1k2w: Difference between revisions

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-[[Image:1k2w.jpg|left|200px]]<br /><applet load="1k2w" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1k2w, resolution 2.4&Aring;" />
-'''Crystal structure of sorbitol dehydrogenase from R. sphaeroides'''<br />
-==Overview==
+==Crystal structure of sorbitol dehydrogenase from R. sphaeroides==
-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.
+<StructureSection load='1k2w' size='340' side='right'caption='[[1k2w]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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>
+</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.
-==About this Structure==
+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>
-K2W is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Active as [http://en.wikipedia.org/wiki/L-iditol_2-dehydrogenase L-iditol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.14 1.1.1.14] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1K2W OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15805591 15805591]
+</div>
-[[Category: L-iditol 2-dehydrogenase]]
+<div class="pdbe-citations 1k2w" style="background-color:#fffaf0;"></div>
-[[Category: Rhodobacter sphaeroides]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Philippsen, A.]]
+__TOC__
-[[Category: Schirmer, T.]]
+</StructureSection>
-[[Category: Stetefeld, J.]]
+[[Category: Cereibacter sphaeroides]]
-[[Category: enzyme]]
+[[Category: Large Structures]]
-[[Category: short-chain dehydrogenase]]
+[[Category: Philippsen A]]
+[[Category: Schirmer T]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:48:26 2007''
+[[Category: Stetefeld J]]