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2qrl

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[[Image:2qrl.gif|left|200px]]<br /><applet load="2qrl" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:2qrl.gif|left|200px]]
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caption="2qrl, resolution 1.600&Aring;" />
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'''Crystal Structure of Oxalylglycine-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae'''<br />
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{{Structure
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|PDB= 2qrl |SIZE=350|CAPTION= <scene name='initialview01'>2qrl</scene>, resolution 1.600&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=OGA:N-OXALYOLGLYCINE'>OGA</scene>
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|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]
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|GENE= LYS1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
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}}
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'''Crystal Structure of Oxalylglycine-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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2QRL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with <scene name='pdbligand=OGA:'>OGA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QRL OCA].
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2QRL 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=2QRL OCA].
==Reference==
==Reference==
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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]
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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]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:41:42 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:28:53 2008''

Revision as of 16:28, 20 March 2008

Image:2qrl.gif


PDB ID 2qrl

Drag the structure with the mouse to rotate
, resolution 1.600Å
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 Oxalylglycine-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae


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.

About this Structure

2QRL is a Single protein structure of sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA.

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:17939687

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