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Information on EC 1.8.5.3 - respiratory dimethylsulfoxide reductase and Organism(s) Rhodobacter capsulatus and UniProt Accession Q52675
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1.8.5.3 respiratory dimethylsulfoxide reductaseIUBMB Comments
The enzyme participates in bacterial electron transfer pathways in which dimethylsulfoxide (DMSO) is the terminal electron acceptor. It is composed of three subunits - DmsA contains a bis(guanylyl molybdopterin) cofactor and a [4Fe-4S] cluster, DmsB is an iron-sulfur protein, and DmsC is a transmembrane protein that anchors the enzyme and accepts electrons from the quinol pool. The electrons are passed through DmsB to DmsA and on to DMSO. The enzyme can also reduce pyridine-N-oxide and trimethylamine N-oxide to the corresponding amines with lower activity.
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Word Map
- 1.8.5.3
- rhodobacter
- sphaeroides
-
molybdoenzyme
- molybdopterin
- capsulatus
-
dithiolene
-
pyranopterins
- narghi
- tord
-
bismolybdopterin
-
mo-containing
-
high-g
- menaquinol
- wiv
- frdabcd
The taxonomic range for the selected organisms is: Rhodobacter capsulatus
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
dmso reductase, dimethyl sulfoxide reductase, dmsor, dmsabc, dimethylsulfoxide reductase, dimethyl sulfoxide/trimethylamine n-oxide reductase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
dimethylsulfoxide reductase
-
-
-
-
DMSO reductase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
dimethylsulfide + menaquinone + H2O = dimethylsulfoxide + menaquinol
according to density functional theory, the reaction between dimethyl sulfoxide and the model complex [Mo(OPh)(C2S2H2)2]- proceeds in one associative step. In the optimized transition state, the bond between the metal and dimethyl sulfoxide is being formed through the oxygen atom of dimethyl sulfoxide while the S-O bond in the substrate is weakening
dimethylsulfide + menaquinone + H2O = dimethylsulfoxide + menaquinol
computational studies show that the enzyme follows a two-step associative mechanism with the binding of dimethylsulfoxide in the first step and the oxygen-atom transfer and dissociation of the dimethylsulfide product in the second step. The first transition state is close in energy to the intermediate (within about 10 kJ/mol), whereas the rate-limiting barrier is observed for the second step
dimethylsulfide + menaquinone + H2O = dimethylsulfoxide + menaquinol
reaction mechanism, overview. The distorted trigonal prismatic active site structure in DMSO reductase imparts significant electronic structure contributions to enzymatic catalysis
SYSTEMATIC NAME
IUBMB Comments
dimethyl sulfide:menaquinone oxidoreductase
The enzyme participates in bacterial electron transfer pathways in which dimethylsulfoxide (DMSO) is the terminal electron acceptor. It is composed of three subunits - DmsA contains a bis(guanylyl molybdopterin) cofactor and a [4Fe-4S] cluster, DmsB is an iron-sulfur protein, and DmsC is a transmembrane protein that anchors the enzyme and accepts electrons from the quinol pool. The electrons are passed through DmsB to DmsA and on to DMSO. The enzyme can also reduce pyridine-N-oxide and trimethylamine N-oxide to the corresponding amines with lower activity.
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
dimethyl sulfoxide + reduced methyl viologen
dimethyl sulfide + H2O + oxidized methyl viologen
-
-
-
r
dimethylsulfoxide + menaquinol
dimethylsulfide + menaquinone + H2O
-
-
-
?
(R)-ethyl 2-pyridyl sulfoxide + reduced methyl viologen + H2O
ethyl 2-pyridyl sulfide + oxidized methyl viologen
-
-
-
-
?
(R)-methoxymethyl phenyl sulfoxide + reduced methyl viologen + H2O
methoxymethyl phenyl sulfide + oxidized methyl viologen
-
-
-
-
?
(R)-methyl p-tolyl sulfoxide + reduced methyl viologen + H2O
methyl p-tolyl sulfide + oxidized methyl viologen
-
-
-
-
?
