2VXH

The crystal structure of chlorite dismutase: a detox enzyme producing molecular oxygen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Chlorite Dismutase, a Detoxifying Enzyme Producing Molecular Oxygen

De Geus, D.C.Thomassen, E.A.J.Hagedoorn, P.L.Pannu, N.S.Van Duijn, E.Abrahams, J.P.

(2009) J Mol Biol 387: 192

  • DOI: 10.1016/j.jmb.2009.01.036
  • Primary Citation of Related Structures:  
    2VXH

  • PubMed Abstract: 
  • Chlorite dismutase (Cld) is a key enzyme of perchlorate and chlorate respiration. This heme-based protein reduces the toxic compound chlorite into the innocuous chloride anion in a very efficient way while producing molecular oxygen. A sequence comparison between Cld homologues shows a highly conserved family ...

    Chlorite dismutase (Cld) is a key enzyme of perchlorate and chlorate respiration. This heme-based protein reduces the toxic compound chlorite into the innocuous chloride anion in a very efficient way while producing molecular oxygen. A sequence comparison between Cld homologues shows a highly conserved family. The crystal structure of Azospira oryzae strain GR-1 Cld is reported to 2.1 A resolution. The structure reveals a hexameric organization of the Cld, while each monomer exhibits a ferredoxin-like fold. The six subunits are organized in a ring structure with a maximal diameter of 9 nm and an inner diameter of 2 nm. The heme active-site pocket is solvent accessible both from the inside and the outside of the ring. Moreover, a second anion binding site that could accommodate the assumed reaction intermediate ClO(-) for further transformation has been identified near the active site. The environment of the heme cofactor was investigated with electron paramagnetic resonance spectroscopy. Apart from the high-spin ferric signal of the five-coordinate resting-state enzyme, two low-spin signals were found corresponding to six-coordinate species. The current crystal structure confirms and complements a recently proposed catalytic mechanism that proceeds via a ferryl species and a ClO(-) anion. Our structural data exclude cooperativity between the iron centers.


    Organizational Affiliation

    Department of Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands. d.de.geus@chem.leidenuniv.nl



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CHLORITE DISMUTASEA, B, C, D, E, F251Dechlorosoma suillumMutation(s): 0 
EC: 1.13.11.49
Find proteins for E2DI02 (Dechlorosoma suillum)
Explore E2DI02 
Go to UniProtKB:  E2DI02
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
G [auth A], J [auth B], M [auth C], P [auth D], R [auth E], U [auth F]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CO3
Query on CO3

Download Ideal Coordinates CCD File 
I [auth A], L [auth B], O [auth C], T [auth E], W [auth F]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
SCN
Query on SCN

Download Ideal Coordinates CCD File 
H [auth A], K [auth B], N [auth C], Q [auth D], S [auth E], V [auth F]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.458α = 90
b = 169.335β = 90
c = 60.792γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CRANKphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance