Protein Family Models

This domain is found in a group of proteins from tailed bacteriophages and prophages mainly found in proteobacteria, including Type VI secretion system spike protein VgrG3 from Vibrio cholerae. VgrG3 degrades the peptidoglycan cell wall of rival bacteria via its C-terminal region through its muramidase activity. This domain adopts a canonical phage- T4-lysozyme-like fold showing eight alpha-helices and two 3-10 helices, which pack against a three-stranded antiparallel beta-sheet [1,2]. Paper describing PDB structure 4noo. [1]. 24699653. Molecular mechanism for self-protection against the type VI secretion system in Vibrio cholerae. Yang X, Xu M, Wang Y, Xia P, Wang S, Ye B, Tong L, Jiang T, Fan Z;. Acta Crystallogr D Biol Crystallogr. 2014;70:1094-1103. Paper describing PDB structure 4nso. [2]. 24751834. Structural basis for recognition of the type VI spike protein VgrG3 by a cognate immunity protein. Zhang J, Zhang H, Gao Z, Hu H, Dong C, Dong YH;. FEBS Lett. 2014;588:1891-1898. (from Pfam)

Date:

2024-10-16

This conserved domain is found in Xanthomonas VirD4 interacting proteins (XVIPs) and other type IV secretion system (T4SS) specialised in translocating effector proteins (toxic effector proteins, X-Tfes) into competing gram-negative species, leading to target cell death. This domain interacts with the central all-alpha domain of VirD4. Its structure shows two well ordered N-terminal antiparallel alpha-helices that pack against a carboxyl-terminal three-stranded antiparallel beta sheet [1-3]. [1]. 15774874. Identification of new protein-protein interactions involving the products of the chromosome- and plasmid-encoded type IV secretion loci of the phytopathogen Xanthomonas axonopodis pv. citri. Alegria MC, Souza DP, Andrade MO, Docena C, Khater L, Ramos CH, da Silva AC, Farah CS;. J Bacteriol. 2005;187:2315-2325. [2]. 25743609. Bacterial killing via a type IV secretion system. Souza DP, Oka GU, Alvarez-Martinez CE, Bisson-Filho AW, Dunger G, Hobeika L, Cavalcante NS, Alegria MC, Barbosa LR, Salinas RK, Guzzo CR, Farah CS;. Nat Commun. 2015;6:6453. [3]. 34983846. Structural basis for effector recognition by an antibacterial type IV secretion system. Oka GU, Souza DP, Cenens W, Matsuyama BY, Cardoso MVC, Oliveira LC, da Silva Lima F, Cuccovia IM, Guzzo CR, Salinas RK, Farah CS;. Proc Natl Acad Sci U S A. 2022; [Epub ahead of print] (from Pfam)

Date:

2024-10-16

This domain is composed of three alpha helices [1]. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [2]. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins [3]. The domain is found to bind peptidoglycan experimentally [4]. This paper gives the crystal structure for this domain. However no function is given for this domain. [1]. 7121588. Structure of a Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase at 2.5 A resolution. Dideberg O, Charlier P, Dive G, Joris B, Frere JM, Ghuysen JM;. Nature 1982;299:469-470. [2]. 1683402. Cloning, expression, sequence analysis and biochemical characterization of an autolytic amidase of Bacillus subtilis 168 trpC2. Foster SJ;. J Gen Microbiol 1991;137:1987-1998. [3]. 7656014. The NMR structure of the inhibited catalytic domain of human stromelysin-1. Gooley PR, O'Connell JF, Marcy AI, Cuca GC, Salowe SP, Bush BL, Hermes JD, Esser CK, Hagmann WK, Springer JP, et al;. Nat Struct Biol 1994;1:111-118. [4]. 17697255. Muralytic activity and modular structure of the endolysins of Pseudomonas aeruginosa bacteriophages phiKZ and EL. Briers Y, Volckaert G, Cornelissen A, Lagaert S, Michiels CW, Hertveldt K, Lavigne R;. Mol Microbiol. 2007;65:1334-1344. (from Pfam)

Date:

2024-10-16

peptidoglycan-binding domain-containing protein may be involved in bacterial cell wall degradation, similar to Vibrio cholerae type VI secretion system (T6SS) effector protein VgrG3 and bacteriophage phi KZ lytic transglycosylase gp144

Date:

2022-09-09