1MJG | pdb_00001mjg

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 (Depositor) 
  • R-Value Work: 
    0.215 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.6 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
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(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 (PDB Primary Data), 1.2.7.4 (UniProt)
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
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(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 (PDB Primary Data), 2.3.1.169 (UniProt)
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]
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 (Depositor) 
  • R-Value Work:  0.215 (Depositor) 
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

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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
  • Version 1.6: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary