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PDBsum entry 1eu1
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protein ligands metals links
Oxidoreductase PDB id
1eu1

 

 

 

 

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JSmol PyMol  
Contents
Protein chain
767 a.a. *
Ligands
GLC ×3
SO4
MGD ×2
__O ×2
EPE
Metals
_CD
6MO
Waters ×1039
* Residue conservation analysis
PDB id:
1eu1
Name: Oxidoreductase
Title: The crystal structure of rhodobacter sphaeroides dimethylsulfoxide reductase reveals two distinct molybdenum coordination environments.
Structure: Dimethyl sulfoxide reductase. Chain: a. Synonym: dmso reductase, dmsor. Engineered: yes
Source: Rhodobacter sphaeroides. Organism_taxid: 1063. Expressed in: bacteria. Expression_system_taxid: 2
Resolution:
1.30Å     R-factor:   0.121     R-free:   0.145
Authors: H.K.Li,K.Temple,K.V.Rajagopalan,H.Schindelin
Key ref: H.Schindelin et al. (1996). Crystal structure of DMSO reductase: redox-linked changes in molybdopterin coordination. Science, 272, 1615-1621. PubMed id: 8658134 DOI: 10.1126/science.272.5268.1615
Date:
13-Apr-00     Release date:   02-Aug-00    
Supersedes: 1cxt
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Q57366  (DSTOR_CERSP) -  Dimethyl sulfoxide/trimethylamine N-oxide reductase from Cereibacter sphaeroides
Seq:
Struc: 		 
Seq:
Struc: 		822 a.a.
769 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: E.C.1.7.2.3  - trimethylamine-N-oxide reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: trimethylamine + 2 Fe(III)-[cytochrome c] + H2O = trimethylamine N-oxide + 2 Fe(II)-[cytochrome c] + 3 H+
trimethylamine
 + 2 × Fe(III)-[cytochrome c]
 + H2O
 = trimethylamine N-oxide
 + 2 × Fe(II)-[cytochrome c]
 + 3 × H(+)
      Cofactor: Mo-bis(molybdopterin guanine dinucleotide)
   Enzyme class 2: E.C.1.8.5.3  - respiratory dimethylsulfoxide reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: dimethyl sulfide + a menaquinone + H2O = dimethyl sulfoxide + a menaquinol
dimethyl sulfide
 + 2 × menaquinone
 + H2O
 = dimethyl sulfoxide
 + 2 × menaquinol
      Cofactor: Iron-sulfur; Mo-molybdopterin
Iron-sulfur
 Mo-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

 

 
    reference    
 
 
DOI no: 10.1126/science.272.5268.1615 Science 272:1615-1621 (1996)
PubMed id: 8658134  
 
 
Crystal structure of DMSO reductase: redox-linked changes in molybdopterin coordination.
H.Schindelin, C.Kisker, J.Hilton, K.V.Rajagopalan, D.C.Rees.
 
