2AWC

deoxy-DcrH-Hr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis for O(2) Sensing by the Hemerythrin-like Domain of a Bacterial Chemotaxis Protein: Substrate Tunnel and Fluxional N Terminus

Isaza, C.E.Silaghi-Dumitrescu, R.Iyer, R.B.Kurtz, D.M.Chan, M.K.

(2006) Biochemistry 45: 9023-9031

  • DOI: https://doi.org/10.1021/bi0607812
  • Primary Citation of Related Structures:  
    2AVK, 2AWC, 2AWY

  • PubMed Abstract: 

    The methyl-accepting chemotaxis protein, DcrH, from the anaerobic sulfate-reducing bacterium, Desulfovibrio vulgaris (Hildenborough), has a hemerythrin-like domain, DcrH-Hr, at its C terminus. DcrH-Hr was previously shown to contain a diiron site that binds O2, suggesting an O2-sensing function. X-ray crystal structures of diferric (met-), azido-diferric (azidomet-), and diferrous (deoxy-) DcrH-Hr reveal a "substrate tunnel" distinct from that in invertebrate hemerythrins. This tunnel is proposed to facilitate the rapid autoxidation of oxy-DcrH-Hr and suggests that sensing is triggered by O2 binding and subsequent oxidation of the diferrous active site. The N-terminal loop of DcrH-Hr is highly ordered in both met- and azidomet-DcrH-Hr but is disordered in deoxy-DcrH-Hr. These redox-dependent conformational differences presumably transduce the sensory signal of DcrH-Hr to the neighboring methylation domain in the full-length receptor. Given the putative cytoplasmic localization of its Hr-like O2-sensing domain, DcrH is proposed to serve a role in negative aerotaxis (anaerotaxis).


  • Organizational Affiliation

    The Ohio State Biophysics Program, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hemerythrin-like domain protein DcrH130Nitratidesulfovibrio vulgarisMutation(s): 0 
UniProt
Find proteins for Q9REU3 (Nitratidesulfovibrio vulgaris)
Explore Q9REU3 
Go to UniProtKB:  Q9REU3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9REU3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FEO
Query on FEO

Download Ideal Coordinates CCD File 
B [auth A]MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.98α = 90
b = 33.12β = 96.02
c = 44.7γ = 90
Software Package:
Software NamePurpose
CNSrefinement
Blu-Icedata collection
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations