3t00

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Current revision (13:13, 14 March 2024) (edit) (undo)
 
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<StructureSection load='3t00' size='340' side='right'caption='[[3t00]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='3t00' size='340' side='right'caption='[[3t00]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3t00]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ensifer_meliloti Ensifer meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T00 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T00 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3t00]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_meliloti_1021 Sinorhizobium meliloti 1021]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T00 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T00 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3szy|3szy]], [[3szz|3szz]], [[3t01|3t01]], [[3t02|3t02]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">phnA, RB0978, SM_b21538 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266834 Ensifer meliloti])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nucleotide_diphosphatase Nucleotide diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.9 3.6.1.9] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3t00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t00 OCA], [https://pdbe.org/3t00 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t00 RCSB], [https://www.ebi.ac.uk/pdbsum/3t00 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t00 ProSAT]</span></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=3t00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t00 OCA], [https://pdbe.org/3t00 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t00 RCSB], [https://www.ebi.ac.uk/pdbsum/3t00 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t00 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q92UV8_RHIME Q92UV8_RHIME]
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Bacteria have evolved pathways to metabolize phosphonates as a nutrient source for phosphorus. In Sinorhizobium meliloti 1021, 2-aminoethylphosphonate is catabolized to phosphonoacetate, which is converted to acetate and inorganic phosphate by phosphonoacetate hydrolase (PhnA). Here we present detailed biochemical and structural characterization of PhnA that provides insights into the mechanism of C-P bond cleavage. The 1.35 A resolution crystal structure reveals a catalytic core similar to those of alkaline phosphatases and nucleotide pyrophosphatases but with notable differences, such as a longer metal-metal distance. Detailed structure-guided analysis of active site residues and four additional cocrystal structures with phosphonoacetate substrate, acetate, phosphonoformate inhibitor, and a covalently bound transition state mimic provide insight into active site features that may facilitate cleavage of the C-P bond. These studies expand upon the array of reactions that can be catalyzed by enzymes of the alkaline phosphatase superfamily.
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Structural and mechanistic insights into C-p bond hydrolysis by phosphonoacetate hydrolase.,Agarwal V, Borisova SA, Metcalf WW, van der Donk WA, Nair SK Chem Biol. 2011 Oct 28;18(10):1230-40. PMID:22035792<ref>PMID:22035792</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3t00" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Ensifer meliloti]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Nucleotide diphosphatase]]
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[[Category: Sinorhizobium meliloti 1021]]
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[[Category: Agarwal, V]]
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[[Category: Agarwal V]]
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[[Category: Nair, S K]]
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[[Category: Nair SK]]
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[[Category: Alkaline phosphatase superfamily]]
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[[Category: Hydrolase]]
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[[Category: Transition state mimic]]
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Current revision

Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with vanadate

PDB ID 3t00

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OCA

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