Protein Family Models

This is the N-terminal domain found in Escherichia coli RimK proteins (Ribosomal protein S6-L-glutamate ligase). This domain precedes the ATP-grasp domain Pfam:PF08443 [1]. [1]. 23609986. Structure and function of Escherichia coli RimK, an ATP-grasp fold, L-glutamyl ligase enzyme. Zhao G, Jin Z, Wang Y, Allewell NM, Tuchman M, Shi D;. Proteins. 2013;81:1847-1854. (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

Date:

2024-08-14

RimK family alpha-L-glutamate ligase, similar to Escherichia coli RimK which can catalyze the synthesis of poly-alpha-glutamate in vitro, via ATP hydrolysis from unprotected Glu residues

Date:

2018-07-12

Responsible for the addition of glutamate residues to the C-terminus of ribosomal protein S6

Gene:

rimK

Date:

2022-06-03

This family, related to bacterial glutathione synthetases, contains at least three different alpha-L-glutamate ligases. One is RimK, as in E. coli, which adds additional Glu residues to the native Glu-Glu C-terminus of ribosomal protein S6, but not to Lys-Glu mutants. Most species with a member of this subfamily lack an S6 homolog ending in Glu-Glu, however. Members in Methanococcus jannaschii act instead as a tetrahydromethanopterin:alpha-l-glutamate ligase (MJ0620) and a gamma-F420-2:alpha-l-glutamate ligase (MJ1001).

Date:

2021-04-27