| Root |
Created: 28 October 1997
| Prosthetic group | Formal oxidation states | ||
|---|---|---|---|
 |
|||
| a | 
[MoO](S1'pterin)2(S2'pterin)2O |
Mo(S1'pterin)2S2'pterinO |
|
| b | 
[MoO2]S1'pterinS2'pterinO |
||
| c | 
[MoX](S1'pterin)2(S2'pterin)2Se |
Mo(S1'pterin)2(S2'pterin)2Se |
|
| d | 
[MoX](S1'pterin)2(S2'pterin)2S |
Mo(S1'pterin)2(S2'pterin)2S |
|
  Cys)4 |
|||
Enzymes of the dimethylsulphoxide (DMSO) reductase family contain molybdenum
or tungsten and catalyse a variety of reactions that involve oxygen atom
transfer to or from an available electron lone pair of a substrate
(1-5) or the
cleavage of a C-H bond (6,
7).
All these enzymes are found either in bacteria or archaea and possess
the bis(dithiolene) coordination to the Mo or W ion by two molybdopterin
(adenine, guanine or hypoxanthine dinucleotide) molecules
[1-3].
The 3D structures of DMSO reductases from
Rhodobacter sphaeroides [4] and
Rhodobacter capsulatus [5],
Escherichia coli FDHH [6]
and Desulfovibrio desulfuricans NAP [7]
have been determined (see Figure 1FDO).
All the proteins are folded into four
The coordination of the molybdenum differs significantly in the three enzymes
(cf. schemes a, b,
c and d).
In the oxidised R. sphaeroides DMSO reductase
(a),
the four dithiolene sulphur atoms of the molybdopterins coordinate the
Mo ion asymmetrically. S2' of QMGD is positioned 3.1 Å away from
Mo, whereas the remaining three sulphur ligands are 2.4 Å away.
The S1'-S2' distances in the PMGD and QMGD are 3.1 Å and
2.3 Å, respectively, which suggests a partial disulphidebond
character for the dithiolene group of the QMGD.
The Mo is hexacoordinated by the four sulphurs,
O
Some of these enzymes, in particular periplasmic DMSO reductase from
Rhodobacter spp., possess a molybdenum cofactor (Moco) as their sole
redoxactive centre. Others, like Escherichia coli membrane
DMSO reductase and dissimilatory nitrate reductase, consist of at least
three different subunits, with the 
subunit binding Moco and the ß subunit binding several
[Fe4S4] clusters. Some dissimilatory nitrate reductases
and polysulphide reductase include a transmembrane
subunit containing
btype cytochrome. E. coli formate dehydrogenase H
(FDHH) and periplasmic dissimilatory nitrate reductase from
Desulfovibrio desulfuricans (NAP) contain both a Moco and a
[Fe4S4] cluster within the same polypeptide chain.
/ß domains.
A large funnellike cavity penetrates into the protein and leads to the
Mo ion, which is located approximately in the centre of the molecule.
The Moco consists of two molybdopterin guanine dinucleotide (MGD) molecules,
arranged in an antiparallel fashion, and one Mo ion. The two MGDs are
arbitrarily referred to as P and QMGD.
In DMSO reductases, the Nterminal domain I is the only domain that
does not interact directly with the Moco. In FDHH, domain I binds
[Fe4S4] cluster.
Domains II and III are each
ß
sandwiches with overall topology that resembles the classical dinucleotide
binding fold. Domain II coordinates PMGD while domain III coordinates
QMGD. The Cterminal domain IV consists of a sixstranded
ßbarrel and several helices.
of Ser147
and an oxo group in distorted trigonal prismatic coordination geometry.
In the MoIV form, only four
of the Mo ligands remain - the oxo group is lost and S2' of QMGD
is shifted to a position 3.7 Å from the Mo
[4].
In the MoVI R. capsulatus DMSO reductase
(b), the Mo is
pentacoordinated with a square pyramidal geometry. Only two sulphur ligands of
PMGD, O
DMSO reductase
(R. sphaeroides)(a)
of
Ser147, and one oxo group are equatorial ligands, while another
oxo group forms an apical ligand. The S1'-S2' distance in the QMGD is
2.5 Å [5].
In both the reduced and oxidised FDHH, Mo is ligated to the four
dithiolene sulphurs of the MGD cofactors and the selenium of SeCys140
(c).
In the reduced (MoIV) form, the molybdenum is pentacoordinated with
an approximately square pyramidal coordination geometry with the four sulphurs
equatorial and the selenium ligand axial
(Figure 1FDO i). In the oxidised
(MoVI) FDHH, either oxo or nitritebound,
the Mo is hexacoordinated with a trigonal prismatic coordination geometry
[6]
(Figure 1FDO g, h).