  ABSTRACT  
 
The molybdoenzyme dimethylsulfoxide (DMSO) reductase contributes to the release of dimethylsulfide, a compound that has been implicated in cloud nucleation and global climate regulation. The crystal structure of DMSO reductase from Rhodobacter sphaeroides reveals a monooxo molybdenum cofactor containing two molybdopterin guanine dinucleotides that asymmetrically coordinate the molybdenum through their dithiolene groups. One of the pterins exhibits different coordination modes to the molybdenum between the oxidized and reduced states, whereas the side chain oxygen of Ser147 coordinates the metal in both states. The change in pterin coordination between the Mo(VI) and Mo(IV) forms suggests a mechanism for substrate binding and reduction by this enzyme. Sequence comparisons of DMSO reductase with a family of bacterial oxotransferases containing molybdopterin guanine dinucleotide indicate a similar polypeptide fold and active site with two molybdopterins within this family.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Mechanistic insight into the reactivity of oxotransferases by novel asymmetric dioxomolybdenum(VI) model complexes.
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19290363 C.A.Bayse (2009).
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19082848 K.I.Chen, A.G.McEwan, and P.V.Bernhardt (2009).
Mediated electrochemistry of dimethyl sulfoxide reductase from Rhodobacter capsulatus.
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Molybdenum and tungsten enzymes: a crystallographic and mechanistic overview.
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19368556 M.Neumann, G.Mittelstädt, C.Iobbi-Nivol, M.Saggu, F.Lendzian, P.Hildebrandt, and S.Leimkühler (2009).
A periplasmic aldehyde oxidoreductase represents the first molybdopterin cytosine dinucleotide cofactor containing molybdo-flavoenzyme from Escherichia coli.
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19890522 R.G.Hadt, V.N.Nemykin, J.G.Olsen, and P.Basu (2009).
Comparative calculation of EPR spectral parameters in [Mo(V)OX4]-, [Mo(V)OX5]2-, and [Mo(V)OX4(H2O)]- complexes.
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19479286 U.Ryde, C.Schulzke, and K.Starke (2009).
Which functional groups of the molybdopterin ligand should be considered when modeling the active sites of the molybdenum and tungsten cofactors? A density functional theory study.
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18535145 G.J.Workun, K.Moquin, R.A.Rothery, and J.H.Weiner (2008).
Evolutionary persistence of the molybdopyranopterin-containing sulfite oxidase protein fold.
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19020675 H.Sugimoto, and H.Tsukube (2008).
Chemical analogues relevant to molybdenum and tungsten enzyme reaction centres toward structural dynamics and reaction diversity.
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18536726 M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, and S.Iwata (2008).
Molecular mechanism of energy conservation in polysulfide respiration.
  Nat Struct Mol Biol, 15, 730-737.
PDB codes: 2vpw 2vpx 2vpy 2vpz
18270755 S.Fukuzumi, and T.Kojima (2008).
Control of redox reactivity of flavin and pterin coenzymes by metal ion coordination and hydrogen bonding.
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18667702 T.Reda, C.M.Plugge, N.J.Abram, and J.Hirst (2008).
Reversible interconversion of carbon dioxide and formate by an electroactive enzyme.
  Proc Natl Acad Sci U S A, 105, 10654-10658.  
18175314 Y.Qiu, R.Zhang, T.A.Binkowski, V.Tereshko, A.Joachimiak, and A.Kossiakoff (2008).
The 1.38 A crystal structure of DmsD protein from Salmonella typhimurium, a proofreading chaperone on the Tat pathway.
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PDB code: 1s9u
18485362 Y.Zhang, and V.N.Gladyshev (2008).
Molybdoproteomes and evolution of molybdenum utilization.
