Crystal structures of ligand-bound saccharopine dehydrogenase from Saccharomyces cerevisiae.
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.
Andi
Babak
B
Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, Oklahoma 73019, USA.
Xu
Hengyu
H
Cook
Paul F
PF
West
Ann H
AH
D001665:Binding Sites; D018360:Crystallography, X-Ray; D008024:Ligands; D008239:Lysine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D008954:Models, Biological; D008958:Models, Molecular; D011485:Protein Binding; D012441:Saccharomyces cerevisiae / Q000201:enzymology*; D012443:Saccharopine Dehydrogenases / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism
D008024:Ligands; D012443:Saccharopine Dehydrogenases; D008239:Lysine; C100169:saccharopine