2qrk: Difference between revisions
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[[Image:2qrk.gif|left|200px]] | [[Image:2qrk.gif|left|200px]] | ||
'''Crystal Structure of AMP-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae''' | {{Structure | ||
|PDB= 2qrk |SIZE=350|CAPTION= <scene name='initialview01'>2qrk</scene>, resolution 1.750Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=AMP:ADENOSINE MONOPHOSPHATE'>AMP</scene> | |||
|ACTIVITY= [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] | |||
|GENE= LYS1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]) | |||
}} | |||
'''Crystal Structure of AMP-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2QRK is a [ | 2QRK is a [[Single protein]] structure of 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]. | ||
==Reference== | ==Reference== | ||
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:// | 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://www.ncbi.nlm.nih.gov/pubmed/17939687 17939687] | ||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Saccharopine dehydrogenase (NAD(+), L-lysine-forming)]] | [[Category: Saccharopine dehydrogenase (NAD(+), L-lysine-forming)]] | ||
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[[Category: rossmann fold]] | [[Category: rossmann fold]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:28:51 2008'' | ||
Revision as of 19:28, 20 March 2008
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| , resolution 1.750Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | LYS1 (Saccharomyces cerevisiae) | ||||||
| Activity: | Saccharopine dehydrogenase (NAD(+), L-lysine-forming), with EC number 1.5.1.7 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of AMP-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae
OverviewOverview
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.
About this StructureAbout this Structure
2QRK is a Single protein structure of sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA.
ReferenceReference
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
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