PDBsum entry 1dcd

Electron transport

PDB id: 1dcd

Contents

Protein chains

36 a.a. *

Metals

_CD ×2

Waters ×53

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural studies by X-Ray diffraction on metal substituted desulforedoxin, A rubredoxin-Type protein.

Authors

M.Archer, A.L.Carvalho, S.Teixeira, I.Moura, J.J.Moura, F.Rusnak, M.J.Romão.

Ref.

Protein Sci, 1999, 8, 1536-1545. [DOI no: 10.1110/ps.8.7.1536]

PubMed id

10422844

Abstract

Desulforedoxin (Dx), isolated from the sulfate reducing bacterium Desulfovibrio gigas, is a small homodimeric (2 x 36 amino acids) protein. Each subunit contains a high-spin iron atom tetrahedrally bound to four cysteinyl sulfur atoms, a metal center similar to that found in rubredoxin (Rd) type proteins. The simplicity of the active center in Dx and the possibility of replacing the iron by other metals make this protein an attractive case for the crystallographic analysis of metal-substituted derivatives. This study extends the relevance of Dx to the bioinorganic chemistry field and is important to obtain model compounds that can mimic the four sulfur coordination of metals in biology. Metal replacement experiments were carried out by reconstituting the apoprotein with In3+, Ga3+, Cd2+, Hg2+, and Ni2+ salts. The In3+ and Ga3+ derivatives are isomorphous with the iron native protein; whereas Cd2+, Hg2+, and Ni2+ substituted Dx crystallized under different experimental conditions, yielding two additional crystal morphologies; their structures were determined by the molecular replacement method. A comparison of the three-dimensional structures for all metal derivatives shows that the overall secondary and tertiary structures are maintained, while some differences in metal coordination geometry occur, namely, bond lengths and angles of the metal with the sulfur ligands. These data are discussed in terms of the entatic state theory.

Secondary reference #1

Title

Crystal structure of desulforedoxin from desulfovibrio gigas determined at 1.8 a resolution: a novel non-Heme iron protein structure.

Authors

M.Archer, R.Huber, P.Tavares, I.Moura, J.J.Moura, M.A.Carrondo, L.C.Sieker, J.Legall, M.J.Romão.

Ref.

J Mol Biol, 1995, 251, 690-702. [DOI no: 10.1006/jmbi.1995.0465]

PubMed id

7666420

Figure 1.
Figure 1. Electron density 2Fobs-- Fcalc map (contour level 1s) around the iron center for monomer B.

Figure 11.
Figure 11. Stereo view of the Dx Fe(Cys)4 center, with NH : S hydrogen bonds marked.

The above figures are reproduced from the cited reference with permission from Elsevier