2cy0

From Proteopedia

(Difference between revisions)

Current revision

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

Structural highlights

2cy0 is a 2 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

AROE_THET8 Involved in the biosynthesis of the chorismate, which leads to the biosynthesis of aromatic amino acids. Catalyzes the reversible NADPH linked reduction of 3-dehydroshikimate (DHSA) to yield shikimate (SA).[HAMAP-Rule:MF_00222]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bagautdinov B, Kunishima N. Crystal structures of shikimate dehydrogenase AroE from Thermus thermophilus HB8 and its cofactor and substrate complexes: insights into the enzymatic mechanism. J Mol Biol. 2007 Oct 19;373(2):424-38. Epub 2007 Aug 21. PMID:17825835 doi:10.1016/j.jmb.2007.08.017

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2cy0"

Categories: Large Structures | Thermus thermophilus HB8 | Bagautdinov B | Kunishima N

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Shikimate 5-Dehydrogenase (AroE) from Thermus Thermophilus HB8 in complex with NADP==
-<StructureSection load='2cy0' size='340' side='right' caption='[[2cy0]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='2cy0' size='340' side='right'caption='[[2cy0]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2cy0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CY0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CY0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2cy0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CY0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CY0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wxd|1wxd]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AroE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cy0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cy0 OCA], [https://pdbe.org/2cy0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cy0 RCSB], [https://www.ebi.ac.uk/pdbsum/2cy0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cy0 ProSAT], [https://www.topsan.org/Proteins/RSGI/2cy0 TOPSAN]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cy0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cy0 OCA], [http://pdbe.org/2cy0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2cy0 RCSB], [http://www.ebi.ac.uk/pdbsum/2cy0 PDBsum], [http://www.topsan.org/Proteins/RSGI/2cy0 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/AROE_THET8 AROE_THET8]] Involved in the biosynthesis of the chorismate, which leads to the biosynthesis of aromatic amino acids. Catalyzes the reversible NADPH linked reduction of 3-dehydroshikimate (DHSA) to yield shikimate (SA).[HAMAP-Rule:MF_00222]
+[https://www.uniprot.org/uniprot/AROE_THET8 AROE_THET8] Involved in the biosynthesis of the chorismate, which leads to the biosynthesis of aromatic amino acids. Catalyzes the reversible NADPH linked reduction of 3-dehydroshikimate (DHSA) to yield shikimate (SA).[HAMAP-Rule:MF_00222]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cy/2cy0_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cy/2cy0_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2cy0 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 32: / Line 31: @@
 ==See Also==
-*[[Shikimate dehydrogenase|Shikimate dehydrogenase]]
+*[[Shikimate dehydrogenase 3D structures|Shikimate dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Shikimate dehydrogenase]]
+[[Category: Large Structures]]
-[[Category: Thet8]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Bagautdinov, B]]
+[[Category: Bagautdinov B]]
-[[Category: Kunishima, N]]
+[[Category: Kunishima N]]
-[[Category: Structural genomic]]
-[[Category: Cofactor]]
-[[Category: Dimer]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Oxidoreductase]]
-[[Category: Rsgi]]
-[[Category: Shikimate]]

2cy0

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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