3QBU

Crystal structure of putative peptidoglycan deactelyase (HP0310) from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5701 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structure of Helicobacter pylori HP0310 Reveals an Atypical Peptidoglycan Deacetylase.

Shaik, M.M.Cendron, L.Percudani, R.Zanotti, G.

(2011) Plos One 6: e19207-e19207

  • DOI: 10.1371/journal.pone.0019207

  • PubMed Abstract: 
  • Peptidoglycan deacetlyase (HP0310, HpPgdA) from the gram-negative pathogen Helicobacter pylori, has been indicated as the enzyme responsible for a peptidoglycan modification that counteracts the host immune response. HpPgdA has been cloned, purified ...

    Peptidoglycan deacetlyase (HP0310, HpPgdA) from the gram-negative pathogen Helicobacter pylori, has been indicated as the enzyme responsible for a peptidoglycan modification that counteracts the host immune response. HpPgdA has been cloned, purified and expressed in good yield in E. coli. It has been crystallized, its structure determined and activity tests in vitro performed. The enzyme, which belongs to the polysaccharide deacetylases protein family, is a homo-tetramer. The four polypeptide chains, each folded into a single domain characterized by a non-canonical TIM-barrel fold, are arranged around a four-fold symmetry axis. The active site, one per monomer, contains a heavy ion coordinated in a way similar to other deacetylases. However, the enzyme showed no in vitro activity on the typical polysaccharide substrates of peptidoglycan deacetylases. In striking contrast with the known peptidoglycan deacetylases, HpPgdA does not exhibit a solvent-accessible polysaccharide binding groove, suggesting that the enzyme binds a small molecule at the active site.


    Organizational Affiliation

    Department of Biological Chemistry, University of Padua, Padua, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
A, B, C, D
326Helicobacter pylori (strain G27)Mutation(s): 0 
Gene Names: pgdA
EC: 3.5.1.-
Find proteins for B5ZA76 (Helicobacter pylori (strain G27))
Go to UniProtKB:  B5ZA76
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5701 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 154.560α = 90.00
b = 154.730β = 90.00
c = 158.680γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
PHENIXrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-11-20
    Type: Structure summary