(R)-methylthiomethyl methyl sulfoxide + reduced methyl viologen + H2O
methylthiomethyl methyl sulfide + oxidized methyl viologen
-
-
-
-
?
(S)-ethyl 2-pyridyl sulfoxide + reduced methyl viologen + H2O
ethyl 2-pyridyl sulfide + oxidized methyl viologen
-
-
-
-
?
(S)-methoxymethyl phenyl sulfoxide + reduced methyl viologen + H2O
methoxymethyl phenyl sulfide + oxidized methyl viologen
-
-
-
-
?
(S)-methyl p-tolyl sulfoxide + reduced methyl viologen + H2O
methyl p-tolyl sulfide + oxidized methyl viologen
-
catalyses the selective removal of (S)-methyl p-tolyl sulfoxide from a racemic mixture of methyl p-tolyl sulfoxide, resulting in an 88 O/o recovery of enantiomerically pure (R)-methyl p-tolyl sulfoxide
-
-
?
(S)-methylthiomethyl methyl sulfoxide + reduced methyl viologen + H2O
methylthiomethyl methyl sulfide + oxidized methyl viologen
-
-
-
-
?
dimethylsulfide + H2O + oxidized benzyl viologen
dimethylsulfoxide + reduced benzyl viologen
-
-
-
-
r
dimethylsulfide + H2O + oxidized methyl viologen
dimethylsulfoxide + reduced methyl viologen
-
-
-
-
r
dimethylsulfoxide + reduced benzyl viologen
dimethylsulfide + H2O + oxidized benzyl viologen
-
-
-
-
r
dimethylsulfoxide + reduced methyl viologen
dimethylsulfide + H2O + oxidized methyl viologen
-
-
-
-
r
trimethylamine-N-oxide + reduced methyl viologen
trimethylamine + H2O + oxidized methyl viologen
-
-
-
-
r
additional information
?
-
formation of the intermediate formed by reaction of DMSOR with dimethylsulfide occurs at a redox potential that is 80 mV higher than that required for reduction of Mo(VI) to Mo(IV) in the free enzyme. In the back-assay the Mo(IV) state may at least in part be by-passed via two successive one electron-reactions of the intermediate with the electron-acceptor
-
-
?
additional information
?
-
-
formation of the intermediate formed by reaction of DMSOR with dimethylsulfide occurs at a redox potential that is 80 mV higher than that required for reduction of Mo(VI) to Mo(IV) in the free enzyme. In the back-assay the Mo(IV) state may at least in part be by-passed via two successive one electron-reactions of the intermediate with the electron-acceptor
-
-
?
additional information
?
-
-
enzyme catalyses the enantioselective reduction of (R)-sulfoxides
-
-
?
additional information
?
-
-
enzyme catalyses the enantioselective reduction of (S)-sulfoxides
-
-
?
additional information
?
-
-
Second-order rate constants for the two-electron reduction and reoxidation reactions at pH 5.5 are 190000 and 430 per M and s, respectively, while at pH 8.0, the catalytic step is rate-limiting. Kinetically, for the two-electron reactions, the enzyme is more effective in dimethylsulfide oxidation than in dimethylsulfoxide reduction. Reduction of DMSOR by dimethylsulfide is incomplete below 1 mM dimethylsulfide but complete at higher concentrations. Reoxidation of the dimethylsulfide-reduced state by dimethylsulfoxide is always incomplete
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
dimethylsulfoxide + menaquinol
dimethylsulfide + menaquinone + H2O
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
bis(molybdopterin guanine dinucleotide)molybdenum cofactor
-
the bis-molybdopterin guanine dinucleotide cofactor of the single chain protein has the molybdenum ion bound to the cis-dithiolene group of only one molybdopterin guanine dinucleotide molecule. Three additional ligands, two oxo groups and the oxygen of a serine side-chain, are bound to the molybdenum ion. The second molybdopterin system is not part of the ligand sphere of the metal center
molybdenum bis-molybdopterin guanine dinucleotide
-
the molybdenum cofactor in dimethylsulfoxide reductase is bis(molybdopterin guanine dinucleotide) molybdenum. Protein contains 1 mol Mo and 2 mol GMP. Approximately 2 mol. electrons/2 mol molybdopterin guanine dinucleotide reduce 2,6-dichloroindophenol. Presence of one molybdopterin guanine dinucleotide moiety with a pyrazine ring at the oxidation level of a dihydropteridine and one molybdopterin guanine dinucleotide moiety with a pyrazine ring at the oxidation level of a fully aromatic pteridine
molybdenum cofactor
-
residue W116 forms a hydrogen bond with a single oxo ligand bound to the molybdenum ion. Mutation of this residue to phenylalanine affects the UV/visible spectrum of the purified MoVI form of dimethylsulfoxide reductase resulting in the loss of the characteristic transition at 720 nm. W116 plays a critical role in stabilizing the hexacoordinate monooxo MoVI form of the enzyme and prevents the formation of a dioxo pentacoordinate MoVI species
