1k2w: Difference between revisions

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[[Image:1k2w.png|left|200px]]


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==Crystal structure of sorbitol dehydrogenase from R. sphaeroides==
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<StructureSection load='1k2w' size='340' side='right'caption='[[1k2w]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1k2w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides Cereibacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K2W FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1k2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k2w OCA], [https://pdbe.org/1k2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k2w RCSB], [https://www.ebi.ac.uk/pdbsum/1k2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k2w ProSAT]</span></td></tr>
{{STRUCTURE_1k2w|  PDB=1k2w  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/SDH_CERSP SDH_CERSP] Catalyzes the oxidation of D-sorbitol (D-glucitol) to D-fructose. Can also catalyze the oxidation of galactitol to D-tagatose and the oxidation of L-iditol, with lower efficiency.<ref>PMID:7551049</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k2/1k2w_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </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/main_output.php?pdb_ID=1k2w ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Recombinant sorbitol dehydrogenase (SDH) from Rhodobacter sphaeroides has been crystallized in the absence of the cofactor NAD(H) and its structure determined to 2.4 A resolution using molecular replacement (refined R and R free factors of 18.8 and 23.8%, respectively). As expected from the sequence and shown by the conserved fold, SDH can be assigned to the short-chain dehydrogenase/reductase protein family. The cofactor NAD and the substrate sorbitol have been modelled into the structure and the active-site architecture, which displays the highly conserved catalytic tetrad of Asn-Ser-Tyr-Lys residues, is discussed in relation to the enzyme mechanism. This is the first structure of a bacterial SDH belonging to the SDR family.


===Crystal structure of sorbitol dehydrogenase from R. sphaeroides===
Structure of zinc-independent sorbitol dehydrogenase from Rhodobacter sphaeroides at 2.4 A resolution.,Philippsen A, Schirmer T, Stein MA, Giffhorn F, Stetefeld J Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):374-9. Epub 2005, Mar 24. PMID:15805591<ref>PMID:15805591</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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(as it appears on PubMed at http://www.pubmed.gov), where 15805591 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_15805591}}
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</StructureSection>
==About this Structure==
[[Category: Cereibacter sphaeroides]]
1K2W is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K2W OCA].
[[Category: Large Structures]]
 
[[Category: Philippsen A]]
==Reference==
[[Category: Schirmer T]]
<ref group="xtra">PMID:15805591</ref><references group="xtra"/>
[[Category: Stetefeld J]]
[[Category: L-iditol 2-dehydrogenase]]
[[Category: Rhodobacter sphaeroides]]
[[Category: Philippsen, A.]]
[[Category: Schirmer, T.]]
[[Category: Stetefeld, J.]]
[[Category: Enzyme]]
[[Category: Short-chain dehydrogenase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:40:08 2009''

Latest revision as of 11:49, 16 August 2023

Crystal structure of sorbitol dehydrogenase from R. sphaeroidesCrystal structure of sorbitol dehydrogenase from R. sphaeroides

Structural highlights

1k2w is a 2 chain structure with sequence from Cereibacter sphaeroides. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SDH_CERSP Catalyzes the oxidation of D-sorbitol (D-glucitol) to D-fructose. Can also catalyze the oxidation of galactitol to D-tagatose and the oxidation of L-iditol, with lower efficiency.[1]

Evolutionary Conservation

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

Publication Abstract from PubMed

Recombinant sorbitol dehydrogenase (SDH) from Rhodobacter sphaeroides has been crystallized in the absence of the cofactor NAD(H) and its structure determined to 2.4 A resolution using molecular replacement (refined R and R free factors of 18.8 and 23.8%, respectively). As expected from the sequence and shown by the conserved fold, SDH can be assigned to the short-chain dehydrogenase/reductase protein family. The cofactor NAD and the substrate sorbitol have been modelled into the structure and the active-site architecture, which displays the highly conserved catalytic tetrad of Asn-Ser-Tyr-Lys residues, is discussed in relation to the enzyme mechanism. This is the first structure of a bacterial SDH belonging to the SDR family.

Structure of zinc-independent sorbitol dehydrogenase from Rhodobacter sphaeroides at 2.4 A resolution.,Philippsen A, Schirmer T, Stein MA, Giffhorn F, Stetefeld J Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):374-9. Epub 2005, Mar 24. PMID:15805591[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Schauder S, Schneider KH, Giffhorn F. Polyol metabolism of Rhodobacter sphaeroides: biochemical characterization of a short-chain sorbitol dehydrogenase. Microbiology (Reading). 1995 Aug;141 ( Pt 8):1857-1863. PMID:7551049 doi:10.1099/13500872-141-8-1857
  2. ↑ Philippsen A, Schirmer T, Stein MA, Giffhorn F, Stetefeld J. Structure of zinc-independent sorbitol dehydrogenase from Rhodobacter sphaeroides at 2.4 A resolution. Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):374-9. Epub 2005, Mar 24. PMID:15805591 doi:10.1107/S0907444904034390

1k2w, resolution 2.40Å

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