3FPV

Crystal Structure of HbpS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The oligomeric assembly of the novel haem-degrading protein HbpS is essential for interaction with its cognate two-component sensor kinase

Ortiz de Orue Lucana, D.Bogel, G.Zou, P.Groves, M.R.

(2009) J Mol Biol 386: 1108-1122

  • DOI: 10.1016/j.jmb.2009.01.017
  • Primary Citation of Related Structures:  
    3FPV, 3FPW

  • PubMed Abstract: 
  • HbpS, a novel protein of previously unknown function from Streptomyces reticuli, is up-regulated in response to haemin- and peroxide-based oxidative stress and interacts with the SenS/SenR two-component signal transduction system. In this study, we report the high-resolution crystal structures (2 ...

    HbpS, a novel protein of previously unknown function from Streptomyces reticuli, is up-regulated in response to haemin- and peroxide-based oxidative stress and interacts with the SenS/SenR two-component signal transduction system. In this study, we report the high-resolution crystal structures (2.2 and 1.6 A) of octomeric HbpS crystallized in the presence and in the absence of haem and demonstrate that iron binds to surface-exposed lysine residues of an octomeric assembly. Based on an analysis of the crystal structures, we propose that the iron atom originates from the haem group and report subsequent biochemical experiments that demonstrate that HbpS possesses haem-degrading activity in vitro. Further examination of the crystal structures has identified amino acids that are essential for assembly of the octomer. The role of these residues is confirmed by biophysical experiments. Additionally, we show that while the octomeric assembly state of HbpS is not essential for haem-degrading activity, the assembly of HbpS is required for its interaction with the cognate sensor kinase, SenS. Homologs of HbpS and SenS/SenR have been identified in a number of medically and ecologically relevant bacterial species (including Vibrio cholerae, Klebsiella pneumoniae, Corynebacterium diphtheriae, Arthrobacter aurescens and Pseudomonas putida), suggesting the existence of a previously undescribed bacterial oxidative stress-response pathway common to Gram-negative and Gram-positive bacteria. Thus, the data presented provide the first insight into the function of a novel protein family and an example of an iron-mediated interaction between an accessory protein and its cognate two-component sensor kinase.


    Related Citations: 
    • Crystallization and preliminary characterization of a novel haem-binding protein of Streptomyces reticuli
      Zou, P., Groves, M.R., Viale-Bouroncle, S.D., Ortiz de Orue Lucana, D.
      (2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 386

    Organizational Affiliation

    Universität Osnabrück, FB Biologie/Chemie, Angewandte Genetik der Mikroorganismen, Barbarastrasse 13, 49069 Osnabrück, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular haem-binding proteinA, B, C, D, E, F, G, H192Streptomyces reticuliMutation(s): 0 
Gene Names: hbpS
UniProt
Find proteins for Q9RIM2 (Streptomyces reticuli)
Explore Q9RIM2 
Go to UniProtKB:  Q9RIM2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.522α = 90
b = 152.522β = 90
c = 152.522γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SOLVEphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description