molybdenum cofactor
pterin-based cofactor MoCo, the unique cofactor contains the ligand pyranopterin ene-1,2-dithiolate. Mechanism for mature Moco formation, overview. Bacterial DMSO reductase family enzymes possess a bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor that is obtained by adding GMP to the MPT terminal phosphates. Enzymes that belong to the DMSO reductase enzyme family possess two coordinated MPTs, with one of the MPTs adopting an SO family configuration and the other a more distorted XO enzyme family structure, role of MPT in catalysis
molybdenum cofactor
two desoxo molybdenum(V) complexes are synthesized and characterized as models for the paramagnetic high-g split intermediate observed in the catalytic cycle of dimethyl sulfoxide reductase (DMSOR), analysis of extended X-ray absorption fine structure (EXAFS) and electron paramagnetic resonance (EPR) data. A 6-coordinate [(PDT)2Mo(OH)(OSer)]- structure (PDT = pyranopterin dithiolene) is supported for a high-g split with four S donors from two PDT ligands, a coordinated hydroxyl ligand, and a serinate O donor. This geometry orients the redox orbital toward the substrate access channel for the two-electron reduction of substrates. Detailed overview
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Molybdenum
Tungsten
may replace molybdenum. Tungsten is ligated by the dithiolene group of the two pyranopterins, the oxygen atom of Ser147 plus another oxygen atom, and is located in a very similar site to that of molybdenum in Mo-DMSOR. W-DMSOR is significantly more active than Mo-DMSOR in catalysing the reduction of dimethylsulfoxide but shows no significant ability to catalyse the oxidation of dimethylsulfide
Molybdenum
-
the bis-molybdopterin guanine dinucleotide cofactor of the single chain protein has the molybdenum ion bound to the cis-dithiolene group of only one molybdopterin guanine dinucleotide molecule. Three additional ligands, two oxo groups and the oxygen of a serine side-chain, are bound to the molybdenum ion. The second molybdopterin system is not part of the ligand sphere of the metal center
Molybdenum
formation of the intermediate formed by reaction of DMSOR with dimethylsulfide occurs at a redox potential that is 80 mV higher than that required for reduction of Mo(VI) to Mo(IV) in the free enzyme. In the back-assay the Mo(IV) state may at least in part be by-passed via two successive one electron-reactions of the intermediate with the electron-acceptor
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0097
Dimethylsulfoxide
-
wild-type, pH not specified in the publication, temperature not specified in the publication
0.0261
Dimethylsulfoxide
-
mutant W116F, pH not specified in the publication, temperature not specified in the publication
0.0959
Trimethylamine-N-oxide
-
mutant W116F, pH not specified in the publication, temperature not specified in the publication
0.193
Trimethylamine-N-oxide
-
wild-type, pH not specified in the publication, temperature not specified in the publication
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
21
dimethyl sulfoxide
enzyme Mo-DMSOR with molybdenum in the catalytic centre, pH not specified in the publication, temperature not specified in the publication
470
dimethyl sulfoxide
enzyme W-DMSOR with tungsten in the catalytic centre, pH not specified in the publication, temperature not specified in the publication
7
Dimethylsulfoxide
-
mutant W116F, pH not specified in the publication, temperature not specified in the publication
42.9
Dimethylsulfoxide
-
wild-type, pH not specified in the publication, temperature not specified in the publication
11.3
Trimethylamine-N-oxide
-
mutant W116F, pH not specified in the publication, temperature not specified in the publication
134.5
Trimethylamine-N-oxide
-
wild-type, pH not specified in the publication, temperature not specified in the publication
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
300
Dimethylsulfoxide
-
mutant W116F, pH not specified in the publication, temperature not specified in the publication
4400
Dimethylsulfoxide
-
wild-type, pH not specified in the publication, temperature not specified in the publication
100
Trimethylamine-N-oxide
-
mutant W116F, pH not specified in the publication, temperature not specified in the publication
700
Trimethylamine-N-oxide
-
wild-type, pH not specified in the publication, temperature not specified in the publication
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
