2AWC | pdb_00002awc

deoxy-DcrH-Hr

• PDB DOI: https://doi.org/10.2210/pdb2AWC/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Nitratidesulfovibrio vulgaris
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-08-31 Released: 2006-08-15 
• Deposition Author(s): Isaza, C.E., Silaghi-Dumitrescu, R., Iyer, R.B., Kurtz, D.M., Chan, M.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.253 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

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

• PubMed: 16866347 
• DOI: https://doi.org/10.1021/bi0607812
• Primary Citation 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).

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.72 kDa 
• Atom Count: 1,232 
• Modeled Residue Count: 130 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hemerythrin-like domain protein DcrH	A	130	Nitratidesulfovibrio vulgaris	Mutation(s): 0
UniProt
Find proteins for Q9REU3 (Nitratidesulfovibrio vulgaris) Explore Q9REU3  Go to UniProtKB:  Q9REU3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FEO	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 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.98	α = 90
b = 33.12	β = 96.02
c = 44.7	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
Blu-Ice	data collection
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-15 
Deposition Author(s): Isaza, C.E., Silaghi-Dumitrescu, R., Iyer, R.B., Kurtz, D.M., Chan, M.K.

Revision History  

• 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