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

References listed in PDB file

Key reference

Title

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

Authors

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

Ref.

Nat Struct Biol, 2003, 10, 271-279. [DOI no: 10.1038/nsb912]

PubMed id

12627225

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.

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.