Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 53.18 kDa 
• Atom Count: 3740 
• Modelled Residue Count: 420 
• Deposited Residue Count: 439 
• Unique protein chains: 1

5D2R

Inhibitor Bound Cell Shape Determinant Protein Csd4 from Helicobacter pylori

• DOI: 10.2210/pdb5D2R/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Helicobacter pylori G27
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-06 Released: 2016-01-20 
• Deposition Author(s): Chan, A.C., Murphy, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.219 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

A Bacterial Cell Shape-Determining Inhibitor.

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

(2016) ACS Chem Biol 11: 981-991

• PubMed: 26735022 
• DOI: 10.1021/acschembio.5b01039
• Primary Citation of Related Structures:  
  5D2R


• PubMed Abstract: 
  

Helicobacter pylori and Campylobacter jejuni are human pathogens and causative agents of gastric ulcers/cancer and gastroenteritis, respectively. Recent studies have uncovered a series of proteases that are responsible for maintaining the helical shape of these organisms. The H. pylori metalloprotease Csd4 and its C. jejuni homologue Pgp1 cleave the amide bond between meso-diaminopimelate and iso-d-glutamic acid in truncated peptidoglycan side chains. Deletion of either csd4 or pgp1 results in bacteria with a straight rod phenotype, a reduced ability to move in viscous media, and reduced pathogenicity. In this work, a phosphinic acid-based pseudodipeptide inhibitor was designed to act as a tetrahedral intermediate analog against the Csd4 enzyme. The phosphinic acid was shown to inhibit the cleavage of the alternate substrate, Ac-l-Ala-iso-d-Glu-meso-Dap, with a Ki value of 1.5 μM. Structural analysis of the Csd4-inhibitor complex shows that the phosphinic acid displaces the zinc-bound water and chelates the metal in a bidentate fashion. The phosphinate oxygens also interact with the key acid/base residue, Glu222, and the oxyanion-stabilizing residue, Arg86. The results are consistent with the "promoted-water pathway" mechanism for carboxypeptidase A catalysis. Studies on cultured bacteria showed that the inhibitor causes significant cell straightening when incubated with H. pylori at millimolar concentrations. A diminished, yet observable, effect on the morphology of C. jejuni was also apparent. Cell straightening was more pronounced with an acapsular C. jejuni mutant strain compared to the wild type, suggesting that the capsule impaired inhibitor accessibility. These studies demonstrate that a highly polar compound is capable of crossing the outer membrane and altering cell shape, presumably by inhibiting cell shape determinant proteases. Peptidoglycan proteases acting as cell shape determinants represent novel targets for the development of antimicrobials against these human pathogens.

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Organizational Affiliation: 

Contribution from the Department of Chemistry, University of British Columbia , Vancouver, British Columbia V6T 1Z1, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved hypothetical secreted protein	A	439	Helicobacter pylori G27	Mutation(s): 0  Gene Names: HPG27_353
UniProt
Find proteins for B5ZAD9 (Helicobacter pylori (strain G27)) Explore B5ZAD9  Go to UniProtKB:  B5ZAD9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
56W (Subject of Investigation/LOI)	X [auth A]	(2R,6R)-2-{[(R)-[(3R)-3-(acetylamino)-3-carboxypropyl](hydroxy)phosphoryl]methyl}-6-aminoheptanedioic acid C14 H25 N2 O9 P AWMPEAXWUINOES-HBNTYKKESA-N
IOD	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [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]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
56W	Binding MOAD:  5D2R	Ki: 1500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.219 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.84	α = 90
b = 66.61	β = 90
c = 144.48	γ = 90

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2015-08-06 
• Released Date: 2016-01-20 
Deposition Author(s): Chan, A.C., Murphy, M.E.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2016-04-27
  Changes: Database references