1ZXI

Reconstituted CO dehydrogenase from Oligotropha carboxidovorans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and functional reconstruction in situ of the [CuSMoO(2)] active site of carbon monoxide dehydrogenase from the carbon monoxide oxidizing eubacterium Oligotropha carboxidovorans

Resch, M.Dobbek, H.Meyer, O.

(2005) J.Biol.Inorg.Chem. 10: 518-528

  • DOI: 10.1007/s00775-005-0006-4

  • PubMed Abstract: 
  • Carbon monoxide dehydrogenase from the bacterium Oligotropha carboxidovorans catalyzes the oxidation of CO to CO(2) at a unique [CuSMoO(2)] cluster. In the bacteria the cluster is assembled post-translational. The integration of S, and particularly o ...

    Carbon monoxide dehydrogenase from the bacterium Oligotropha carboxidovorans catalyzes the oxidation of CO to CO(2) at a unique [CuSMoO(2)] cluster. In the bacteria the cluster is assembled post-translational. The integration of S, and particularly of Cu, is rate limiting in vivo, which leads to CO dehydrogenase preparations containing the mature and fully functional enzyme along with forms of the enzyme deficient in one or both of these elements. The active sites of mature and immature forms of CO dehydrogenase were converted into a [MoO(3)] centre by treatment with potassium cyanide. We have established a method, which rescues 50% of the CO dehydrogenase activity by in vitro reconstitution of the active site through the supply of sulphide first and subsequently of Cu(I) under reducing conditions. Immature forms of CO dehydrogenase isolated from the bacterium, which were deficient in S and/or Cu at the active site, were similarly activated. X-ray crystallography and electron paramagnetic resonance spectroscopy indicated that the [CuSMoO(2)] cluster was properly reconstructed. However, reconstituted CO dehydrogenase contains mature along with immature forms. The chemical reactions of the reconstitution of CO dehydrogenase are summarized in a model, which assumes resulphuration of the Mo-ion at both equatorial positions at a 1:1 molar ratio. One equatorial Mo-S group reacts with Cu(I) in a productive fashion yielding a mature, functional [CuSMoO(2)] cluster. The other Mo-S group reacts with Cu(I), then Cu(2)S is released and an oxo group is introduced from water, yielding an inactive [MoO(3)] centre.


    Organizational Affiliation

    Lehrstuhl für Mikrobiologie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95440 Bayreuth, Germany.




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 / KCTC 32145 / OM5)Mutation(s): 0 
Gene Names: coxS
EC: 1.2.5.3
Find proteins for P19921 (Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / KCTC 32145 / OM5))
Go to UniProtKB:  P19921
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Carbon monoxide dehydrogenase large chain
B, E
809Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / KCTC 32145 / OM5)Mutation(s): 0 
Gene Names: coxL
EC: 1.2.5.3
Find proteins for P19919 (Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / KCTC 32145 / OM5))
Go to UniProtKB:  P19919
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Carbon monoxide dehydrogenase medium chain
C, F
288Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / KCTC 32145 / OM5)Mutation(s): 0 
Gene Names: coxM
EC: 1.2.5.3
Find proteins for P19920 (Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / KCTC 32145 / OM5))
Go to UniProtKB:  P19920
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CUM
Query on CUM

Download SDF File 
Download CCD File 
B, E
CU(I)-S-MO(VI)(=O)OH CLUSTER
Cu H Mo O2 S
VFYYAMWTODUIEV-UHFFFAOYSA-M
 Ligand Interaction
PO4
Query on PO4

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

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

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

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Download CCD File 
A, D
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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Download CCD File 
B, E
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 118.840α = 90.00
b = 131.320β = 90.00
c = 159.990γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Refinement description