1MJG | pdb_00001mjg

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

• PDB DOI: https://doi.org/10.2210/pdb1MJG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Neomoorella thermoacetica
• Mutation(s): No 


• Deposited: 2002-08-27 Released: 2003-01-28 
• Deposition Author(s): Doukov, T.I., Iverson, T.M., Seravalli, J., Ragsdale, S.W., Drennan, C.L.

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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

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

• PubMed: 12386327 
• DOI: https://doi.org/10.1126/science.1075843
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 624.9 kDa 
• Atom Count: 44,653 
• Modeled Residue Count: 5,600 
• Deposited Residue Count: 5,612 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBON MONOXIDE DEHYDROGENASE BETA SUBUNIT	A, B, C, D	674	Neomoorella thermoacetica	Mutation(s): 0  EC: 1.2.99.2 (PDB Primary Data), 1.2.7.4 (UniProt)
UniProt
Find proteins for P27989 (Neomoorella thermoacetica) Explore P27989  Go to UniProtKB:  P27989

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase alpha subunit	E [auth M], F [auth N], G [auth O], H [auth P]	729	Neomoorella thermoacetica	Mutation(s): 0  EC: 1.2.99.2 (PDB Primary Data), 2.3.1.169 (UniProt)
UniProt
Find proteins for P27988 (Neomoorella thermoacetica) Explore P27988  Go to UniProtKB:  P27988

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XCC	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	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	AA [auth O], EA [auth P], S [auth M], W [auth N]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N
ACT	CA [auth O], GA [auth P], U [auth M], Y [auth N]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NI	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 = 99.749	α = 101.45
b = 136.973	β = 109.05
c = 141.532	γ = 103.94

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SHELXD	phasing
DM	model building
DMMulti	model building
EPMR	phasing
CNS	refinement
DENZO	data reduction
DM	phasing
DMMulti	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-28 
Deposition Author(s): Doukov, T.I., Iverson, T.M., Seravalli, J., Ragsdale, S.W., Drennan, C.L.

Revision History  

• 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