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| | <StructureSection load='2qrl' size='340' side='right'caption='[[2qrl]], [[Resolution|resolution]] 1.60Å' scene=''> | | <StructureSection load='2qrl' size='340' side='right'caption='[[2qrl]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2qrl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. 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> | + | <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> |
| - | </td></tr><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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2q99|2q99]]</div></td></tr>
| + | <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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LYS1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Saccharopine_dehydrogenase_(NAD(+),_L-lysine-forming) Saccharopine dehydrogenase (NAD(+), L-lysine-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.7 1.5.1.7] </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=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> | | <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> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/LYS1_YEAST LYS1_YEAST]] Catalyzes the NAD(+)-dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate.
| + | [https://www.uniprot.org/uniprot/LYS1_YEAST LYS1_YEAST] Catalyzes the NAD(+)-dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 18824]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Andi, B]] | + | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Cook, P F]] | + | [[Category: Andi B]] |
| - | [[Category: West, A H]] | + | [[Category: Cook PF]] |
| - | [[Category: Xu, H]] | + | [[Category: West AH]] |
| - | [[Category: Acetylation]] | + | [[Category: Xu H]] |
| - | [[Category: Alpha-aminoadipate pathway]]
| + | |
| - | [[Category: Amino-acid biosynthesis]]
| + | |
| - | [[Category: Cytoplasm]]
| + | |
| - | [[Category: Fungal lysine biosynthesis]]
| + | |
| - | [[Category: Nad]]
| + | |
| - | [[Category: Oxalylglycine]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| Structural highlights
Function
LYS1_YEAST Catalyzes the NAD(+)-dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate.
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
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 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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Andi B, Xu H, Cook PF, West AH. Crystal structures of ligand-bound saccharopine dehydrogenase from Saccharomyces cerevisiae. Biochemistry. 2007 Nov 6;46(44):12512-21. Epub 2007 Oct 16. PMID:17939687 doi:10.1021/bi701428m
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