1k2w: Difference between revisions

Latest revision as of 08:49, 16 August 2023

Crystal 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

↑ 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
↑ 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

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OCA

[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

[1]

[2]

@@ Line 3: / Line 3: @@
 <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/"rhodococcus_capsulatus"_molisch_1907 "rhodococcus capsulatus" molisch 1907]. 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>
+<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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/L-iditol_2-dehydrogenase L-iditol 2-dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.14 1.1.1.14] </span></td></tr>
+</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/DHSO_RHOSH DHSO_RHOSH]] Catalyzes the oxidation of D-glucitol (sorbitol) to D-fructose, galactitol to D-tagatose and of L-iditol.
+[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]]
@@ Line 32: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Rhodococcus capsulatus molisch 1907]]
+[[Category: Cereibacter sphaeroides]]
-[[Category: L-iditol 2-dehydrogenase]]
 [[Category: Large Structures]]
-[[Category: Philippsen, A]]
+[[Category: Philippsen A]]
-[[Category: Schirmer, T]]
+[[Category: Schirmer T]]
-[[Category: Stetefeld, J]]
+[[Category: Stetefeld J]]
-[[Category: Enzyme]]
-[[Category: Oxidoreductase]]
-[[Category: Short-chain dehydrogenase]]

1k2w: Difference between revisions

Latest revision as of 08:49, 16 August 2023

Crystal structure of sorbitol dehydrogenase from R. sphaeroides

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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