2ev9: Difference between revisions

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Revision as of 17:44, 20 March 2008

File:2ev9.gif

, resolution 1.90Å

Ligands:

, and

Gene:

AroE (Thermus thermophilus)

Activity:

Shikimate dehydrogenase, with EC number 1.1.1.25

Coordinates:

save as pdb, mmCIF, xml

Crystal Structure of Shikimate 5-Dehydrogenase (AroE) from Thermus Thermophilus HB8 in complex with NADP(H) and shikimate

OverviewOverview

Shikimate dehydrogenase (EC 1.1.1.25) catalyses the fourth step of the shikimate pathway which is required for the synthesis of the aromatic amino acids and other aromatic compounds in bacteria, microbial eukaryotes, and plants. The crystal structures of the shikimate dehydrogenase AroE from Thermus thermophilus HB8 in its ligand-free form, binary complexes with cofactor NADP+ or substrate shikimate, and the ternary complex with both NADP(H) and shikimate were determined by X-ray diffraction method at atomic resolutions. The crystals are nearly isomorphous with the asymmetric unit containing a dimer, each subunit of which has a bi-domain structure of compact alpha/beta sandwich folds. The two subunits of the enzyme display asymmetry in the crystals due to different relative orientations between the N- and C-terminal domains resulting in a slightly different closure of the interdomain clefts. NADP(H) is bound to the more closed form only. This closed conformation with apparent higher affinity to the cofactor is also observed in the unliganded crystal form, indicating that the NADP(H) binding to TtAroE may follow the selection mode where the cofactor binds to the subunit that happens to be in the closed conformation in solution. Crystal structures of the closed subunits with and without NADP(H) show no significant structural difference, suggesting that the cofactor binding to the closed subunit corresponds to the lock-and-key model in TtAroE. On the other hand, shikimate binds to both open and closed subunit conformers of both apo and NADP(H)-liganded holo enzyme forms. The ternary complex TtAroE:NADP(H):shikimate allows unambiguous visualization of the SDH permitting elucidation of the roles of conserved residues Lys64 and Asp100 in the hydride ion transfer between NADP(H) and shikimate.

About this StructureAbout this Structure

2EV9 is a Single protein structure of sequence from Thermus thermophilus. Full crystallographic information is available from OCA.

ReferenceReference

Crystal structures of shikimate dehydrogenase AroE from Thermus thermophilus HB8 and its cofactor and substrate complexes: insights into the enzymatic mechanism., Bagautdinov B, Kunishima N, J Mol Biol. 2007 Oct 19;373(2):424-38. Epub 2007 Aug 21. PMID:17825835

Page seeded by OCA on Thu Mar 20 16:44:47 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2ev9.gif|left|200px]]<br /><applet load="2ev9" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:2ev9.gif|left|200px]]
-caption="2ev9, resolution 1.90&Aring;" />
-'''Crystal Structure of Shikimate 5-Dehydrogenase (AroE) from Thermus Thermophilus HB8 in complex with NADP(H) and shikimate'''<br />
+ {{Structure
+|PDB= 2ev9 |SIZE=350|CAPTION= <scene name='initialview01'>2ev9</scene>, resolution 1.90&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SKM:(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC+ACID'>SKM</scene> and <scene name='pdbligand=NAP:NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE'>NAP</scene>
+|ACTIVITY= [http://en.wikipedia.org/wiki/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25]
+|GENE= AroE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])
+}}
+'''Crystal Structure of Shikimate 5-Dehydrogenase (AroE) from Thermus Thermophilus HB8 in complex with NADP(H) and shikimate'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-EV9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=SKM:'>SKM</scene> and <scene name='pdbligand=NAP:'>NAP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EV9 OCA].
+EV9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EV9 OCA].
 ==Reference==
-Crystal structures of shikimate dehydrogenase AroE from Thermus thermophilus HB8 and its cofactor and substrate complexes: insights into the enzymatic mechanism., Bagautdinov B, Kunishima N, J Mol Biol. 2007 Oct 19;373(2):424-38. Epub 2007 Aug 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17825835 17825835]
+Crystal structures of shikimate dehydrogenase AroE from Thermus thermophilus HB8 and its cofactor and substrate complexes: insights into the enzymatic mechanism., Bagautdinov B, Kunishima N, J Mol Biol. 2007 Oct 19;373(2):424-38. Epub 2007 Aug 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17825835 17825835]
 [[Category: Shikimate dehydrogenase]]
 [[Category: Single protein]]
@@ Line 22: / Line 31: @@
 [[Category: cofactor]]
 [[Category: dimer]]
-[[Category: national project on protein structural and functional analyses]]
+[[Category: national project on protein structural and functional analyse]]
 [[Category: nppsfa]]
 [[Category: oxidoreductase]]
@@ Line 28: / Line 37: @@
 [[Category: rsgi]]
 [[Category: shikimate]]
-[[Category: structural genomics]]
+[[Category: structural genomic]]
 [[Category: substrate]]
 [[Category: x-ray diffraction]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:14:52 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:44:47 2008''