4TSD

Crystal structure of Helicobacter pylori HP1029


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The crystal structure of Helicobacter pylori HP1029 highlights the functional diversity of the sialic acid-related DUF386 family.

Vallese, F.Percudani, R.Fischer, W.Zanotti, G.

(2015) FEBS J 282: 3311-3322

  • DOI: 10.1111/febs.13344
  • Primary Citation of Related Structures:  
    4TSD

  • PubMed Abstract: 
  • The proteins of the YhcH/YjgK/YiaL (DUF386) family have been implicated in the bacterial metabolism of host-derived sialic acids and biofilm formation, although their precise biochemical function remains enigmatic. We present here the crystal structure of protein HP1029 from Helicobacter pylori ...

    The proteins of the YhcH/YjgK/YiaL (DUF386) family have been implicated in the bacterial metabolism of host-derived sialic acids and biofilm formation, although their precise biochemical function remains enigmatic. We present here the crystal structure of protein HP1029 from Helicobacter pylori. The protein is a homodimer, in which each monomer comprises a molecular core formed by 12 antiparallel β-strands arranged in two β-sheets flanked by helices. The sandwich formed by the sheets assumes the shape of a funnel opened at one end, with a zinc ion present at the bottom of the funnel. The crystal structure unequivocally shows that HP1029 belongs to the DUF386 family. Although no bioinformatics evidence has been found for sialic acid catabolism in H. pylori, the genomic context of HP1029 in Helicobacter and related organisms suggests a possible role in the metabolism of bacterial surface saccharides, such as pseudaminic acid and its derivatives.


    Organizational Affiliation

    Department of Biomedical Sciences, University of Padua, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HP1029B [auth A],
A [auth B]
195Helicobacter pylori 26695Mutation(s): 0 
Gene Names: C694_05325HP_1029
UniProt
Find proteins for O25673 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25673 
Go to UniProtKB:  O25673
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25673
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth B],
D [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.788α = 90
b = 77.49β = 90
c = 99.134γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
MOLREPphasing
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
University of PaduaItalyProgetto di Ateneo 2011
MIURItalyPRIN 2010-2011

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-06-17
    Changes: Database references
  • Version 1.2: 2015-07-08
    Changes: Database references
  • Version 1.3: 2015-09-09
    Changes: Database references