3I01

Native structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica, water-bound C-cluster.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystallographic snapshots of cyanide- and water-bound C-clusters from bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase.

Kung, Y.Doukov, T.I.Seravalli, J.Ragsdale, S.W.Drennan, C.L.

(2009) Biochemistry 48: 7432-7440

  • DOI: https://doi.org/10.1021/bi900574h
  • Primary Citation of Related Structures:  
    3I01, 3I04

  • PubMed Abstract: 

    Nickel-containing carbon monoxide dehydrogenases (CODHs) reversibly catalyze the oxidation of carbon monoxide to carbon dioxide and are of vital importance in the global carbon cycle. The unusual catalytic CODH C-cluster has been crystallographically characterized as either a NiFe(4)S(4) or a NiFe(4)S(5) metal center, the latter containing a fifth, additional sulfide that bridges Ni and a unique Fe site. To determine whether this bridging sulfide is catalytically relevant and to further explore the mechanism of the C-cluster, we obtained crystal structures of the 310 kDa bifunctional CODH/acetyl-CoA synthase complex from Moorella thermoacetica bound both with a substrate H(2)O/OH(-) molecule and with a cyanide inhibitor. X-ray diffraction data were collected from native crystals and from identical crystals soaked in a solution containing potassium cyanide. In both structures, the substrate H(2)O/OH(-) molecule exhibits binding to the unique Fe site of the C-cluster. We also observe cyanide binding in a bent conformation to Ni of the C-cluster, adjacent the substrate H(2)O/OH(-) molecule. Importantly, the bridging sulfide is not present in either structure. As these forms of the C-cluster represent the coordination environment immediately before the reaction takes place, our findings do not support a fifth, bridging sulfide playing a catalytic role in the enzyme mechanism. The crystal structures presented here, along with recent structures of CODHs from other organisms, have led us toward a unified mechanism for CO oxidation by the C-cluster, the catalytic center of an environmentally important enzyme.


  • Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
A, B, C, D
674Moorella thermoaceticaMutation(s): 0 
EC: 1.2.7.4 (PDB Primary Data), 1.2.99.2 (PDB Primary Data)
UniProt
Find proteins for P27989 (Moorella thermoacetica)
Explore P27989 
Go to UniProtKB:  P27989
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27989
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alphaE [auth M],
F [auth N],
G [auth O],
H [auth P]
729Moorella thermoaceticaMutation(s): 0 
EC: 2.3.1.169
UniProt
Find proteins for P27988 (Moorella thermoacetica)
Explore P27988 
Go to UniProtKB:  P27988
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27988
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XCC
Query on XCC

Download Ideal Coordinates CCD File 
K [auth A],
N [auth B],
R [auth C],
U [auth D]
FE(4)-NI(1)-S(4) CLUSTER
Fe4 Ni S4
QGLWBXDZIHZONR-UHFFFAOYSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
BA [auth N]
GA [auth O]
I [auth A]
J [auth A]
LA [auth P]
BA [auth N],
GA [auth O],
I [auth A],
J [auth A],
LA [auth P],
M [auth B],
P [auth C],
Q [auth C],
T [auth D],
W [auth M]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
GOL
Query on GOL

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L [auth A],
O [auth B],
S [auth C],
V [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU1
Query on CU1

Download Ideal Coordinates CCD File 
CA [auth N],
HA [auth O],
MA [auth P],
X [auth M]
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
ACT
Query on ACT

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EA [auth N],
JA [auth O],
OA [auth P],
Z [auth M]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NI
Query on NI

Download Ideal Coordinates CCD File 
DA [auth N],
IA [auth O],
NA [auth P],
Y [auth M]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
NA
Query on NA

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AA [auth M],
FA [auth N],
KA [auth O],
PA [auth P]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.651α = 101.26
b = 136.87β = 109.11
c = 140.864γ = 104.08
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description