DMSO reductase
(R. capsulatus)(b)
In the oxidised D. desulfuricans NAP, MoVI is ligated to the
four dithiolene sulphurs of the MGD cofactors, sulphur of Cys140 and a
hydroxo/water ligand in a trigonal prismatic coordination geometry
(d).
In absence of crystallographic data for the reduced (MoIV) form,
it is proposed that the MoIV is pentacoordinated with
an approximately square pyramidal coordination geometry with the four
dithiolene sulphurs equatorial and the Cys140 sulphur ligand axial
[7].
FDHH (E. coli)
(c)
NAP (D. desulfuricans)
(d)
DMSO reductase family in enzyme databases
| ENZYME | LIGAND | BRENDA | Official name | Alternative name |
|---|---|---|---|---|
| 1.2.1.2 | 1.2.1.2 | 1.2.1.2 | Formate dehydrogenase | Formate:NAD+ oxidoreductase |
| 1.2.1.43 | 1.2.1.43 | 1.2.1.43 | Formate dehydrogenase (NADP+) | Formate:NADP+ oxidoreductase |
| 1.2.99.5 | 1.2.99.5 | Formylmethanofuran dehydrogenase | ||
| 1.6.6.9 | 1.6.6.9 | 1.6.6.9 | TrimethylamineNoxide reductase | Trimethylamine oxidase |
| 1.7.99.4 | 1.7.99.4 | 1.7.99.4 | Nitrate reductase | Respiratory nitrate reductase |
| PRINTS ID | PRINTS AC | PROSITE/BLOCKS ID | PROSITE AC | BLOCKS AC |
|---|---|---|---|---|
| 4FE4SFRDOXIN | PR00353 | 4FE4S_FERREDOXIN | PS00198 | BL00198 |
| 7FE8SFRDOXIN | PR00354 | |||
| MOLYBDOPTERIN_PROK_1
MOLYBDOPTERIN_PROK_2 MOLYBDOPTERIN_PROK_3 |
PS00551
PS00490 PS00932 |
BL00551 |
| Protein (Super)Family | Protein Homology Domain | Pfam | LPFC 3D alignment |
|---|---|---|---|
|
00138;
nitrate reductase chain
80559; (biotin sulfoxide reductase) 06380; (dimethylsulfoxide reductase chain)
21378; (formylmethanofuran dehydrogenase A chain) 21433; (formylmethanofuran dehydrogenase A chain) | PF00384; molybdopterin | ||
|
00139;
nitrate reductase ß chain
03802; (dimethylsulfoxide reductase ß chain) 80599; (formylmethanofuran dehydrogenase B chain) | 00121; ferredoxin 2[4Fe-4S] | PF00037; fer4 | |
|
21435;
(formylmethanofuran dehydrogenase E chain)
80612; (formylmethanofuran dehydrogenase F chain) 21427; (formylmethanofuran dehydrogenase G chain) |
|||
|
00140;
nitrate reductase chain
80581; (formylmethanofuran dehydrogenase C chain) 18609; dimethylsulfoxide reductase chain
| |||
| 21428; (formylmethanofuran dehydrogenase D chain) |
| PDB | scop | BSM | RELI Base |
Header | 
¹ |
|---|---|---|---|---|---|
| 1aa6 | 1aa6 | 1aa6 | 1aa6 | Formate dehydrogenase H (MoIV); Escherichia coli | |
| 1cxs | 1cxs | 1cxs | 1cxs | DMSO reductase (MoVI; oxo); Rhodobacter sphaeroides | MS7MC2A |
| 1cxt | 1cxt | 1cxt | 1cxt | DMSO reductase (MoIV); Rhodobacter sphaeroides | MS7MC2A |
| 1dmr | 1dmr | 1dmr | DMSO reductase (MoVI; dioxo); Rhodobacter capsulatus | 1fdi | 1fdi | 1fdi | Formate dehydrogenase H (MoVI; complex with NO2¯); Escherichia coli |
| 1fdo | 1fdo | 1fdo | 1fdo | Formate dehydrogenase H (MoVI; complex with OH¯); Escherichia coli | |
| 2dmr | 2dmr | 2dmr | DMSO reductase (MoIV; oxo; complex with SO2); Rhodobacter capsulatus | ||
| 3dmr | 3dmr | 3dmr | DMSO reductase (MoVI; dioxo) (pH 7.0); Rhodobacter capsulatus | 4dmr | 4dmr | 4dmr | DMSO reductase (MoIV; oxo; complex with DMSO); Rhodobacter capsulatus |
¹ Macromolecular Structures abstract.
Full text is available to BioMedNet
Members
References
|
Bibliography on structural studies of DMSO reductase family |
(CH3)2S + H2O