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18021072 E.V.Morozkina, and R.A.Zvyagilskaya (2007).
Nitrate reductases: structure, functions, and effect of stress factors.
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17360611 G.B.Seiffert, G.M.Ullmann, A.Messerschmidt, B.Schink, P.M.Kroneck, and O.Einsle (2007).
Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase.
  Proc Natl Acad Sci U S A, 104, 3073-3077.
PDB code: 2e7z
17392955 G.Lyashenko, G.Saischek, A.Pal, R.Herbst-Irmer, and N.C.Mösch-Zanetti (2007).
Molecular oxygen activation by a molybdenum(IV) monooxo bis(beta-ketiminato) complex.
  Chem Commun (Camb), (), 701-703.  
17361996 G.N.George, K.J.Nelson, H.H.Harris, C.J.Doonan, and K.V.Rajagopalan (2007).
Interaction of product analogues with the active site of rhodobacter sphaeroides dimethyl sulfoxide reductase.
  Inorg Chem, 46, 3097-3104.  
17636351 M.Hofmann (2007).
Density functional theory studies of model complexes for molybdenum-dependent nitrate reductase active sites.
  J Biol Inorg Chem, 12, 989.  
17471372 X.Ma, C.Schulzke, H.G.Schmidt, and M.Noltemeyer (2007).
Structural, electrochemical and oxygen atom transfer properties of a molybdenum selenoether complex [Mo2O4(OC3H6SeC3H6O)2] and its thioether analogue [Mo2O4(OC3H6SC3H6O)2].
  Dalton Trans, (), 1773-1780.  
16234939 A.Thapper, A.Behrens, J.Fryxelius, M.H.Johansson, F.Prestopino, M.Czaun, D.Rehder, and E.Nordlander (2005).
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15716436 J.A.Müller, and S.DasSarma (2005).
Genomic analysis of anaerobic respiration in the archaeon Halobacterium sp. strain NRC-1: dimethyl sulfoxide and trimethylamine N-oxide as terminal electron acceptors.
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15284442 A.Messerschmidt, H.Niessen, D.Abt, O.Einsle, B.Schink, and P.M.Kroneck (2004).
Crystal structure of pyrogallol-phloroglucinol transhydroxylase, an Mo enzyme capable of intermolecular hydroxyl transfer between phenols.
  Proc Natl Acad Sci U S A, 101, 11571-11576.
PDB codes: 1ti2 1ti4 1ti6 1vld 1vle 1vlf
15322772 H.R.Luckarift, H.Dalton, N.D.Sharma, D.R.Boyd, and R.A.Holt (2004).
Isolation and characterisation of bacterial strains containing enantioselective DMSO reductase activity: application to the kinetic resolution of racemic sulfoxides.
  Appl Microbiol Biotechnol, 65, 678-685.  
15311335 J.J.Moura, C.D.Brondino, J.Trincão, and M.J.Romão (2004).
Mo and W bis-MGD enzymes: nitrate reductases and formate dehydrogenases.
  J Biol Inorg Chem, 9, 791-799.  
15306815 J.Kuper, A.Llamas, H.J.Hecht, R.R.Mendel, and G.Schwarz (2004).
Structure of the molybdopterin-bound Cnx1G domain links molybdenum and copper metabolism.
  Nature, 430, 803-806.
PDB codes: 1uux 1uuy
15486691 T.Tomiki, and N.Saitou (2004).
Phylogenetic analysis of proteins associated in the four major energy metabolism systems: photosynthesis, aerobic respiration, denitrification, and sulfur respiration.
  J Mol Evol, 59, 158-176.  
12910261 M.G.Bertero, R.A.Rothery, M.Palak, C.Hou, D.Lim, F.Blasco, J.H.Weiner, and N.C.Strynadka (2003).
Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A.
  Nat Struct Biol, 10, 681-687.
PDB code: 1q16
12948771 M.Jormakka, B.Byrne, and S.Iwata (2003).
Formate dehydrogenase--a versatile enzyme in changing environments.
  Curr Opin Struct Biol, 13, 418-423.  
12067345 C.A.McDevitt, P.Hugenholtz, G.R.Hanson, and A.G.McEwan (2002).
Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes.
  Mol Microbiol, 44, 1575-1587.  
11934270 C.Sandu, and R.Brandsch (2002).
Functional analysis of the Escherichia coli molybdopterin cofactor biosynthesis protein MoeA by site-directed mutagenesis.
  Biol Chem, 383, 319-323.  
12165429 J.Simon (2002).
Enzymology and bioenergetics of respiratory nitrite ammonification.
  FEMS Microbiol Rev, 26, 285-309.  
12114025 R.Hille (2002).
