1N60

Crystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Cyanide-inactivated Form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


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.USA 99: 15971-15976

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

  • 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-buty ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbon monoxide dehydrogenase small chain
A, D
166Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)Gene Names: coxS
EC: 1.2.7.4
Find proteins for P19921 (Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5))
Go to UniProtKB:  P19921
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Carbon monoxide dehydrogenase large chain
B, E
809Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)Gene Names: coxL
EC: 1.2.7.4
Find proteins for P19919 (Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5))
Go to UniProtKB:  P19919
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Carbon monoxide dehydrogenase medium chain
C, F
288Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)Gene Names: coxM
EC: 1.2.7.4
Find proteins for P19920 (Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5))
Go to UniProtKB:  P19920
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OMO
Query on OMO

Download SDF File 
Download CCD File 
B, E
MO(VI)(=O)(OH)2 CLUSTER
H2 Mo O3
GKDPEXRCAVYDOG-UHFFFAOYSA-L
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MCN
Query on MCN

Download SDF File 
Download CCD File 
B, E
PTERIN CYTOSINE DINUCLEOTIDE
C19 H22 N8 O13 P2 S2
RBWYFPNWTRZKKZ-LOIMWUFNSA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
C, F
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
A, D
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 118.566α = 90.00
b = 130.642β = 90.00
c = 158.492γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
REFMACrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance