5OPZ | pdb_00005opz

Crystal structure of Serratia marcescens L-Ala D-Glu endopeptidase ChiX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 
    0.120 (Depositor), 0.120 (DCC) 
  • R-Value Work: 
    0.089 (Depositor) 
  • R-Value Observed: 
    0.091 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5OPZ

This is version 1.2 of the entry. See complete history

Literature

Structure and activity of ChiX: a peptidoglycan hydrolase required for chitinase secretion by Serratia marcescens.

Owen, R.A.Fyfe, P.K.Lodge, A.Biboy, J.Vollmer, W.Hunter, W.N.Sargent, F.

(2018) Biochem J 475: 415-428

  • DOI: https://doi.org/10.1042/BCJ20170633
  • Primary Citation Related Structures: 
    5OPZ, 5OQ1

  • PubMed Abstract: 

    The Gram-negative bacterium Serratia marcescens secretes many proteins that are involved in extracellular chitin degradation. This so-called chitinolytic machinery includes three types of chitinase enzymes and a lytic polysaccharide monooxygenase. An operon has been identified in S. marcescens , chiWXYZ , that is thought to be involved in the secretion of the chitinolytic machinery. Genetic evidence points to the ChiX protein being a key player in the secretion mechanism, since deletion of the chiX gene in S. marcescens led to a mutant strain blocked for secretion of all members of the chitinolytic machinery. In this work, a detailed structural and biochemical characterisation of ChiX is presented. The high-resolution crystal structure of ChiX reveals the protein to be a member of the LAS family of peptidases. ChiX is shown to be a zinc-containing metalloenzyme, and in vitro assays demonstrate that ChiX is an l-Ala d-Glu endopeptidase that cleaves the cross-links in bacterial peptidoglycan. This catalytic activity is shown to be intimately linked with the secretion of the chitinolytic machinery, since substitution of the ChiX Asp-120 residue results in a variant protein that is both unable to digest peptidoglycan and cannot rescue the phenoytype of a chiX mutant strain.


  • Organizational Affiliation
    • School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.

Macromolecule Content 

  • Total Structure Weight: 31.14 kDa 
  • Atom Count: 2,742 
  • Modeled Residue Count: 266 
  • Deposited Residue Count: 274 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ChiX
A, B
137Serratia marcescensMutation(s): 0 
Gene Names: ERS381432_02813chiX

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free:  0.120 (Depositor), 0.120 (DCC) 
  • R-Value Work:  0.089 (Depositor) 
  • R-Value Observed: 0.091 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.627α = 90
b = 55.531β = 90
c = 51.78γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--
Wellcome TrustUnited Kingdom094090

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Refinement description