2qrk: Difference between revisions

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-[[Image:2qrk.png|left|200px]]
-{{STRUCTURE_2qrk|  PDB=2qrk  |  SCENE=  }}
+==Crystal Structure of AMP-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae==
+<StructureSection load='2qrk' size='340' side='right'caption='[[2qrk]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2qrk]] 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=2QRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QRK 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]] 1.75&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=2qrk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qrk OCA], [https://pdbe.org/2qrk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qrk RCSB], [https://www.ebi.ac.uk/pdbsum/2qrk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qrk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LYS1_YEAST LYS1_YEAST] Catalyzes the NAD(+)-dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate.
+== 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/qr/2qrk_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=2qrk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Three structures of saccharopine dehydrogenase (l-lysine-forming) (SDH) have been determined in the presence of sulfate, adenosine monophosphate (AMP), and oxalylglycine (OxGly). In the sulfate-bound structure, a sulfate ion binds in a cleft between the two domains of SDH, occupies one of the substrate carboxylate binding sites, and results in partial closure of the active site of the enzyme due to a domain rotation of almost 12 degrees in comparison to the apoenzyme structure. In the second structure, AMP binds to the active site in an area where the NAD+ cofactor is expected to bind. All of the AMP moieties (adenine ring, ribose, and phosphate) interact with specific residues of the enzyme. In the OxGly-bound structure, carboxylates of OxGly interact with arginine residues representative of the manner in which substrate (alpha-ketoglutarate and saccharopine) may bind. The alpha-keto group of OxGly interacts with Lys77 and His96, which are candidates for acid-base catalysis. Analysis of ligand-enzyme interactions, comparative structural analysis, corroboration with kinetic data, and discussion of a ternary complex model are presented in this study.
-===Crystal Structure of AMP-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae===
+Crystal structures of ligand-bound saccharopine dehydrogenase from Saccharomyces cerevisiae.,Andi B, Xu H, Cook PF, West AH Biochemistry. 2007 Nov 6;46(44):12512-21. Epub 2007 Oct 16. PMID:17939687<ref>PMID:17939687</ref>
-{{ABSTRACT_PUBMED_17939687}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2qrk" style="background-color:#fffaf0;"></div>
-[[2qrk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QRK OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:017939687</ref><references group="xtra"/>
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Andi, B.]]
+[[Category: Andi B]]
-[[Category: Cook, P F.]]
+[[Category: Cook PF]]
-[[Category: West, A H.]]
+[[Category: West AH]]
-[[Category: Xu, H.]]
+[[Category: Xu H]]
-[[Category: Alpha-aminoadipate pathway]]
-[[Category: Amino-acid biosynthesis]]
-[[Category: Amp]]
-[[Category: Fungal lysine biosynthesis]]
-[[Category: Nad]]
-[[Category: Oxidoreductase]]
-[[Category: Rossmann fold]]