Dataset Information

Structural basis of murein peptide specificity of a gamma-D-glutamyl-l-diamino acid endopeptidase.

ABSTRACT: The crystal structures of two homologous endopeptidases from cyanobacteria Anabaena variabilis and Nostoc punctiforme were determined at 1.05 and 1.60 A resolution, respectively, and contain a bacterial SH3-like domain (SH3b) and a ubiquitous cell-wall-associated NlpC/P60 (or CHAP) cysteine peptidase domain. The NlpC/P60 domain is a primitive, papain-like peptidase in the CA clan of cysteine peptidases with a Cys126/His176/His188 catalytic triad and a conserved catalytic core. We deduced from structure and sequence analysis, and then experimentally, that these two proteins act as gamma-D-glutamyl-L-diamino acid endopeptidases (EC 3.4.22.-). The active site is located near the interface between the SH3b and NlpC/P60 domains, where the SH3b domain may help define substrate specificity, instead of functioning as a targeting domain, so that only muropeptides with an N-terminal L-alanine can bind to the active site.

SUBMITTER: Xu Q

PROVIDER: S-EPMC2667786 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature

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Structural basis of murein peptide specificity of a gamma-D-glutamyl-l-diamino acid endopeptidase.

Xu Qingping Q Sudek Sebastian S McMullan Daniel D Miller Mitchell D MD Geierstanger Bernhard B Jones David H DH Krishna S Sri SS Spraggon Glen G Bursalay Badry B Abdubek Polat P Acosta Claire C Ambing Eileen E Astakhova Tamara T Axelrod Herbert L HL Carlton Dennis D Caruthers Jonathan J Chiu Hsiu-Ju HJ Clayton Thomas T Deller Marc C MC Duan Lian L Elias Ylva Y Elsliger Marc-André MA Feuerhelm Julie J Grzechnik Slawomir K SK Hale Joanna J Han Gye Won GW Haugen Justin J Jaroszewski Lukasz L Jin Kevin K KK Klock Heath E HE Knuth Mark W MW Kozbial Piotr P Kumar Abhinav A Marciano David D Morse Andrew T AT Nigoghossian Edward E Okach Linda L Oommachen Silvya S Paulsen Jessica J Reyes Ron R Rife Christopher L CL Trout Christina V CV van den Bedem Henry H Weekes Dana D White Aprilfawn A Wolf Guenter G Zubieta Chloe C Hodgson Keith O KO Wooley John J Deacon Ashley M AM Godzik Adam A Lesley Scott A SA Wilson Ian A IA

Structure (London, England : 1993) 20090201 2

The crystal structures of two homologous endopeptidases from cyanobacteria Anabaena variabilis and Nostoc punctiforme were determined at 1.05 and 1.60 A resolution, respectively, and contain a bacterial SH3-like domain (SH3b) and a ubiquitous cell-wall-associated NlpC/P60 (or CHAP) cysteine peptidase domain. The NlpC/P60 domain is a primitive, papain-like peptidase in the CA clan of cysteine peptidases with a Cys126/His176/His188 catalytic triad and a conserved catalytic core. We deduced from st ...[more]

PMID: 19217401

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Project description:Some Gram-negative bacteria target their competitors by exploiting the type VI secretion system to extrude toxic effector proteins. To prevent self-harm, these bacteria also produce highly specific immunity proteins that neutralize these antagonistic effectors. Here, the peptidoglycan endopeptidase specificity of two type VI secretion-system-associated effectors from Serratia marcescens is characterized. These small secreted proteins, Ssp1 and Ssp2, cleave between ?-D-glutamic acid and L-meso-diaminopimelic acid with different specificities. Ssp2 degrades the acceptor part of cross-linked tetratetrapeptides. Ssp1 displays greater promiscuity and cleaves monomeric tripeptides, tetrapeptides and pentapeptides and dimeric tetratetra and tetrapenta muropeptides on both the acceptor and donor strands. Functional assays confirm the identity of a catalytic cysteine in these endopeptidases and crystal structures provide information on the structure-activity relationships of Ssp1 and, by comparison, of related effectors. Functional assays also reveal that neutralization of these effectors by their cognate immunity proteins, which are called resistance-associated proteins (Raps), contributes an essential role to cell fitness. The structures of two immunity proteins, Rap1a and Rap2a, responsible for the neutralization of Ssp1 and Ssp2-like endopeptidases, respectively, revealed two distinct folds, with that of Rap1a not having previously been observed. The structure of the Ssp1-Rap1a complex revealed a tightly bound heteromeric assembly with two effector molecules flanking a Rap1a dimer. A highly effective steric block of the Ssp1 active site forms the basis of effector neutralization. Comparisons with Ssp2-Rap2a orthologues suggest that the specificity of these immunity proteins for neutralizing effectors is fold-dependent and that in cases where the fold is conserved sequence differences contribute to the specificity of effector-immunity protein interactions.

Dataset Information

Structural basis of murein peptide specificity of a gamma-D-glutamyl-l-diamino acid endopeptidase.

Publications

Structural basis of murein peptide specificity of a gamma-D-glutamyl-l-diamino acid endopeptidase.

Similar Datasets

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