Protein Family Models

An uncharacterized alpha+beta fold domain that is mostly fused to a RimK-like ATP-grasp and is found in bacteria and euryarchaea. Members of this family are almost always associated in gene neighborhoods with a GNAT-like acetyltransferase fused to a papain-like petidase. Additionally M20-like peptidases, GCS2, 4Fe-4S Ferredoxins, a distinct metal-sulfur cluster protein and ribosomal proteins are found in the gene neighborhoods. Contextual analysis suggests a role for these in peptide biosynthesis [1]. [1]. 20023723. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L;. Mol Biosyst. 2009;5:1636-1660. (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

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

RimK family protein containing a C-terminal domain similar to ribosomal protein S6--L-glutamate ligase RimK that catalyzes the ATP-dependent post-translational addition of glutamate residues to the C-terminus of ribosomal protein S6

Date:

2019-05-23