2qrk
Crystal Structure of AMP-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae
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| , resolution 1.750Å | |||||||
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| 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 | ||||||
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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