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Crystal structure of truncated FlgD (monoclinic form) from the human pathogen Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of truncated FlgD from the human pathogen Helicobacter pylori.

Pulic, I.Cendron, L.Salamina, M.Polverino de Laureto, P.Matkovic-Calogovic, D.Zanotti, G.

(2016) J.Struct.Biol. 194: 147-155

  • DOI: 10.1016/j.jsb.2016.02.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Flagellin component D (FlgD) participates in the assembly of flagella, helical tubular structures that provide motility in non-filamentous bacteria. FlgD guides and controls the polymerization of FlgE that builds the hook, a short curved and hollow c ...

    Flagellin component D (FlgD) participates in the assembly of flagella, helical tubular structures that provide motility in non-filamentous bacteria. FlgD guides and controls the polymerization of FlgE that builds the hook, a short curved and hollow cylinder that connects the flagellar basal body spanning the cell envelope to the protruding filament. Crystal structures of truncated forms of Helicobacter pylori FlgD from two different strains in two space groups, I422 and P2, are reported here, at 2.2Å and 2.8Å resolution, respectively. Analogously to Pseudomonas aeruginosa and Xanthomonas campestris FlgD proteins, crystallization experiments set up for the full length protein resulted in crystals of a truncated form, lacking both N- and C-terminus ends. The crystal structures of the central domain show that the monomer is composed of a tudor and a fibronectin type III domain. The full length HpFlgD contains a long N-terminal signal region, probably partially flexible, a central globular region and a C-terminal segment with a peculiar repetitive pattern of amino acids. The spatial orientation of the two domains in HpFlgD differs from that of the homologous FlgD family members, P. aeruginosa and X. campestris. This difference together with the observation that HpFlgD assembles into tetramers, both in the solution and in the two crystal forms, strongly suggests that significant differences exist in the molecular organization of the flagella in different bacterial species.


    Organizational Affiliation

    University of Zagreb, Faculty of Science, Department of Chemistry, Division of General and Inorganic Chemistry, Horvatovac 102a, Zagreb 10000, Croatia; Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua 35131, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Basal-body rod modification protein FlgD
A, B, C, D
146Helicobacter pylori (strain G27)Mutation(s): 0 
Gene Names: flgD
Find proteins for B5Z7R3 (Helicobacter pylori (strain G27))
Go to UniProtKB:  B5Z7R3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.221 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 77.420α = 90.00
b = 34.220β = 99.58
c = 131.640γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Community's Seventh Framework Program (FP7/2007-2013)Italy283570
PRIN 2010-2011 (MIUR)Italy--
Ministry of Science, Education and SportsCroatia119-1193079-1084

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references