2dx7: Difference between revisions

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-{{Seed}}
-[[Image:2dx7.png|left|200px]]
-<!--
+==Crystal structure of Pyrococcus horikoshii OT3 aspartate racemase complex with citric acid==
-The line below this paragraph, containing "STRUCTURE_2dx7", creates the "Structure Box" on the page.
+<StructureSection load='2dx7' size='340' side='right'caption='[[2dx7]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2dx7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DX7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DX7 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene></td></tr>
-{{STRUCTURE_2dx7|  PDB=2dx7  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dx7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dx7 OCA], [https://pdbe.org/2dx7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dx7 RCSB], [https://www.ebi.ac.uk/pdbsum/2dx7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dx7 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RACD_PYRHO RACD_PYRHO]
+== 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/dx/2dx7_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2dx7 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Pyrococcus horikoshii OT3 aspartate racemase (PhAspR) catalyzes the interconversion between L- and D-aspartate. The X-ray structure of PhAspR revealed a pseudo mirror-symmetric distribution of the residues around its active site, which is very reasonable for its chiral substrates, L-aspartate and D-aspartate. In this study, we have determined the crystal structure of an inactive mutant PhAspR complexed with a citric acid (Cit) at a resolution of 2.0 A. Cit contains the substrate analogue moieties of both L- and D-aspartate and exhibits a low competitive inhibition activity against PhAspR. In the structure, Cit binds to the catalytic site of PhAspR, which induced the conformational change to close the active site. The distance between the thiolates was estimated to be 7.4 A, representing a catalytic state and the substrate binding modes of PhAspR. Two conserved basic residues, Arg48 and Lys164, seem to be indispensable for PhAspR activity. Arg48 is thought to be responsible for recognizing carboxyl groups of the substrates L-/D-aspartates and stabilizing a reaction intermediate, and Lys164 is responsible for stabilizing a closed state structure. In this structure, the L-aspartate moiety of Cit is likely to take the substrate position of the PhAspR-substrate complex, which is very similar to that of Glutamate racemase. There is also another possibility that the two substrate analogue moieties of the bound Cit reflect the binding modes of both L- and D-aspartates. Based on the PhAspR-Cit complex structure, the reaction mechanism of aspartate racemase was elucidated.
-===Crystal structure of Pyrococcus horikoshii OT3 aspartate racemase complex with citric acid===
+Structure of aspartate racemase complexed with a dual substrate analogue, citric acid, and implications for the reaction mechanism.,Ohtaki A, Nakano Y, Iizuka R, Arakawa T, Yamada K, Odaka M, Yohda M Proteins. 2008 Mar;70(4):1167-74. PMID:17847084<ref>PMID:17847084</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17847084}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2dx7" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17847084 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17847084}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-DX7 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DX7 OCA].
+[[Category: Pyrococcus horikoshii OT3]]
+[[Category: Arakawa T]]
-==Reference==
+[[Category: Iizuka R]]
-Structure of aspartate racemase complexed with a dual substrate analogue, citric acid, and implications for the reaction mechanism., Ohtaki A, Nakano Y, Iizuka R, Arakawa T, Yamada K, Odaka M, Yohda M, Proteins. 2008 Mar;70(4):1167-74. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17847084 17847084]
+[[Category: Odaka M]]
-[[Category: Aspartate racemase]]
+[[Category: Ohtaki A]]
-[[Category: Pyrococcus horikoshii ot3]]
+[[Category: Yohda M]]
-[[Category: Arakawa, T.]]
-[[Category: Iizuka, R.]]
-[[Category: Odaka, M.]]
-[[Category: Ohtaki, A.]]
-[[Category: Yohda, M.]]
-[[Category: Aspartate racemase]]
-[[Category: Isomerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan  7 08:24:55 2009''