2qrk: Difference between revisions

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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 with as ligand. Active as Saccharopine dehydrogenase (NAD(+), L-lysine-forming), with EC number 1.5.1.7 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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 ==Overview==
-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.
+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 Structure==
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 ==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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17939687 17939687]
+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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17939687 17939687]
 [[Category: Saccharomyces cerevisiae]]
 [[Category: Saccharopine dehydrogenase (NAD(+), L-lysine-forming)]]
 [[Category: Single protein]]
 [[Category: Andi, B.]]
-[[Category: Cook, P.F.]]
+[[Category: Cook, P F.]]
-[[Category: West, A.H.]]
+[[Category: West, A H.]]
 [[Category: Xu, H.]]
 [[Category: AMP]]
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 [[Category: rossmann fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:57:24 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:41:42 2008''