PDBsum entry 2wdf

Hydrolase

PDB id: 2wdf

Contents

Protein chain

544 a.a. *

Ligands

TBU

Metals

_MN ×2

Waters ×336

* Residue conservation analysis

PDB id:

2wdf

Name:

Hydrolase

Title:

Termus thermophilus sulfate thiohydrolase soxb

Structure:

Sulfur oxidation protein soxb. Chain: a. Fragment: residues 24-573. Synonym: soxb. Engineered: yes. Other_details: thermus thermophilus hb27 soxb

Source:

Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: de3.

Resolution:

2.08Å R-factor: 0.182 R-free: 0.228

Authors:

V.Sauve,P.Roversi,K.J.Leath,E.F.Garman,R.Antrobus,S.M.Lea,B.C.Berks

Key ref:

V.Sauvé et al. (2009). Mechanism for the hydrolysis of a sulfur-sulfur bond based on the crystal structure of the thiosulfohydrolase SoxB. J Biol Chem, 284, 21707-21718. PubMed id: 19535341 DOI: 10.1074/jbc.M109.002709

Date:

24-Mar-09 Release date: 16-Jun-09

Protein chain

Q72IT0  (Q72IT0_THET2) -  Sulfur oxidation protein soxB from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 573 a.a.

Struc: 544 a.a.

Enzyme reactions

• Enzyme class: E.C.3.12.2.1

DOI no: 10.1074/jbc.M109.002709

J Biol Chem 284:21707-21718 (2009)

PubMed id: 19535341

Mechanism for the hydrolysis of a sulfur-sulfur bond based on the crystal structure of the thiosulfohydrolase SoxB.

V.Sauvé, P.Roversi, K.J.Leath, E.F.Garman, R.Antrobus, S.M.Lea, B.C.Berks.

ABSTRACT

SoxB is an essential component of the bacterial Sox sulfur oxidation pathway. SoxB contains a di-manganese(II) site and is proposed to catalyze the release of sulfate from a protein-bound cysteine S-thiosulfonate. A direct assay for SoxB activity is described. The structure of recombinant Thermus thermophilus SoxB was determined by x-ray crystallography to a resolution of 1.5 A. Structures were also determined for SoxB in complex with the substrate analogue thiosulfate and in complex with the product sulfate. A mechanistic model for SoxB is proposed based on these structures.

Selected figure(s)

Figure 2.
Structure of T. thermophilus SoxB and the effect of binding the substrate analogue thiosulfate.A, cartoon representation of the overall structure of SoxB using the SoxB-glycerol coordinates. The N-terminal domain is shown in blue with the N-terminal loop subdomain in green. The interdomain helix is shown in yellow, the C-terminal domain is in red, and the manganese ions are in purple. The route of access to the active site is indicated with an arrow. B, a representation of the residues that are critical for the relative orientation of the substrate analogue thiosulfate and the reactive bridging hydroxide ion based on the SoxB-Mn^2+-thiosulfate structure. The manganese ions are in purple, and the oxygen of the reactive bridging hydroxide is in red. Thiosulfate is shown in stick representation. The footprint of the thiosulfate S–S bond on the protein surface is green. Distances between selected atoms (indicated by dashed lines) are given. C, the two conformations of loop 465–476. The closed conformation observed when the active site is empty (SoxB-Mn^2+ structure) is shown in yellow, and the open conformation adopted upon binding of the substrate analogue thiosulfate at the active site (SoxB-Mn^2+-thiosulfate structure) is in red. The manganese ions are shown in purple, and the thiosulfate molecule present in the open conformation in a stick representation.

Figure 5.
Proposed mechanism for SoxB. The three steps of the cycle depicted here are based on the SoxB-Mn^2+, SoxB-Mn^2+-thiosulfate, and SoxB-Mn^2+-sulfate (conformer 2) structures.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 21707-21718) copyright 2009.

Figures were selected by an automated process.