Molybdenum and tungsten in biology.
  Trends Biochem Sci, 27, 360-367.  
11148038 A.F.Bell, X.He, J.P.Ridge, G.R.Hanson, A.G.McEwan, and P.J.Tonge (2001).
Active site heterogeneity in dimethyl sulfoxide reductase from Rhodobacter capsulatus revealed by Raman spectroscopy.
  Biochemistry, 40, 440-448.  
11258926 K.Heffron, C.Léger, R.A.Rothery, J.H.Weiner, and F.A.Armstrong (2001).
Determination of an optimal potential window for catalysis by E. coli dimethyl sulfoxide reductase and hypothesis on the role of Mo(V) in the reaction pathway.
  Biochemistry, 40, 3117-3126.  
11170471 V.V.Pollock, and M.J.Barber (2001).
Kinetic and mechanistic properties of biotin sulfoxide reductase.
  Biochemistry, 40, 1430-1440.  
10747793 C.A.Temple, G.N.George, J.C.Hilton, M.J.George, R.C.Prince, M.J.Barber, and K.V.Rajagopalan (2000).
Structure of the molybdenum site of Rhodobacter sphaeroides biotin sulfoxide reductase.
  Biochemistry, 39, 4046-4052.  
10985771 R.C.Bray, B.Adams, A.T.Smith, B.Bennett, and S.Bailey (2000).
Reversible dissociation of thiolate ligands from molybdenum in an enzyme of the dimethyl sulfoxide reductase family.
  Biochemistry, 39, 11258-11269.
PDB codes: 1e5v 1e60 1e61
11063566 W.T.Lowther, N.Brot, H.Weissbach, and B.W.Matthews (2000).
Structure and mechanism of peptide methionine sulfoxide reductase, an "anti-oxidation" enzyme.
  Biochemistry, 39, 13307-13312.
PDB codes: 1fva 1fvg
10841552 W.T.Lowther, N.Brot, H.Weissbach, J.F.Honek, and B.W.Matthews (2000).
Thiol-disulfide exchange is involved in the catalytic mechanism of peptide methionine sulfoxide reductase.
  Proc Natl Acad Sci U S A, 97, 6463-6468.  
10387097 B.Adams, A.T.Smith, S.Bailey, A.G.McEwan, and R.C.Bray (1999).
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.  
10413473 C.S.Butler, J.M.Charnock, B.Bennett, H.J.Sears, A.J.Reilly, S.J.Ferguson, C.D.Garner, D.J.Lowe, A.J.Thomson, B.C.Berks, and D.J.Richardson (1999).
Models for molybdenum coordination during the catalytic cycle of periplasmic nitrate reductase from Paracoccus denitrificans derived from EPR and EXAFS spectroscopy.
  Biochemistry, 38, 9000-9012.  
10518782 D.Baas, and J.Rétey (1999).
Cloning, sequencing and heterologous expression of pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici.
  Eur J Biochem, 265, 896-901.  
10216869 J.Buc, C.L.Santini, R.Giordani, M.Czjzek, L.F.Wu, and G.Giordano (1999).
Enzymatic and physiological properties of the tungsten-substituted molybdenum TMAO reductase from Escherichia coli.
  Mol Microbiol, 32, 159-168.  
10231485 M.Hensel, A.P.Hinsley, T.Nikolaus, G.Sawers, and B.C.Berks (1999).
The genetic basis of tetrathionate respiration in Salmonella typhimurium.
  Mol Microbiol, 32, 275-287.  
10587462 M.J.Almendra, C.D.Brondino, O.Gavel, A.S.Pereira, P.Tavares, S.Bursakov, R.Duarte, J.Caldeira, J.J.Moura, and I.Moura (1999).
Purification and characterization of a tungsten-containing formate dehydrogenase from Desulfovibrio gigas.
  Biochemistry, 38, 16366-16372.  
10447686 R.U.Meckenstock, R.Krieger, S.Ensign, P.M.Kroneck, and B.Schink (1999).
Acetylene hydratase of Pelobacter acetylenicus. Molecular and spectroscopic properties of the tungsten iron-sulfur enzyme.
  Eur J Biochem, 264, 176-182.  
  9515915 A.Hasona, R.M.Ray, and K.T.Shanmugam (1998).
Physiological and genetic analyses leading to identification of a biochemical role for the moeA (molybdate metabolism) gene product in Escherichia coli.
  J Bacteriol, 180, 1466-1472.  
9585550 A.Magalon, M.Asso, B.Guigliarelli, R.A.Rothery, P.Bertrand, G.Giordano, and F.Blasco (1998).
Molybdenum cofactor properties and [Fe-S] cluster coordination in Escherichia coli nitrate reductase A: investigation by site-directed mutagenesis of the conserved his-50 residue in the NarG subunit.
  Biochemistry, 37, 7363-7370.  
9990727 C.Kisker, H.Schindelin, D.Baas, J.Rétey, R.U.Meckenstock, and P.M.Kroneck (1998).
