PDBsum entry 1oao

Oxidoreductase/transferase

PDB id: 1oao

Contents

Protein chains

673 a.a. *

729 a.a. *

Ligands

SF4 ×5

XCC-FOR ×2

SO4 ×31

GOL ×8

BCT

_SX

ACT

Metals

FE2 ×2

_ZN

_NI ×3

Waters ×1271

* Residue conservation analysis

PDB id:

1oao

Name:

Oxidoreductase/transferase

Title:

Nizn[fe4s4] and nini[fe4s4] clusters in closed and open alpha subunits of acetyl-coa synthase/carbon monoxide dehydrogenase

Structure:

Carbon monoxide dehydrogenase/acetyl-coa synthase subunit beta. Chain: a, b. Synonym: codh. Carbon monoxide dehydrogenase/acetyl-coa synthase subunit alpha. Chain: c, d. Synonym: codh. Ec: 2.3.1.169

Source:

Moorella thermoacetica. Organism_taxid: 1525. Organism_taxid: 1525

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.90Å R-factor: 0.149 R-free: 0.179

Authors:

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

Key ref:

C.Darnault et al. (2003). Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] clusters in closed and open subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase. Nat Struct Biol, 10, 271-279. PubMed id: 12627225 DOI: 10.1038/nsb912

Date:

20-Jan-03 Release date: 11-Apr-03

Protein chains

P27989  (DCMB_MOOTH) -  Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta from Moorella thermoacetica

Seq: 674 a.a.

Struc: 673 a.a.

Protein chains

P27988  (DCMA_MOOTH) -  Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha from Moorella thermoacetica

Seq: 729 a.a.

Struc: 730 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.1.2.7.4 - anaerobic carbon-monoxide dehydrogenase.
• Reaction: CO + 2 oxidized [2Fe-2S]-[ferredoxin] + H2O = 2 reduced [2Fe-2S]- [ferredoxin] + CO2 + 2 H⁺

CO (Bound ligand (Het Group name = FOR) corresponds exactly) + 2 × oxidized [2Fe-2S]-[ferredoxin] + H2O = 2 × reduced [2Fe-2S]- [ferredoxin] + CO2 (Bound ligand (Het Group name = BCT) matches with 75.00% similarity) + 2 × H(+)

• Cofactor: Fe cation; Ni(2+); Zn(2+)
• Enzyme class 3: Chains C, D: E.C.2.3.1.169 - CO-methylating acetyl-CoA synthase.
• Reaction: Co(I)-[corrinoid Fe-S protein] + acetyl-CoA + H⁺ = methyl-Co(III)- [corrinoid Fe-S protein] + CO + CoA

Co(I)-[corrinoid Fe-S protein] + 2 × acetyl-CoA + H(+) = 2 × methyl-Co(III)- [corrinoid Fe-S protein] + CO (Bound ligand (Het Group name = FOR) corresponds exactly) + 2 × CoA

• Cofactor: Cu(2+); Iron-sulfur; Ni(2+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nsb912

Nat Struct Biol 10:271-279 (2003)

PubMed id: 12627225

Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] clusters in closed and open subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase.

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

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.

Selected figure(s)

Figure 3.
Figure 3. Stereo view of a superposition of the A[o]- and A[c]-clusters. The coordination of Ni[p] in the A[o] cluster (atoms color-coded as in Fig. 2) indicates a square planar arrangement with three cysteine thiolates and one unidentified exogenous ligand (L). In the A[c]-cluster (gray), the coordination of the proximal Zn ion is distorted tetrahedral (see also Fig. 5b). A 7 electron density peak is found in a mF[o] - F[c] map that is 1.3 Å removed from Ni[p] and that occupies, as shown, a position equivalent to the Zn in the A[c]-cluster.

Figure 4.
Figure 4. Stereo views of the structure of the C-cluster in the subunit. a, Electron density, contoured at the 1 level, corresponding to a 2mF[o] - DF[c] difference electron density map42 using 1.9 Å resolution refined model phases of CO-treated crystal CO[a]. b, Residual mF[o] - F[c] electron density peaks, contoured at the 5.5 level, correponding to (i) a putative persulfide formed between a labile S atom and Cys316, (ii) an alternative position for the unique Fe, as indicated by arrows and (iii) alternative conformations of Cys550. Atoms at alternative positions are shown as translucid spheres. Atoms are colored as in Fig. 2.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 271-279) copyright 2003.

Figures were selected by an automated process.