2hk8: Difference between revisions

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-[[Image:2hk8.jpg|left|200px]]
- {{Structure
+==Crystal structure of shikimate dehydrogenase from aquifex aeolicus at 2.35 angstrom resolution==
-|PDB= 2hk8 |SIZE=350|CAPTION= <scene name='initialview01'>2hk8</scene>, resolution 2.35&Aring;
+<StructureSection load='2hk8' size='340' side='right'caption='[[2hk8]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<table><tr><td colspan='2'>[[2hk8]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HK8 FirstGlance]. <br>
-|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]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35&#8491;</td></tr>
-|GENE= aroE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hk8 OCA], [https://pdbe.org/2hk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hk8 RCSB], [https://www.ebi.ac.uk/pdbsum/2hk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hk8 ProSAT]</span></td></tr>
-}}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AROE_AQUAE AROE_AQUAE]
+== 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/hk/2hk8_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/main_output.php?pdb_ID=2hk8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The shikimate biosynthetic pathway is essential to microorganisms, plants, and parasites but absent from mammals. Therefore, shikimate dehydrogenase (SD) and other enzymes in the pathway are attractive targets for developing nontoxic antimicrobial agents, herbicides, and antiparasite drugs. SD catalyzes the fourth reaction in the pathway, the nicotinamide adenine dinucleotide phosphate- (NADP-) dependent reduction of 3-dehydroshikimic acid to shikimic acid (SA), as well as its reverse, by the transfer of a hydride. Previous structural studies reveal that the enzyme exists in two major conformations, an open and a closed form. For the reaction to occur, it is believed that the catalytic complex assumes the closed conformation. Nonetheless, the only structure containing both SA and NADP+ exhibits an open conformation (PDB entry 2EV9). Here, we present two crystal structures of Aquifex aeolicus SD, including a ternary complex with both SA and NADP+, which assumes the closed conformation and therefore contains a catalytically competent active site. On the basis of preexisting and novel structural and biochemical data, a catalytic mechanism is proposed.
-'''Crystal structure of shikimate dehydrogenase from aquifex aeolicus at 2.35 angstrom resolution'''
+Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism.,Gan J, Wu Y, Prabakaran P, Gu Y, Li Y, Andrykovitch M, Liu H, Gong Y, Yan H, Ji X Biochemistry. 2007 Aug 21;46(33):9513-22. Epub 2007 Jul 25. PMID:17649975<ref>PMID:17649975</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2hk8" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The shikimate biosynthetic pathway is essential to microorganisms, plants, and parasites but absent from mammals. Therefore, shikimate dehydrogenase (SD) and other enzymes in the pathway are attractive targets for developing nontoxic antimicrobial agents, herbicides, and antiparasite drugs. SD catalyzes the fourth reaction in the pathway, the nicotinamide adenine dinucleotide phosphate- (NADP-) dependent reduction of 3-dehydroshikimic acid to shikimic acid (SA), as well as its reverse, by the transfer of a hydride. Previous structural studies reveal that the enzyme exists in two major conformations, an open and a closed form. For the reaction to occur, it is believed that the catalytic complex assumes the closed conformation. Nonetheless, the only structure containing both SA and NADP+ exhibits an open conformation (PDB entry 2EV9). Here, we present two crystal structures of Aquifex aeolicus SD, including a ternary complex with both SA and NADP+, which assumes the closed conformation and therefore contains a catalytically competent active site. On the basis of preexisting and novel structural and biochemical data, a catalytic mechanism is proposed.
+*[[Shikimate dehydrogenase 3D structures|Shikimate dehydrogenase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-HK8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HK8 OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism., Gan J, Wu Y, Prabakaran P, Gu Y, Li Y, Andrykovitch M, Liu H, Gong Y, Yan H, Ji X, Biochemistry. 2007 Aug 21;46(33):9513-22. Epub 2007 Jul 25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17649975 17649975]
 [[Category: Aquifex aeolicus]]
-[[Category: Shikimate dehydrogenase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Andrykovitch M]]
-[[Category: Andrykovitch, M.]]
+[[Category: Gan JH]]
-[[Category: Gan, J H.]]
+[[Category: Gu YJ]]
-[[Category: Gu, Y J.]]
+[[Category: Ji X]]
-[[Category: Ji, X.]]
+[[Category: Li Y]]
-[[Category: Li, Y.]]
+[[Category: Liu HH]]
-[[Category: Liu, H H.]]
+[[Category: Prabakaran P]]
-[[Category: Prabakaran, P.]]
+[[Category: Yan H]]
-[[Category: Yan, H.]]
-[[Category: drug design]]
-[[Category: oxidoreductase]]
-[[Category: shikimate dehydrogenase]]
-[[Category: shikimate pathway]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:18:13 2008''