1N5W

Crystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Oxidized form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.135 

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This is version 1.2 of the entry. See complete history


Literature

Catalysis at a dinuclear [CuSMo(=O)OH] cluster in a CO dehydrogenase resolved at 1.1-A resolution

Dobbek, H.Gremer, L.Kiefersauer, R.Huber, R.Meyer, O.

(2002) Proc Natl Acad Sci U S A 99: 15971-15976

  • DOI: 10.1073/pnas.212640899
  • Primary Citation of Related Structures:  
    1N60, 1N5W, 1N63, 1N62, 1N61

  • PubMed Abstract: 
  • The CO dehydrogenase of the eubacterium Oligotropha carboxidovorans is a 277-kDa Mo- and Cu-containing iron-sulfur flavoprotein. Here, the enzyme's active site in the oxidized or reduced state, after inactivation with potassium cyanide or with n-butylisocyanide bound to the active site, has been reinvestigated by multiple wavelength anomalous dispersion measurements at atomic resolution, electron spin resonance spectroscopy, and chemical analyses ...

    The CO dehydrogenase of the eubacterium Oligotropha carboxidovorans is a 277-kDa Mo- and Cu-containing iron-sulfur flavoprotein. Here, the enzyme's active site in the oxidized or reduced state, after inactivation with potassium cyanide or with n-butylisocyanide bound to the active site, has been reinvestigated by multiple wavelength anomalous dispersion measurements at atomic resolution, electron spin resonance spectroscopy, and chemical analyses. We present evidence for a dinuclear heterometal [CuSMoO)OH] cluster in the active site of the oxidized or reduced enzyme, which is prone to cyanolysis. The cluster is coordinated through interactions of the Mo with the dithiolate pyran ring of molybdopterin cytosine dinucleotide and of the Cu with the Sgamma of Cys-388, which is part of the active-site loop VAYRC(388)SFR. The previously reported active-site structure [Dobbek, H., Gremer, L., Meyer, O. & Huber, R. (1999) Proc. Natl. Acad. Sci. USA 96, 8884-8889] of an Mo with three oxygen ligands and an SeH-group bound to the Sgamma atom of Cys-388 could not be confirmed. The structure of CO dehydrogenase with the inhibitor n-butylisocyanide bound has led to a model for the catalytic mechanism of CO oxidation which involves a thiocarbonate-like intermediate state. The dinuclear [CuSMo(O)OH] cluster of CO dehydrogenase establishes a previously uncharacterized class of dinuclear molybdoenzymes containing the pterin cofactor.


    Organizational Affiliation

    Abteilung Strukturforschung, Max-Planck-Institut für Biochemie, and Proteros Biostructures GmbH, D-82152 Martinsried, Germany Europe. dobbek@biochem.mpg.de



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbon monoxide dehydrogenase small chain AD166Afipia carboxidovorans OM5Mutation(s): 0 
Gene Names: coxSOCA5_pHCG300300
EC: 1.2.99.2 (PDB Primary Data), 1.2.5.3 (UniProt)
Find proteins for P19921 (Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / KCTC 32145 / OM5))
Explore P19921 
Go to UniProtKB:  P19921
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Carbon monoxide dehydrogenase large chain BE809Afipia carboxidovorans OM5Mutation(s): 0 
Gene Names: coxLOCA5_pHCG300310
EC: 1.2.99.2 (PDB Primary Data), 1.2.5.3 (UniProt)
Find proteins for P19919 (Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / KCTC 32145 / OM5))
Explore P19919 
Go to UniProtKB:  P19919
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Carbon monoxide dehydrogenase medium chain CF288Afipia carboxidovorans OM5Mutation(s): 0 
Gene Names: coxMOCA5_pHCG300290
EC: 1.2.99.2 (PDB Primary Data), 1.2.5.3 (UniProt)
Find proteins for P19920 (Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / KCTC 32145 / OM5))
Explore P19920 
Go to UniProtKB:  P19920
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.135 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.295α = 90
b = 132.088β = 90
c = 159.825γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMACrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-23
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance