2q99: Difference between revisions

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-[[Image:2q99.jpg|left|200px]]<br /><applet load="2q99" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2q99, resolution 1.640&Aring;" />
-'''Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cerevisiae'''<br />
-==Overview==
+==Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cerevisiae==
-The 1.64 A structure of the apoenzyme form of saccharopine dehydrogenase, (SDH) from Saccharomyces cerevisiae shows the enzyme to be composed of two, domains with similar dinucleotide binding folds with a deep cleft at the, interface. The structure reveals homology to alanine dehydrogense, despite, low primary sequence similarity. A model of the ternary complex of SDH, NAD, and saccharopine identifies residues Lys77 and Glu122 as potentially, important for substrate binding and/or catalysis, consistent with a proton, shuttle mechanism. Furthermore, the model suggests that a conformational, change is required for catalysis and that residues Lys99 and Asp281 may be, instrumental in mediating this change. Analysis of the crystal structure, in the context of other homologous enzymes from pathogenic fungi and human, sources sheds light into the suitability of SDH as a target for, antimicrobial drug development.
+<StructureSection load='2q99' size='340' side='right'caption='[[2q99]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2q99]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q99 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]] 1.64&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=2q99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q99 OCA], [https://pdbe.org/2q99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q99 RCSB], [https://www.ebi.ac.uk/pdbsum/2q99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q99 ProSAT]</span></td></tr>
+</table>
+== 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/q9/2q99_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2q99 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The 1.64 A structure of the apoenzyme form of saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae shows the enzyme to be composed of two domains with similar dinucleotide binding folds with a deep cleft at the interface. The structure reveals homology to alanine dehydrogenase, despite low primary sequence similarity. A model of the ternary complex of SDH, NAD, and saccharopine identifies residues Lys77 and Glu122 as potentially important for substrate binding and/or catalysis, consistent with a proton shuttle mechanism. Furthermore, the model suggests that a conformational change is required for catalysis and that residues Lys99 and Asp281 may be instrumental in mediating this change. Analysis of the crystal structure in the context of other homologous enzymes from pathogenic fungi and human sources sheds light into the suitability of SDH as a target for antimicrobial drug development.
-==About this Structure==
+Structural studies of the final enzyme in the alpha-aminoadipate pathway-saccharopine dehydrogenase from Saccharomyces cerevisiae.,Burk DL, Hwang J, Kwok E, Marrone L, Goodfellow V, Dmitrienko GI, Berghuis AM J Mol Biol. 2007 Oct 26;373(3):745-54. Epub 2007 Aug 24. PMID:17854830<ref>PMID:17854830</ref>
-Q99 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Active as [http://en.wikipedia.org/wiki/Saccharopine_dehydrogenase_(NAD(+),_L-lysine-forming) Saccharopine dehydrogenase (NAD(+), L-lysine-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.7 1.5.1.7] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q99 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structural Studies of the Final Enzyme in the alpha-Aminoadipate Pathway-Saccharopine Dehydrogenase from Saccharomyces cerevisiae., Burk DL, Hwang J, Kwok E, Marrone L, Goodfellow V, Dmitrienko GI, Berghuis AM, J Mol Biol. 2007 Oct 26;373(3):745-54. Epub 2007 Aug 24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17854830 17854830]
+</div>
+<div class="pdbe-citations 2q99" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Saccharopine dehydrogenase (NAD(+), L-lysine-forming)]]
+[[Category: Berghuis AM]]
-[[Category: Single protein]]
+[[Category: Burk DL]]
-[[Category: Berghuis, A.M.]]
-[[Category: Burk, D.L.]]
-[[Category: alpha-aminoadipate pathway]]
-[[Category: alpha/beta protein]]
-[[Category: dehydrogenase]]
-[[Category: fungal lysine synthesis]]
-[[Category: oxidoreductase]]
-[[Category: rossmann fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 12:22:43 2008''