1N62

Crystal Structure of the Mo,Cu-CO Dehydrogenase (CODH), n-butylisocyanide-bound state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 

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 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbon monoxide dehydrogenase small chainA, D166Afipia carboxidovorans OM5Mutation(s): 0 
Gene Names: coxSOCA5_pHCG300300
EC: 1.2.99.2 (PDB Primary Data), 1.2.5.3 (UniProt)
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 chainB, E809Afipia carboxidovorans OM5Mutation(s): 0 
Gene Names: coxLOCA5_pHCG300310
EC: 1.2.99.2 (PDB Primary Data), 1.2.5.3 (UniProt)
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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Carbon monoxide dehydrogenase medium chainC, F288Afipia carboxidovorans OM5Mutation(s): 0 
Gene Names: coxMOCA5_pHCG300290
EC: 1.2.99.2 (PDB Primary Data), 1.2.5.3 (UniProt)
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
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
L [auth C], Q [auth F]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MCN (Subject of Investigation/LOI)
Query on MCN

Download Ideal Coordinates CCD File 
K [auth B], P [auth E]PTERIN CYTOSINE DINUCLEOTIDE
C19 H22 N8 O13 P2 S2
RBWYFPNWTRZKKZ-LOIMWUFNSA-N
 Ligand Interaction
CUB (Subject of Investigation/LOI)
Query on CUB

Download Ideal Coordinates CCD File 
J [auth B], O [auth E]CU(I)-S-MO(IV)(=O)O-NBIC CLUSTER
C5 H9 Cu Mo N O2 S
KNSQHRMNQABPBN-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], M [auth D], N [auth D]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.86α = 90
b = 130.019β = 90
c = 156.231γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMACrefinement
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-18
    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