PDBsum entry 3d4t

Oxidoreductase

PDB id: 3d4t

Contents

Protein chain

97 a.a. *

Ligands

BME ×2

Waters ×103

* Residue conservation analysis

PDB id:

3d4t

Name:

Oxidoreductase

Title:

Crystal structure of the periplasmic thioredoxin soxs from paracoccus pantotrophus (oxidized form)

Structure:

Putative uncharacterized protein. Chain: a. Fragment: periplasmic domain, unp residues 32-130. Synonym: thiol-disulfide oxidoreductase soxs. Engineered: yes

Source:

Paracoccus denitrificans. Strain: gb17. Gene: soxs. Expressed in: escherichia coli.

Resolution:

2.05Å R-factor: 0.177 R-free: 0.216

Authors:

Y.Carius,C.G.Friedrich,A.J.Scheidig

Key ref:

Y.Carius et al. (2009). The structure of the periplasmic thiol-disulfide oxidoreductase SoxS from Paracoccus pantotrophus indicates a triple Trx/Grx/DsbC functionality in chemotrophic sulfur oxidation. Acta Crystallogr D Biol Crystallogr, 65, 229-240. PubMed id: 19237745 DOI: 10.1107/S0907444908043023

Date:

15-May-08 Release date: 15-Jul-08

Protein chain

Q8KM22  (Q8KM22_PARDE) -  Thioredoxin-like fold domain-containing protein from Paracoccus denitrificans

Seq: 130 a.a.

Struc: 97 a.a.

DOI no: 10.1107/S0907444908043023

Acta Crystallogr D Biol Crystallogr 65:229-240 (2009)

PubMed id: 19237745

The structure of the periplasmic thiol-disulfide oxidoreductase SoxS from Paracoccus pantotrophus indicates a triple Trx/Grx/DsbC functionality in chemotrophic sulfur oxidation.

Y.Carius, D.Rother, C.G.Friedrich, A.J.Scheidig.

ABSTRACT

The periplasmic thiol-disulfide oxidoreductase SoxS is beneficial for the sulfur-oxidizing (Sox) phenotype of the facultative chemotrophic bacterium Paracoccus pantotrophus and is not part of the Sox enzyme system. SoxS combines features of thioredoxins, glutaredoxins and the thiol-disulfide oxidoreductases of the Dsb family in structure, target specificity and reaction. The structure of SoxS was solved in oxidized and reduced forms at 2.1 and 1.9 A resolution, respectively. SoxS revealed high structural homology to typical cytoplasmic bacterial thioredoxins. In contrast, SoxS contained the active-site motif Pro-Gly-Cys-Leu-Tyr-Cys that is not present in other thioredoxins. Interestingly, the sequence of this motif is closely related to the Pro-Gly-Cys-Pro-Tyr-Cys sequence of some glutaredoxins and to the Pro-Xaa-Cys-Xaa-Tyr-Cys sequences of some members of the DsbC and DsbG subfamilies of thiol-disulfide oxidoreductases. Furthermore, the proposed substrate of SoxS, the interprotein disulfide of SoxY, Cys110(Y)-Cys110(Y), is structurally similar to oxidized glutathione. However, SoxS is proposed to specifically reduce the interprotein disulfide between two SoxY subunits, releasing a heterodimeric SoxYZ as an active part of the sulfur-oxidation cycle.

Selected figure(s)

Figure 5.
Figure 5 Stereo representation of the hydrogen-bonding network around the thiolate of cysteine Cys13 in the reduced form of SoxS. The main-chain trace of the protein is displayed as a loop representation. The side chains of relevant residues are depicted in ball-and-stick representation and coloured green, with associated N, O and S atoms in blue, red and yellow, respectively. Direct and water-mediated hydrogen bonds are represented by cyan dashed lines. This figure was prepared using PyMOL (DeLano, 2004[DeLano, W. L. (2004). The PyMOL Molecular Graphics System. http://www.pymol.org .]).

Figure 6.
Figure 6 Molecular-surface representation of SoxS. (a) Representation of the molecular surface coloured according to the electrostatic potential. The yellow asterisk indicates the position of the redox-active Cys13. The molecular surface is coloured according to the electrostatic potential as calculated with the program APBS (Baker et al., 2001[Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. (2001). Proc. Natl Acad. Sci. USA, 98, 10037-10041.]). The molecular surface is colour-ramped according to the electrostatic potential, with red indicating negative potential and blue indicating positive potential; fully saturated colours indicate a potential of or equal to] ±4kT/e (assuming an ionic strength of 150 mM, a protein interior dielectric of 2 and a solvent dielectric of 78.5). The rendered surface representation was prepared with PyMOL (DeLano, 2004[DeLano, W. L. (2004). The PyMOL Molecular Graphics System. http://www.pymol.org .]). (b) The putative binding cleft on the surface of SoxS. The spheres are coloured according to the type of the underlying atom (carbon, green; nitrogen, blue; oxygen, red; sulfur, yellow). For the putative substrate-binding epitope the C atoms are coloured magenta. The S atom of the redox-active cysteinyl residue Cys13 is labelled as well as the aromatic amino-acid residues located at the surface near the active site.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2009, 65, 229-240) copyright 2009.

Figures were selected by an automated process.