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New page: '''Unreleased structure''' The entry 3so7 is ON HOLD Authors: Ely, F, Pedroso, M., Gahan, L. R., Ollis, D. L. , Guddat, L. W. , Schenk, G Description: Organophoshatedegrading enzyme (O... |
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The | ==Organophoshatedegrading enzyme (OpdA)-phosphate complex== | ||
<StructureSection load='3so7' size='340' side='right'caption='[[3so7]], [[Resolution|resolution]] 2.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3so7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SO7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SO7 FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | |||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">opdA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</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=3so7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3so7 OCA], [https://pdbe.org/3so7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3so7 RCSB], [https://www.ebi.ac.uk/pdbsum/3so7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3so7 ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
OpdA is a binuclear metalloenzyme that can hydrolyze organophosphate pesticides and nerve agents. In this study the crystal structure of the complex between OpdA and phosphate has been determined to 2.20A resolution. The structure shows the phosphate bound in a tripodal mode to the metal ions whereby two of the oxygen atoms of PO(4) are terminally bound to each metal ion and a third oxygen bridges the two metal ions, thus displacing the muOH in the active site. In silico modelling demonstrates that the phosphate moiety of a reaction product, e.g. diethyl phosphate, may bind in the same orientation, positioning the diethyl groups neatly into the substrate binding pocket close to the metal center. Thus, similar to the binuclear metallohydrolases urease and purple acid phosphatase the tripodal arrangement of PO(4) is interpreted in terms of a role of the muOH as a reaction nucleophile. | |||
Phosphate-bound structure of an organophosphate-degrading enzyme from Agrobacterium radiobacter.,Ely F, Pedroso MM, Gahan LR, Ollis DL, Guddat LW, Schenk G J Inorg Biochem. 2012 Jan;106(1):19-22. Epub 2011 Sep 17. PMID:22112835<ref>PMID:22112835</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3so7" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Phosphotriesterase 3D structures|Phosphotriesterase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Ely, F]] | |||
[[Category: Gahan, L R]] | |||
[[Category: Guddat, L W]] | |||
[[Category: Ollis, D L]] | |||
[[Category: Pedroso, M]] | |||
[[Category: Schenk, G]] | |||
[[Category: Hydrolase]] | |||
[[Category: Opda]] | |||
[[Category: Phosphotriesterase]] | |||
Latest revision as of 11:03, 29 June 2022
Organophoshatedegrading enzyme (OpdA)-phosphate complexOrganophoshatedegrading enzyme (OpdA)-phosphate complex
Structural highlights
Publication Abstract from PubMedOpdA is a binuclear metalloenzyme that can hydrolyze organophosphate pesticides and nerve agents. In this study the crystal structure of the complex between OpdA and phosphate has been determined to 2.20A resolution. The structure shows the phosphate bound in a tripodal mode to the metal ions whereby two of the oxygen atoms of PO(4) are terminally bound to each metal ion and a third oxygen bridges the two metal ions, thus displacing the muOH in the active site. In silico modelling demonstrates that the phosphate moiety of a reaction product, e.g. diethyl phosphate, may bind in the same orientation, positioning the diethyl groups neatly into the substrate binding pocket close to the metal center. Thus, similar to the binuclear metallohydrolases urease and purple acid phosphatase the tripodal arrangement of PO(4) is interpreted in terms of a role of the muOH as a reaction nucleophile. Phosphate-bound structure of an organophosphate-degrading enzyme from Agrobacterium radiobacter.,Ely F, Pedroso MM, Gahan LR, Ollis DL, Guddat LW, Schenk G J Inorg Biochem. 2012 Jan;106(1):19-22. Epub 2011 Sep 17. PMID:22112835[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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