5ijs: Difference between revisions

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OCA

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-'''Unreleased structure'''
-The entry 5ijs is ON HOLD
+==Crystal structure of autotaxin with orthovanadate bound as a trigonal bipyramidal intermediate analog==
+<StructureSection load='5ijs' size='340' side='right'caption='[[5ijs]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5ijs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IJS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IJS FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5JK:7ALPHA-HYDROXYCHOLESTEROL'>5JK</scene>, <scene name='pdbligand=6BR:THREONINEVANADATE'>6BR</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5ijs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ijs OCA], [https://pdbe.org/5ijs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ijs RCSB], [https://www.ebi.ac.uk/pdbsum/5ijs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ijs ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ENPP2_RAT ENPP2_RAT]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Autotaxin (ATX) is a secreted phosphodiesterase that produces the signalling lipid lysophosphatidic acid (LPA). The bimetallic active site of ATX is structurally related to the alkaline phosphatase superfamily. Here, we present a new crystal structure of ATX in complex with orthovanadate (ATX-VO5), which binds the Ogamma nucleophile of Thr209 and adopts a trigonal bipyramidal conformation, following the nucleophile attack onto the substrate. We have now a portfolio of ATX structures we discuss as intermediates of the catalytic mechanism: the new ATX-VO5 structure; a unique structure where the nucleophile Thr209 is phosphorylated (ATX-pThr). Comparing these to a complex with the LPA product (ATX-LPA) and with a complex with a phosphate ion (ATX-PO4), that represent the Michaelis complex of the reaction, we observe movements of Thr209, changes in the relative displacement of the zinc ions, and a water molecule that likely fulfils the second nucleophilic attack. We propose that ATX follows the associative two-step in-line displacement mechanism.
-Authors: Hausmann, J., Joosten, R.P., Perrakis, A.
+Structural snapshots of the catalytic cycle of the phosphodiesterase Autotaxin.,Hausmann J, Keune WJ, Hipgrave Ederveen AL, van Zeijl L, Joosten RP, Perrakis A J Struct Biol. 2016 Jun 4. pii: S1047-8477(16)30108-3. doi:, 10.1016/j.jsb.2016.06.002. PMID:27268273<ref>PMID:27268273</ref>
-Description: crystal structure of autotaxin with bound orthovanadate
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Hausmann, J]]
+<div class="pdbe-citations 5ijs" style="background-color:#fffaf0;"></div>
-[[Category: Joosten, R.P]]
-[[Category: Perrakis, A]]
+==See Also==
+*[[Ectonucleotide pyrophosphatase/phosphodiesterase 3D structures|Ectonucleotide pyrophosphatase/phosphodiesterase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Rattus norvegicus]]
+[[Category: Hausmann J]]
+[[Category: Joosten RP]]
+[[Category: Perrakis A]]