2qrl

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(New page: 200px<br /><applet load="2qrl" size="350" color="white" frame="true" align="right" spinBox="true" caption="2qrl, resolution 1.600&Aring;" /> '''Crystal Structure o...)
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[[Image:2qrl.gif|left|200px]]<br /><applet load="2qrl" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2qrl, resolution 1.600&Aring;" />
 
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'''Crystal Structure of Oxalylglycine-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae'''<br />
 
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==Overview==
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==Crystal Structure of Oxalylglycine-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae==
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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.
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<StructureSection load='2qrl' size='340' side='right'caption='[[2qrl]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2qrl]] 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=2QRL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QRL FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qrl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qrl OCA], [https://pdbe.org/2qrl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qrl RCSB], [https://www.ebi.ac.uk/pdbsum/2qrl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qrl ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/LYS1_YEAST LYS1_YEAST] Catalyzes the NAD(+)-dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qr/2qrl_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2qrl ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==About this Structure==
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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>
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2QRL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with <scene name='pdbligand=OGA:'>OGA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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=2QRL OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17939687 17939687]
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</div>
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<div class="pdbe-citations 2qrl" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Saccharopine dehydrogenase (NAD(+), L-lysine-forming)]]
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[[Category: Andi B]]
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[[Category: Single protein]]
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[[Category: Cook PF]]
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[[Category: Andi, B.]]
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[[Category: West AH]]
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[[Category: Cook, P.F.]]
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[[Category: Xu H]]
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[[Category: West, A.H.]]
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[[Category: Xu, H.]]
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[[Category: OGA]]
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[[Category: acetylation]]
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[[Category: alpha-aminoadipate pathway]]
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[[Category: amino-acid biosynthesis]]
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[[Category: cytoplasm]]
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[[Category: fungal lysine biosynthesis]]
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[[Category: nad]]
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[[Category: oxalylglycine]]
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[[Category: oxidoreductase]]
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[[Category: rossmann fold]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:57:29 2008''
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Current revision

Crystal Structure of Oxalylglycine-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae

PDB ID 2qrl

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