A structural comparison of molybdenum cofactor-containing enzymes.
  FEMS Microbiol Rev, 22, 503-521.  
9427745 C.L.Santini, B.Ize, A.Chanal, M.Müller, G.Giordano, and L.F.Wu (1998).
A novel sec-independent periplasmic protein translocation pathway in Escherichia coli.
  EMBO J, 17, 101-112.  
9698384 D.M.Luykx, J.A.Duine, and S.de Vries (1998).
Molybdopterin radical in bacterial aldehyde dehydrogenases.
  Biochemistry, 37, 11366-11375.  
9667924 J.McMaster, and J.H.Enemark (1998).
The active sites of molybdenum- and tungsten-containing enzymes.
  Curr Opin Chem Biol, 2, 201-207.  
  9573158 M.Matsuzaki, Y.Kiso, I.Yamamoto, and T.Satoh (1998).
Isolation of a periplasmic molecular chaperone-like protein of Rhodobacter sphaeroides f. sp. denitrificans that is homologous to the dipeptide transport protein DppA of Escherichia coli.
  J Bacteriol, 180, 2718-2722.  
  9791109 N.J.Mouncey, and S.Kaplan (1998).
Redox-dependent gene regulation in Rhodobacter sphaeroides 2.4.1(T): effects on dimethyl sulfoxide reductase (dor) gene expression.
  J Bacteriol, 180, 5612-5618.  
10189201 R.Hille, J.Rétey, U.Bartlewski-Hof, and W.Reichenbecher (1998).
Mechanistic aspects of molybdenum-containing enzymes.
  FEMS Microbiol Rev, 22, 489-501.  
9485360 R.W.Frazee, A.M.Orville, K.B.Dolbeare, H.Yu, D.H.Ohlendorf, and J.D.Lipscomb (1998).
The axial tyrosinate Fe3+ ligand in protocatechuate 3,4-dioxygenase influences substrate binding and product release: evidence for new reaction cycle intermediates.
  Biochemistry, 37, 2131-2144.
PDB code: 3pcd
9521673 S.V.Khangulov, V.N.Gladyshev, G.C.Dismukes, and T.C.Stadtman (1998).
Selenium-containing formate dehydrogenase H from Escherichia coli: a molybdopterin enzyme that catalyzes formate oxidation without oxygen transfer.
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9473631 T.Palmer, I.P.Goodfellow, R.E.Sockett, A.G.McEwan, and D.H.Boxer (1998).
Characterisation of the mob locus from Rhodobacter sphaeroides required for molybdenum cofactor biosynthesis.
  Biochim Biophys Acta, 1395, 135-140.  
9914255 U.Ermler, W.Grabarse, S.Shima, M.Goubeaud, and R.K.Thauer (1998).
Active sites of transition-metal enzymes with a focus on nickel.
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9428520 C.Kisker, H.Schindelin, A.Pacheco, W.A.Wehbi, R.M.Garrett, K.V.Rajagopalan, J.H.Enemark, and D.C.Rees (1997).
Molecular basis of sulfite oxidase deficiency from the structure of sulfite oxidase.
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PDB code: 1sox
9242907 C.Kisker, H.Schindelin, and D.C.Rees (1997).
Molybdenum-cofactor-containing enzymes: structure and mechanism.
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9036855 J.C.Boyington, V.N.Gladyshev, S.V.Khangulov, T.C.Stadtman, and P.D.Sun (1997).
Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster.
  Science, 275, 1305-1308.
PDB codes: 1aa6 1fdi 1fdo
9210484 P.S.Solomon, I.Lane, G.R.Hanson, and A.G.McEwan (1997).
Characterisation of the pterin molybdenum cofactor in dimethylsulfoxide reductase of Rhodobacter capsulatus.
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Cell biology and molecular basis of denitrification.
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The molybdenum formylmethanofuran dehydrogenase operon and the tungsten formylmethanofuran dehydrogenase operon from Methanobacterium thermoautotrophicum. Structures and transcriptional regulation.
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Cloning and sequence analysis of the dimethylsulfoxide reductase structural gene from Rhodobacter capsulatus.
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Novel metal sites in protein structures.
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The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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