physiological function
bacterial DMSO reductase and trimethylamine-N-oxide reductase (TMAO reductase) are of increasing environmental importance since they catalyze the oxidation of marine osmolytes and facilitate cloud formation and albedo
additional information
evolution
dimethyl sulfoxide reductase (DMSOR) represents the canonical member of the DMSOR family of prokaryotic pyranopterin molybdenum enzymes. DMSOR family enzymes have been classified by type, with type II/III enzymes being characterized by [(PDT)2MoVIO(OSer/Asp)]- oxidized active sites that possess N- and S-oxide reductase activity. Type III Rhodobacter capsulatus DMSOR catalyzes the reduction of dimethyl sulfoxide to dimethyl sulfide (DMS) as part of the global sulfur cycle
evolution
the enzyme belongs to the dimethyl sulfoxide (DMSO) reductase family. The DMSO reductase family enzymes are the most structurally and catalytically diverse of the three pyranopterin Mo enzyme families. The DMSO reductase family enzymes are divided into three classes (Types I, II, and III) that are distinguished from each other by their active site structure and the nature of the donor ligand that is provided by the polypeptide. DMSO reductase family enzymes are quite diverse and not all of the enzymes in this family adhere to this general classification scheme. DMSO reductases are type III enzymes and a combination of EXAFS and high resolution X-ray crystallography shows that the oxidized active site possesses a distorted six-coordinate trigonal prismatic [(MPT)2MoO(OSer)]1- coordination geometry
additional information
structure-function analysis of DMSO reductases, overview. Comparison of oxygen atom transfer (OAT) reactivity in different families of canonical pyranopterin Mo enzymes , including the DMSO reductase family, the sulfite oxidase (SO) family, the xanthine oxidase (XO) family enzymes, and the formate dehydrogenases. The active site structures and the nature of the ligands bound to the metal center appear to be fine-tuned so that the reactions catalyzed by pyranopterin Mo enzymes are close to thermoneutral. The DMSO reductase family enzymes are the most structurally and catalytically diverse of the three pyranopterin Mo enzyme families. The oxidized active site possesses a distorted six-coordinate trigonal prismatic [(MPT)2MoO(OSer)]1- coordination geometry
additional information
two desoxo molybdenum(V) complexes are synthesized and characterized as models for the paramagnetic high-g split intermediate observed in the catalytic cycle of dimethyl sulfoxide reductase (DMSOR), analysis of extended X-ray absorption fine structure (EXAFS) and electron paramagnetic resonance (EPR) data. A 6-coordinate [(PDT)2Mo(OH)(OSer)]- structure (PDT = pyranopterin dithiolene) is supported for a high-g split with four S donors from two PDT ligands, a coordinated hydroxyl ligand, and a serinate O donor. This geometry orients the redox orbital toward the substrate access channel for the two-electron reduction of substrates. Detailed overview
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
damaged enzyme form derived from an intermediate formed by reaction of DMSOR with dimethylsulfide and reaction with oxygen, to 2.0 A resolution. All four thiolate ligands and Ogamma of serine-147 remain coordinated to molybdenum, there are no terminal oxygen ligands and molybdenum is Mo(VI)
protein with tungsten in place of molybdenum, to 2.0 A resolution
to 1.88 A resolution, space group P41212. Spherical protein, consists of four domains with a funnel-like cavity that leads to the freely accessible metal-ion redox center. The bis(molybdopterin guanine dinucleotide) molybdenum cofactor of the single chain protein has the molybdenum ion bound to the cis-dithiolene group of only one molybdopterin guanine dinucleotide molecule. Three additional ligands, two oxo groups and the oxygen of a serine side-chain, are bound to the molybdenum ion. The second molybdopterin system is not part of the ligand sphere of the metal center
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
W116F
-
residue W116 forms a hydrogen bond with a single oxo ligand bound to the molybdenum ion. Mutation of this residue to phenylalanine affects the UV/visible spectrum of the purified MoVI form of dimethylsulfoxide reductase resulting in the loss of the characteristic transition at 720 nm
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Schneider, F.; Lowe, F.; Huber, R.; Schindelin, H.; Kisker, C.; Knablein, J.
