6T7J

As-isolated Ni-free crystal structure of carbon monoxide dehydrogenase from Thermococcus sp. AM4 produced without CooC maturase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The two CO-dehydrogenases of Thermococcus sp. AM4.

Benvenuti, M.Meneghello, M.Guendon, C.Jacq-Bailly, A.Jeoung, J.H.Dobbek, H.Leger, C.Fourmond, V.Dementin, S.

(2020) Biochim Biophys Acta Bioenerg 1861: 148188-148188

  • DOI: https://doi.org/10.1016/j.bbabio.2020.148188
  • Primary Citation of Related Structures:  
    6T7J

  • PubMed Abstract: 

    Ni-containing CO-dehydrogenases (CODHs) allow some microorganisms to couple ATP synthesis to CO oxidation, or to use either CO or CO 2 as a source of carbon. The recent detailed characterizations of some of them have evidenced a great diversity in terms of catalytic properties and resistance to O 2 . In an effort to increase the number of available CODHs, we have heterologously produced in Desulfovibrio fructosovorans, purified and characterized the two CooS-type CODHs (CooS1 and CooS2) from the hyperthermophilic archaeon Thermococcus sp. AM4 (Tc). We have also crystallized CooS2, which is coupled in vivo to a hydrogenase. CooS1 and CooS2 are homodimers, and harbour five metalloclusters: two [Ni4Fe-4S] C clusters, two [4Fe-4S] B clusters and one interfacial [4Fe-4S] D cluster. We show that both are dependent on a maturase, CooC1 or CooC2, which is interchangeable. The homologous protein CooC3 does not allow Ni insertion in either CooS. The two CODHs from Tc have similar properties: they can both oxidize and produce CO. The Michaelis constants (K m ) are in the microM range for CO and in the mM range (CODH 1) or above (CODH 2) for CO 2 . Product inhibition is observed only for CO 2 reduction, consistent with CO 2 binding being much weaker than CO binding. The two enzymes are rather O 2 sensitive (similarly to CODH II from Carboxydothermus hydrogenoformans), and react more slowly with O 2 than any other CODH for which these data are available.


  • Organizational Affiliation

    Aix-Marseille Université, CNRS, BIP UMR 7281, 31 Chemin J. AIGUIER, CS70071, F-13402 Marseille Cedex 20, (France).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbon monoxide dehydrogenaseA [auth B],
B [auth A],
C [auth D]
632Thermococcus sp. AM4Mutation(s): 0 
Gene Names: TAM4_1067
EC: 1.2.7.4
UniProt
Find proteins for B7R5K0 (Thermococcus sp. AM4)
Explore B7R5K0 
Go to UniProtKB:  B7R5K0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7R5K0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MSK (Subject of Investigation/LOI)
Query on MSK

Download Ideal Coordinates CCD File 
F [auth B],
N [auth A],
S [auth D]
Broken Fe4S4 cluster
Fe4 S4
BEJQIPSIAWWLMO-UHFFFAOYSA-N
SF4
Query on SF4

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D [auth B],
L [auth A],
Q [auth D]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CIT
Query on CIT

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P [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
FES
Query on FES

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E [auth B],
M [auth A],
R [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
PEG
Query on PEG

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K [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

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G [auth B],
O [auth A],
T [auth D],
U [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
BU3
Query on BU3

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B],
J [auth B]
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 268.138α = 90
b = 64.061β = 90
c = 100.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyEXC 2008/1 (UniSysCat) - 390540038

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2021-06-02
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description