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==Crystal structure of autotaxin with orthovanadate bound as a trigonal bipyramidal intermediate analog== | ==Crystal structure of autotaxin with orthovanadate bound as a trigonal bipyramidal intermediate analog== | ||
<StructureSection load='5ijs' size='340' side='right' caption='[[5ijs]], [[Resolution|resolution]] 2.20Å' scene=''> | <StructureSection load='5ijs' size='340' side='right'caption='[[5ijs]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5ijs]] is a 1 chain structure. 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 [ | <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5JK:7ALPHA-HYDROXYCHOLESTEROL'>5JK</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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</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> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/ENPP2_RAT ENPP2_RAT] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 19: | Line 19: | ||
</div> | </div> | ||
<div class="pdbe-citations 5ijs" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5ijs" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Ectonucleotide pyrophosphatase/phosphodiesterase 3D structures|Ectonucleotide pyrophosphatase/phosphodiesterase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Rattus norvegicus]] | ||
[[Category: | [[Category: Hausmann J]] | ||
[[Category: | [[Category: Joosten RP]] | ||
[[Category: | [[Category: Perrakis A]] | ||
Latest revision as of 16:58, 30 August 2023
Crystal structure of autotaxin with orthovanadate bound as a trigonal bipyramidal intermediate analogCrystal structure of autotaxin with orthovanadate bound as a trigonal bipyramidal intermediate analog
Structural highlights
FunctionPublication Abstract from PubMedAutotaxin (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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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