Crystal structure of dimethyl sulfoxide reductase from Rhodobacter capsulatus at 1.88 Ang resolution
J. Mol. Biol.
263
53-69
1996
Rhodobacter capsulatus
Adams, B.; Smith, A.T.; Bailey, S.; McEwan, A.G.; Bray, R.C.
Reactions of dimethylsulfoxide reductase from Rhodobacter capsulatus with dimethyl sulfide and with dimethyl sulfoxide: complexities revealed by conventional and stopped-flow spectrophotometry
Biochemistry
38
8501-8511
1999
Rhodobacter capsulatus
Bray, R.C.; Adams, B.; Smith, A.T.; Richards, R.L.; Lowe, D.J.; Bailey, S.
Reactions of dimethylsulfoxide reductase in the presence of dimethyl sulfide and the structure of the dimethyl sulfide-modified enzyme
Biochemistry
40
9810-9820
2001
Rhodobacter capsulatus (Q52675), Rhodobacter capsulatus
Solomon, P.S.; Lane, I.; Hanson, G.R.; McEwan, A.G.
Characterisation of the pterin molybdenum cofactor in dimethylsulfoxide reductase of Rhodobacter capsulatus
Eur. J. Biochem.
246
200-203
1997
Rhodobacter capsulatus
Ridge, J.P.; Aguey-Zinsou, K.F.; Bernhardt, P.V.; Hanson, G.R.; McEwan, A.G.
The critical role of tryptophan-116 in the catalytic cycle of dimethylsulfoxide reductase from Rhodobacter capsulatus
FEBS Lett.
563
197-202
2004
Rhodobacter capsulatus
Stewart, L.J.; Bailey, S.; Bennett, B.; Charnock, J.M.; Garner, C.D.; McAlpine, A.S.
Dimethylsulfoxide reductase: an enzyme capable of catalysis with either molybdenum or tungsten at the active site
J. Mol. Biol.
299
593-600
2000
Rhodobacter capsulatus (Q52675), Rhodobacter capsulatus
Hanlon, S.; Graham, D.; Hogan, P.; Holt, R.; Reeve, C.; Shaw, A.; McEwan, A.
Asymmetric reduction of racemic sulfoxides by dimethyl sulfoxide reductases from Rhodobacter capsulatus, Escherichia coli and Proteus species
Microbiology
144
2247-2253
1998
Escherichia coli, Proteus mirabilis, Rhodobacter capsulatus
Hernandez-Marin, E.; Ziegler, T.
A kinetic study of dimethyl sulfoxide reductase based on density functional theory
Can. J. Chem.
88
683-693
2010
Rhodobacter capsulatus (Q52675)
-
Li, J.; Mata, R.; Ryde, U.
Large density-functional and basis-set effects for the DMSO reductase catalyzed oxo-transfer reaction
J. Chem. Theory Comput.
9
1799-1807
2013
Rhodobacter capsulatus (Q52675)
Kc, K.; Yang, J.; Kirk, M.L.
Addressing serine lability in a paramagnetic dimethyl sulfoxie reductase catalytic intermediate
Inorg. Chem.
60
9233-9237
2021
Rhodobacter capsulatus (Q52675), Cereibacter sphaeroides (Q57366)
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