1OAO | pdb_00001oao

NiZn[Fe4S4] and NiNi[Fe4S4] clusters in closed and open alpha subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb1OAO/pdb

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


• Deposited: 2003-01-20 Released: 2003-04-11 
• Deposition Author(s): Darnault, C., Volbeda, A., Kim, E.J., Legrand, P., Vernede, X., Lindahl, P.A., Fontecilla-Camps, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.179 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase

Darnault, C., Volbeda, A., Kim, E.J., Legrand, P., Vernede, X., Lindahl, P.A., Fontecilla-Camps, J.C.

(2003) Nat Struct Biol 10: 271

• PubMed: 12627225 
• DOI: https://doi.org/10.1038/nsb912
• Primary Citation Related Structures: 
  1OAO


• PubMed Abstract: 
  

  The crystal structure of the tetrameric alpha2beta2 acetyl-coenzyme A synthase/carbon monoxide dehydrogenase from Moorella thermoacetica has been solved at 1.9 A resolution. Surprisingly, the two alpha subunits display different (open and closed) conformations. Furthermore, X-ray data collected from crystals near the absorption edges of several metal ions indicate that the closed form contains one Zn and one Ni at its active site metal cluster (A-cluster) in the alpha subunit, whereas the open form has two Ni ions at the corresponding positions. Alternative metal contents at the active site have been observed in a recent structure of the same protein in which A-clusters contained one Cu and one Ni, and in reconstitution studies of a recombinant apo form of a related acetyl-CoA synthase. On the basis of our observations along with previously reported data, we postulate that only the A-clusters containing two Ni ions are catalytically active.

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Organizational Affiliation: 
• Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale 'Jean-Pierre Ebel', CEA, UJF, CNRS, 41, rue Jules Horowitz, 38027, Grenoble Cedex 1, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 316.52 kDa 
• Atom Count: 23,346 
• Modeled Residue Count: 2,803 
• Deposited Residue Count: 2,806 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT BETA	A, B	674	Neomoorella thermoacetica	Mutation(s): 0  EC: 1.2.99.2 (PDB Primary Data), 1.2.7.4 (PDB Primary Data)
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/ACETYL-COA SYNTHASE SUBUNIT ALPHA	C, D	729	Neomoorella thermoacetica	Mutation(s): 0  EC: 2.3.1.169
UniProt
Find proteins for P27988 (Neomoorella thermoacetica) Explore P27988  Go to UniProtKB:  P27988

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XCC	F [auth A], W [auth B]	FE(4)-NI(1)-S(4) CLUSTER Fe4 Ni S4 QGLWBXDZIHZONR-UHFFFAOYSA-N
SF4	AB [auth D], E [auth A], MA [auth C], U [auth B], V [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
SO4	AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], EB [auth D], FA [auth B], FB [auth D], GA [auth B], H [auth A], HA [auth B], HB [auth D], I [auth A], IB [auth D], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], UA [auth C], WA [auth C], Y [auth B], YA [auth C], Z [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	GB [auth D], IA [auth B], JA [auth B], P [auth A], TA [auth C], VA [auth C], XA [auth C], ZA [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	NA [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
BCT	KA [auth B]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
ACT	DB [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NI	BB [auth D], CB [auth D], OA [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
FE2	LA [auth B], T [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
SX	PA [auth C]	SULFUR OXIDE O S XTQHKBHJIVJGKJ-UHFFFAOYSA-N
FOR	G [auth A], X [auth B]	FORMYL GROUP C H2 O WSFSSNUMVMOOMR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.179 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 244.57	α = 90
b = 81.89	β = 96.19
c = 167.22	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
AMoRE	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-11 
Deposition Author(s): Darnault, C., Volbeda, A., Kim, E.J., Legrand, P., Vernede, X., Lindahl, P.A., Fontecilla-Camps, J.C.

Revision History  

• Version 1.0: 2003-04-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2019-11-27
  Changes: Derived calculations, Other
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2025-10-01
  Changes: Derived calculations, Structure summary