PDBsum entry: 1h5n

Oxidoreductase

PDB id: 1h5n

Contents

Protein chains

765 a.a. *

Ligands

PGD ×4

SO4 ×2

Metals

6MO ×2

Waters ×1234

* Residue conservation analysis

PDB id:

1h5n

Name:

Oxidoreductase

Title:

Dmso reductase modified by the presence of dms and air

Structure:

Dmso reductase. Chain: a, c

Source:

Rhodobacter capsulatus. Organism_taxid: 1061. Strain: h123. Cellular_location: periplasm. Gene: dora

Resolution:

2.0Å R-factor: 0.158 R-free: 0.209

Authors:

S.Bailey,B.Adams,A.T.Smith,R.L.Richards,D.J.Lowe,R.C.Bray

Key ref:

R.C.Bray et al. (2001). Reactions of dimethylsulfoxide reductase in the presence of dimethyl sulfide and the structure of the dimethyl sulfide-modified enzyme. Biochemistry, 40, 9810-9820. PubMed id: 11502174 DOI: 10.1021/bi010559r

Date:

22-May-01 Release date: 17-May-02

Protein chains

Q52675  (DMSA_RHOCA) -  Dimethyl sulfoxide/trimethylamine N-oxide reductase

Seq: 823 a.a.

Struc: 765 a.a.*

* PDB and UniProt seqs differ at 14 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.1.7.2.3 - Trimethylamine-N-oxide reductase (cytochrome c).
• Reaction: Trimethylamine + 2 (ferricytochrome c)-subunit + H₂O = trimethylamine N-oxide + 2 (ferrocytochrome c)-subunit + 2 H⁺
• Cofactor: Bis(molybdopterin guanine dinucleotide)molybdenum cofactor
• Enzyme class 2: E.C.1.8.5.3 - Dimethylsulfoxide reductase.
• Reaction: Dimethylsulfide + menaquinone + H₂O = dimethylsulfoxide + menaquinol
• Cofactor: Iron-sulfur; Molybdopterin

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (1 term)
• Biochemical function: binding (5 terms)

reference

DOI no: 10.1021/bi010559r

Biochemistry 40:9810-9820 (2001)

PubMed id: 11502174

Reactions of dimethylsulfoxide reductase in the presence of dimethyl sulfide and the structure of the dimethyl sulfide-modified enzyme.

R.C.Bray, B.Adams, A.T.Smith, R.L.Richards, D.J.Lowe, S.Bailey.

ABSTRACT

The bis-molybdopterin enzyme dimethylsulfoxide reductase (DMSOR) from Rhodobacter capsulatus catalyzes the conversion of dimethyl sulfoxide (DMSO) to dimethyl sulfide (DMS), reversibly, in the presence of suitable e(-)-donors or e(-)-acceptors. The catalytically significant intermediate formed by reaction of DMSOR with DMS ('the DMS species') and a damaged enzyme form derived by reaction of the latter with O(2) (DMS-modified enzyme, DMSOR(mod)D) have been investigated. Evidence is presented that Mo in the DMS species is not, as widely assumed, Mo(IV). Formation of the DMS species is reversed on removing DMS or by addition of an excess of DMSO. Equilibrium constants for the competing reactions of DMS and DMSO with the oxidized enzyme (K(d) = 0.07 +/- 0.01 and 21 +/- 5 mM, respectively) that control these processes indicate formation of the DMS species occurs at a redox potential that is 80 mV higher than that required, according to the literature, for reduction of Mo(VI) to Mo(IV) in the free enzyme. Specificity studies show that with dimethyl selenide, DMSOR yields a species analogous to the DMS species but with the 550 nm peak blue-shifted by 27 nm. It is concluded from published redox potential data that this band is due to metal-to-ligand charge transfer from Mo(V) to the chalcogenide. Since the DMS species gives no EPR signal in the normal or parallel mode, a free radical is presumed to be in close proximity to the metal, most likely on the S. The species is thus formulated as Mo(V)-O-S(*)Me(2). Existing X-ray crystallographic and Raman data are consistent with this structure. Furthermore, 1e(-) oxidation of the DMS species with phenazine ethosulfate yields a Mo(V) form without an -OH ligand, since its EPR signal shows no proton splittings. This form presumably arises via dissociation of DMSO. The structure of DMSOR(mod)D has been determined by X-ray crystallography. All four thiolate ligands and Ogamma of serine-147 remain coordinated to Mo, but there are no terminal oxygen ligands and Mo is Mo(VI). Thus, it is a dead-end species, neither oxo group acceptance nor e(-)-donation being possible. O(2)-dependent formation of DMSOR(mod)D represents noncatalytic breakdown of the DMS species by a pathway alternative to that in turnover, with oxidation to Mo(VI) presumably preceding product release. Steps in the forward and backward catalytic cycles are discussed in relation to earlier stopped-flow data. The finding that in the back-assay the Mo(IV) state may at least in part be by-passed via two successive 1e(-) reactions of the DMS species with the e(-)-acceptor, may have implications in relation to the existence of separate molybdopterin enzymes catalyzing DMSO reduction and DMS oxidation, respectively.