3FPV

Crystal Structure of HbpS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.201 

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

  • Primary Citation of Related Structures:  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 r ...

    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 64: 386


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Extracellular haem-binding protein
A, B, C, D, E, F, G, H
192Streptomyces reticuliGene Names: hbpS
Find proteins for Q9RIM2 (Streptomyces reticuli)
Go to UniProtKB:  Q9RIM2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C, D, E, F, H
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.201 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 152.522α = 90.00
b = 152.522β = 90.00
c = 152.522γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MAR345data collection
SOLVEphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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