Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.43 kDa 
• Atom Count: 3,907 
• Modelled Residue Count: 415 
• Deposited Residue Count: 439 
• Unique protein chains: 1

 4WCM

Crystal Structure of Cell Shape Determinant protein Csd4 Gln46His variant from Helicobacter pylori

• PDB DOI: 10.2210/pdb4WCM/pdb

• Classification: HYDROLASE
• Organism(s): Helicobacter pylori G27
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-09-05 Released: 2014-12-24 
• Deposition Author(s): Chan, A.C., Murphy, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.210 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Literature

Helical Shape of Helicobacter pylori Requires an Atypical Glutamine as a Zinc Ligand in the Carboxypeptidase Csd4.

Chan, A.C., Blair, K.M., Liu, Y., Frirdich, E., Gaynor, E.C., Tanner, M.E., Salama, N.R., Murphy, M.E.

(2015) J Biol Chem 290: 3622-3638

• PubMed: 25505267 
• DOI: 10.1074/jbc.M114.624734
• Primary Citation of Related Structures:  
  4WCK, 4WCL, 4WCM, 4WCN


• PubMed Abstract: 
  

Peptidoglycan modifying carboxypeptidases (CPs) are important determinants of bacterial cell shape. Here, we report crystal structures of Csd4, a three-domain protein from the human gastric pathogen Helicobacter pylori. The catalytic zinc in Csd4 is coordinated by a rare His-Glu-Gln configuration that is conserved among most Csd4 homologs, which form a distinct subfamily of CPs. Substitution of the glutamine to histidine, the residue found in prototypical zinc carboxypeptidases, resulted in decreased enzyme activity and inhibition by phosphate. Expression of the histidine variant at the native locus in a H. pylori csd4 deletion strain did not restore the wild-type helical morphology. Biochemical assays show that Csd4 can cleave a tripeptide peptidoglycan substrate analog to release m-DAP. Structures of Csd4 with this substrate analog or product bound at the active site reveal determinants of peptidoglycan specificity and the mechanism to cleave an isopeptide bond to release m-DAP. Our data suggest that Csd4 is the archetype of a new CP subfamily with a domain scheme that differs from this large family of peptide-cleaving enzymes.

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Organizational Affiliation: 

From the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada, [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved hypothetical secreted protein	A	439	Helicobacter pylori G27	Mutation(s): 1  Gene Names: HPG27_353
UniProt
Find proteins for B5ZAD9 (Helicobacter pylori (strain G27)) Explore B5ZAD9  Go to UniProtKB:  B5ZAD9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
API	RA [auth A]	2,6-DIAMINOPIMELIC ACID C7 H14 N2 O4 GMKMEZVLHJARHF-SYDPRGILSA-N
IOD	AA [auth A], B [auth A], BA [auth A], C [auth A], CA [auth A], D [auth A], DA [auth A], E [auth A], EA [auth A], F [auth A], FA [auth A], G [auth A], GA [auth A], H [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], JA [auth A], K [auth A], KA [auth A], L [auth A], LA [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
PO4	QA [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	MA [auth A], NA [auth A], OA [auth A], PA [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.210 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.6	α = 90
b = 66.65	β = 90
c = 145.4	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Chan, A.C., Murphy, M.E.

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2014-12-31
  Changes: Database references
• Version 1.2: 2015-02-18
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Database references, Derived calculations, Refinement description, Source and taxonomy