5NKU

Joint neutron/X-ray structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

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Literature

Molecular Mechanism of Enzymatic Chlorite Detoxification: Insights from Structural and Kinetic Studies.

Schaffner, I., Mlynek, G., Flego, N., Puhringer, D., Libiseller-Egger, J., Coates, L., Hofbauer, S., Bellei, M., Furtmuller, P.G., Battistuzzi, G., Smulevich, G., Djinovic-Carugo, K., Obinger, C.

(2017) ACS Catal 7: 7962-7976

  • DOI: 10.1021/acscatal.7b01749
  • Primary Citation of Related Structures:  
    5K8Z, 5K90, 5K91, 5MAU, 5NKU, 5NKV

  • PubMed Abstract: 

    • The heme enzyme chlorite dismutase (Cld) catalyzes the degradation of chlorite to chloride and dioxygen. Although structure and steady-state kinetics of Clds have been elucidated, many questions remain (e.g., the mechanism of chlorite cleavage and the pH dependence of the reaction) ...

    The heme enzyme chlorite dismutase (Cld) catalyzes the degradation of chlorite to chloride and dioxygen. Although structure and steady-state kinetics of Clds have been elucidated, many questions remain (e.g., the mechanism of chlorite cleavage and the pH dependence of the reaction). Here, we present high-resolution X-ray crystal structures of a dimeric Cld at pH 6.5 and 8.5, its fluoride and isothiocyanate complexes and the neutron structure at pH 9.0 together with the pH dependence of the Fe(III)/Fe(II) couple, and the UV-vis and resonance Raman spectral features. We demonstrate that the distal Arg127 cannot act as proton acceptor and is fully ionized even at pH 9.0 ruling out its proposed role in dictating the pH dependence of chlorite degradation. Stopped-flow studies show that (i) Compound I and hypochlorite do not recombine and (ii) Compound II is the immediately formed redox intermediate that dominates during turnover. Homolytic cleavage of chlorite is proposed.

    Organizational Affiliation: 

    Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorite DismutaseA, B188Cyanothece sp. PCC 7425Mutation(s): 0 
Gene Names: Cyan7425_1434
UniProt
Find proteins for B8HNS6 (Cyanothece sp. (strain PCC 7425 / ATCC 29141))
Explore B8HNS6 
Go to UniProtKB:  B8HNS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8HNS6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
F [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
E [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
OH
Query on OH
Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]		HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 
  • Space Group: P 1
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.427α = 107.3
b = 53.015β = 98.54
c = 55.337γ = 109.86
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
Mantiddata processing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 2.0: 2018-11-14
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary