PDBsum entry 1e0c

Sulfurtransferase

PDB id: 1e0c

Contents

Protein chain

271 a.a. *

Ligands

SO4 ×2

EDO ×2

Metals

_MG ×3

Waters ×341

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The crystal structure of a sulfurtransferase from azotobacter vinelandii highlights the evolutionary relationship between the rhodanese and phosphatase enzyme families.

Authors

D.Bordo, D.Deriu, R.Colnaghi, A.Carpen, S.Pagani, M.Bolognesi.

Ref.

J Mol Biol, 2000, 298, 691-704. [DOI no: 10.1006/jmbi.2000.3651]

PubMed id

10788330

Abstract

Rhodanese is an ubiquitous enzyme that in vitro catalyses the transfer of a sulfur atom from suitable donors to nucleophilic acceptors by way of a double displacement mechanism. During the catalytic process the enzyme cycles between a sulfur-free and a persulfide-containing form, via formation of a persulfide linkage to a catalytic Cys residue. In the nitrogen-fixing bacteria Azotobacter vinelandii the rhdA gene has been identified and the encoded protein functionally characterized as a rhodanese. The crystal structure of the A. vinelandii rhodanese has been determined and refined at 1.8 A resolution in the sulfur-free and persulfide-containing forms. Conservation of the overall three-dimensional fold of bovine rhodanese is observed, with substantial modifications of the protein structure in the proximity of the catalytic residue Cys230. Remarkably, the native enzyme is found as the Cys230-persulfide form; in the sulfur-free state the catalytic Cys residue adopts two alternate conformations, reflected by perturbation of the neighboring active-site residues, which is associated with a partly reversible loss of thiosulfate:cyanide sulfurtransferase activity. The catalytic mechanism of A. vinelandii rhodanese relies primarily on the main-chain conformation of the 230 to 235 active-site loop and on a surrounding strong positive electrostatic field. Substrate recognition is based on residues which are entirely different in the prokaryotic and eukaryotic enzymes. The active-site loop of A. vinelandii rhodanese displays striking structural similarity to the active-site loop of the similarly folded catalytic domain of dual specific phosphatase Cdc25, suggesting a common evolutionary origin of the two enzyme families.

Figure 1.
Figure 1. Overall structure of A. vinelandii rhodanese. (a) Stereoview of the C^a trace, with the molecular pseudo 2-fold axis approximately normal to the plane of the image. (b) Ribbon representation of RhdA. The N- and C-terminal domains (brown and green, respectively), the linker peptide (blue). The secondary structure elements of each domain are labeled with letters following the scheme proposed for bovine rhodanese [Ploegman et al 1978]. A single quote indicates elements of the C-terminal domains. The active-site loop is shown in red; the catalytic residue, Cys230, is represented in ball and stick. The drawings were prepared with the programs MOLSCRIPT [Kraulis 1991] and Raster3D [Merrit and Murphy 1994].

Figure 3.
Figure 3. Stereo representation of the active-site environment of the sulfur-free rhodanese. The alternate conformations of Cys230, Arg235, and Trp195 side-chains are shown in grey and green, respectively; hydrogen bonds as red dotted lines.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 298, 691-704) copyright 2000.

Secondary reference #1

Title

Crystallization and preliminary crystallographic investigations of rhodanese from azotobacter vinelandii.

Authors

D.Bordo, R.Colnaghi, D.Deriu, A.Carpen, P.Storici, S.Pagani, M.Bolognesi.

Ref.

Acta Crystallogr D Biol Crystallogr, 1999, 55, 1471-1473. [DOI no: 10.1107/S0907444999006526]

PubMed id

10417419

Figure 1.
Figure 1 Amino-acid sequence alignment of A. vinelandii and bovine (Bos taurus) liver rhodanese. Conserved residues are indicated by |; amino acids for which reliable alignment could not be obtained are shown in lower case. Active-site Cys residues are indicated by *.

The above figure is reproduced from the cited reference with permission from the IUCr