1dms: Difference between revisions

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==STRUCTURE OF DMSO REDUCTASE==
==STRUCTURE OF DMSO REDUCTASE==
<StructureSection load='1dms' size='340' side='right' caption='[[1dms]], [[Resolution|resolution]] 1.88&Aring;' scene=''>
<StructureSection load='1dms' size='340' side='right'caption='[[1dms]], [[Resolution|resolution]] 1.88&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1dms]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DMS FirstGlance]. <br>
<table><tr><td colspan='2'>[[1dms]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DMS FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MM4:MOLYBDENUM+(IV)+OXIDE'>MM4</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene><br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.88&#8491;</td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dms OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dms RCSB], [http://www.ebi.ac.uk/pdbsum/1dms PDBsum]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MO:MOLYBDENUM+(IV)OXIDE'>2MO</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene></td></tr>
<table>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dms OCA], [https://pdbe.org/1dms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dms RCSB], [https://www.ebi.ac.uk/pdbsum/1dms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dms ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DSTOR_RHOCA DSTOR_RHOCA] Catalyzes the reduction of dimethyl sulfoxide (DMSO) and trimethylamine N-oxide (TMAO) to dimethyl sulfide (DMS) and trimethylamine, respectively. The terminal DMSO reductase can also use various sulfoxides and N-oxide compounds as terminal electron acceptor in addition to DMSO and TMAO.<ref>PMID:2001248</ref> <ref>PMID:8856102</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dm/1dms_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dm/1dms_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dms ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The periplasmic dimethyl sulfoxide reductase (DMSOR) from the photosynthetic purple bacterium Rhodobacter capsulatus functions as the terminal electron acceptor in its respiratory chain. The enzyme catalyzes the reduction of highly oxidized substrates like dimethyl sulfoxide to dimethyl sulfide. At a molybdenum redox center, two single electrons are transferred from cytochrome C556 to the substrate dimethyl sulfoxide, generating dimethyl sulfide and (with two protons) water. The enzyme was purified and crystallized in space group P4(1)2(1)2 with unit cell dimensions of a = b = 80.7 A and c = 229.2 A. The crystals diffract beyond 1.8 A with synchrotron radiation. The three-dimensional structure was solved by a combination of multiple isomorphous replacement and molecular replacement techniques. The atomic model was refined to an R-factor of 0.169 for 57,394 independent reflections. The 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 (1541 Da) of the single chain protein (85,033 Da) 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 with its sulfur atoms at distances of 3.5 A and 3.8 A away. It might be involved in electron shuttling from the protein surface to the molybdenum center.
Crystal structure of dimethyl sulfoxide reductase from Rhodobacter capsulatus at 1.88 A resolution.,Schneider F, Lowe J, Huber R, Schindelin H, Kisker C, Knablein J J Mol Biol. 1996 Oct 18;263(1):53-69. PMID:8890912<ref>PMID:8890912</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Rhodobacter capsulatus]]
[[Category: Rhodobacter capsulatus]]
[[Category: Huber, R.]]
[[Category: Huber R]]
[[Category: Kisker, C.]]
[[Category: Kisker C]]
[[Category: Knaeblein, J.]]
[[Category: Knaeblein J]]
[[Category: Loewe, J.]]
[[Category: Loewe J]]
[[Category: Schindelin, H.]]
[[Category: Schindelin H]]
[[Category: Schneider, F.]]
[[Category: Schneider F]]
[[Category: Dmso reductase]]
[[Category: Molydopterin]]
[[Category: Reductase]]

Latest revision as of 09:56, 7 February 2024

STRUCTURE OF DMSO REDUCTASESTRUCTURE OF DMSO REDUCTASE

Structural highlights

1dms is a 1 chain structure with sequence from Rhodobacter capsulatus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.88Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DSTOR_RHOCA Catalyzes the reduction of dimethyl sulfoxide (DMSO) and trimethylamine N-oxide (TMAO) to dimethyl sulfide (DMS) and trimethylamine, respectively. The terminal DMSO reductase can also use various sulfoxides and N-oxide compounds as terminal electron acceptor in addition to DMSO and TMAO.[1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ McEwan AG, Ferguson SJ, Jackson JB. Purification and properties of dimethyl sulphoxide reductase from Rhodobacter capsulatus. A periplasmic molybdoenzyme. Biochem J. 1991 Feb 15;274 ( Pt 1):305-7. PMID:2001248
  2. ↑ Shaw AL, Hanson GR, McEwan AG. Cloning and sequence analysis of the dimethylsulfoxide reductase structural gene from Rhodobacter capsulatus. Biochim Biophys Acta. 1996 Sep 30;1276(3):176-80. PMID:8856102

1dms, resolution 1.88Å

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