1MJG

CRYSTAL STRUCTURE OF BIFUNCTIONAL CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE(CODH/ACS) FROM MOORELLA THERMOACETICA (F. CLOSTRIDIUM THERMOACETICUM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase

Doukov, T.I.Iverson, T.M.Seravalli, J.Ragsdale, S.W.Drennan, C.L.

(2002) Science 298: 567-572

  • DOI: https://doi.org/10.1126/science.1075843
  • Primary Citation of Related Structures:  
    1MJG

  • PubMed Abstract: 

    A metallocofactor containing iron, sulfur, copper, and nickel has been discovered in the enzyme carbon monoxide dehydrogenase/acetyl-CoA (coenzyme A) synthase from Moorella thermoacetica (f. Clostridium thermoaceticum). Our structure at 2.2 angstrom resolution reveals that the cofactor responsible for the assembly of acetyl-CoA contains a [Fe4S4] cubane bridged to a copper-nickel binuclear site. The presence of these three metals together in one cluster was unanticipated and suggests a newly discovered role for copper in biology. The different active sites of this bifunctional enzyme complex are connected via a channel, 138 angstroms long, that provides a conduit for carbon monoxide generated at the C-cluster on one subunit to be incorporated into acetyl-CoA at the A-cluster on the other subunit.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CARBON MONOXIDE DEHYDROGENASE BETA SUBUNIT
A, B, C, D
674Moorella thermoaceticaMutation(s): 0 
EC: 1.2.99.2
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 alpha subunitE [auth M],
F [auth N],
G [auth O],
H [auth P]
729Moorella thermoaceticaMutation(s): 0 
EC: 1.2.99.2
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XCC
Query on XCC

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

Download Ideal Coordinates CCD File 
DA [auth O]
HA [auth P]
I [auth A]
J [auth A]
L [auth B]
DA [auth O],
HA [auth P],
I [auth A],
J [auth A],
L [auth B],
N [auth C],
O [auth C],
Q [auth D],
V [auth M],
Z [auth N]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CU1
Query on CU1

Download Ideal Coordinates CCD File 
AA [auth O],
EA [auth P],
S [auth M],
W [auth N]
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
CA [auth O],
GA [auth P],
U [auth M],
Y [auth N]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NI
Query on NI

Download Ideal Coordinates CCD File 
BA [auth O],
FA [auth P],
T [auth M],
X [auth N]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.215 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.749α = 101.45
b = 136.973β = 109.05
c = 141.532γ = 103.94
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SHELXDphasing
DMmodel building
DMMultimodel building
EPMRphasing
CNSrefinement
DENZOdata reduction
DMphasing
DMMultiphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-28
    Type: Initial release
  • Version 1.1: 2008-05-05
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2019-11-13
    Changes: Structure summary
  • Version 1.5: 2019-11-20
    Changes: Advisory, Derived calculations