This entry contains a number of related ligase enzymes which have EC numbers 6.3.2.* which includes: MurC (Swiss:P17952), MurD (Swiss:P14900), MurE (Swiss:P22188), MurF (Swiss:P11880), Mpl (Swiss:P37773) and FolC (Swiss:P08192). MurC, MurD, MurE and MurF catalyse consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesised by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine [1,3,4]. This entry also includes folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) [2]. [1]. 9218784. Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli. Bertrand JA, Auger G, Fanchon E, Martin L, Blanot D, van Heijenoort J, Dideberg O;. EMBO J 1997;16:3416-3425. [2]. 9652408. Molecular characterization of cyanophycin synthetase, the enzyme catalyzing the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin). Ziegler K, Diener A, Herpin C, Richter R, Deutzmann R, Lockau W;. Eur J Biochem. 1998;254:154-159. [3]. 25130693. The biology of Mur ligases as an antibacterial target. Ko. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

This family includes a variety of pterin binding enzymes that all adopt a TIM barrel fold. The family includes dihydropteroate synthase EC:2.5.1.15 as well as a group methyltransferase enzymes including methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) Swiss:Q46389 that catalyses a key step in the Wood-Ljungdahl pathway of carbon dioxide fixation. It transfers the N5-methyl group from methyltetrahydrofolate (CH3-H4folate) to a cob(I)amide centre in another protein, the corrinoid iron-sulfur protein. MeTr is a member of a family of proteins that includes methionine synthase and methanogenic enzymes that activate the methyl group of methyltetra-hydromethano(or -sarcino)pterin [2]. [1]. 9187658. Crystal structure of the anti-bacterial sulfonamide drug target dihydropteroate synthase. Achari A, Somers DO, Champness JN, Bryant PK, Rosemond J, Stammers DK. Nat Struct Biol 1997;4:490-497. This paper shows similarity by sequence of DHPS and MetH enzymes. [2]. 10997901. Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase. Doukov T, Seravalli J, Stezowski JJ, Ragsdale SW;. Structure Fold Des 2000;8:817-830. (from Pfam)

Date:

2024-10-16

This HMM represents the FolC family of folate pathway proteins. Most examples are bifunctional, active as both folylpolyglutamate synthetase (EC 6.3.2.17) and dihydrofolate synthetase (EC 6.3.2.12). The two activities are similar - ATP + glutamate + dihydropteroate or tetrahydrofolyl-[Glu](n) = ADP + orthophosphate + dihydrofolate or tetrahydrofolyl-[Glu](n+1). A mutation study of the FolC gene of E. coli suggests that both activities belong to the same active site. Because some examples are monofunctional (and these cannot be separated phylogenetically), the model is treated as subfamily, not equivalog.

Gene:

folC

Date:

2024-05-30

This HMM represents dihydropteroate synthase, the enzyme that catalyzes the second to last step in folic acid biosynthesis. The gene is usually designated folP (folic acid biosynthsis) or sul (sulfanilamide resistance). This model represents one branch of the family of pterin-binding enzymes (PF00809) and of a cluster of dihydropteroate synthase and related enzymes (COG0294). Other members of PF00809 and COG0294 are represented by HMM TIGR00284.

Gene:

folP

Date:

2021-04-27