2QRK

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

Summary for 2QRK

• Entry DOI: 10.2210/pdb2qrk/pdb
• Related: 2Q99
• Descriptor: Saccharopine dehydrogenase [NAD+, L-lysine-forming, ADENOSINE MONOPHOSPHATE (3 entities in total)
• Functional Keywords: amp, rossmann fold, alpha-aminoadipate pathway, fungal lysine biosynthesis, acetylation, amino-acid biosynthesis, cytoplasm, nad, oxidoreductase
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Cellular location: Cytoplasm : P38998
• Total number of polymer chains: 1
• Total formula weight: 44404.69

Authors

Andi, B.,Xu, H.,Cook, P.F.,West, A.H. (deposition date: 2007-07-28, release date: 2007-10-30, Last modification date: 2023-08-30)

Primary citation

Andi, B.,Xu, H.,Cook, P.F.,West, A.H.
Crystal Structures of Ligand-Bound Saccharopine Dehydrogenase from Saccharomyces cerevisiae
Biochemistry, 46:12512-12521, 2007

PubMed Abstract: 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.

PubMed: 17939687
DOI: 10.1021/bi701428m

Experimental method

X-RAY DIFFRACTION (1.75 Å)