3don: Difference between revisions

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 <StructureSection load='3don' size='340' side='right'caption='[[3don]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3don]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staeq Staeq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DON FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3don]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_epidermidis_RP62A Staphylococcus epidermidis RP62A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DON FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3doo|3doo]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aroE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176279 STAEQ])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] </span></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=3don FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3don OCA], [https://pdbe.org/3don PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3don RCSB], [https://www.ebi.ac.uk/pdbsum/3don PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3don ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/AROE_STAEQ AROE_STAEQ]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 20: / Line 20: @@
 </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=3don ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Shikimate dehydrogenase (SDH) catalyzes the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway. In this study, we determined the kinetic properties and crystal structures of Staphylococcus epidermidis SDH (SeSDH) both in its ligand-free form and in complex with shikimate. SeSDH has a k(cat) of 22.8 s(-1) and a K(m) of 73 mum towards shikimate, and a K(m) of 100 microM towards NADP. The overall folding of SeSDH comprises the N-terminal alpha/beta domain for substrate binding and the C-terminal Rossmann fold for NADP binding. The active site is within a large groove between the two domains. Residue Tyr211, normally regarded as important for substrate binding, does not interact with shikimate in the binary SeSDH-shikimate complex structure. However, the Y211F mutation leads to a significant decrease in k(cat) and a minor increase in the K(m) for shikimate. The results indicate that the main function of Tyr211 may be to stabilize the catalytic intermediate during catalysis. The NADP-binding domain of SeSDH is less conserved. The usually long helix specifically recognizing the adenine ribose phosphate is substituted with a short 3(10) helix in the NADP-binding domain. Moreover, the interdomain angle of SeSDH is the widest among all known SDH structures, indicating an inactive 'open' state of the SeSDH structure. Thus, a 'closing' process might occur upon NADP binding to bring the cofactor close to the substrate for catalysis.
-X-ray crystallographic and enzymatic analyses of shikimate dehydrogenase from Staphylococcus epidermidis.,Han C, Hu T, Wu D, Qu S, Zhou J, Ding J, Shen X, Qu D, Jiang H FEBS J. 2009 Feb;276(4):1125-39. PMID:19215302<ref>PMID:19215302</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3don" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Shikimate dehydrogenase|Shikimate dehydrogenase]]
+*[[Shikimate dehydrogenase 3D structures|Shikimate dehydrogenase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Shikimate dehydrogenase]]
+[[Category: Staphylococcus epidermidis RP62A]]
-[[Category: Staeq]]
+[[Category: Han C]]
-[[Category: Han, C]]
+[[Category: Hu T]]
-[[Category: Hu, T]]
+[[Category: Jiang H]]
-[[Category: Jiang, H]]
+[[Category: Qu D]]
-[[Category: Qu, D]]
+[[Category: Shen X]]
-[[Category: Shen, X]]
+[[Category: Wu D]]
-[[Category: Wu, D]]
+[[Category: Zhou J]]
-[[Category: Zhou, J]]
-[[Category: Alpha-beta structure]]
-[[Category: Amino-acid biosynthesis]]
-[[Category: Aromatic amino acid biosynthesis]]
-[[Category: Nadp]]
-[[Category: Oxidoreductase]]
-[[Category: Rossmann fold]]