3t00: Difference between revisions

Latest revision as of 10:17, 13 August 2026

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

Structural highlights

3t00 is a 1 chain structure with sequence from Sinorhizobium meliloti 1021. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	NI, VO4, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q92UV8_RHIME

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Agarwal V, Borisova SA, Metcalf WW, van der Donk WA, Nair SK. Structural and mechanistic insights into C-p bond hydrolysis by phosphonoacetate hydrolase. Chem Biol. 2011 Oct 28;18(10):1230-40. PMID:22035792 doi:10.1016/j.chembiol.2011.07.019

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OCA

[1] Agarwal V, Borisova SA, Metcalf WW, van der Donk WA, Nair SK. Structural and mechanistic insights into C-p bond hydrolysis by phosphonoacetate hydrolase. Chem Biol. 2011 Oct 28;18(10):1230-40. PMID:22035792 doi:10.1016/j.chembiol.2011.07.019

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='3t00' size='340' side='right'caption='[[3t00]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<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>
+<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>
-</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>
+</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>
-<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>
+<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>
-<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>
-<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>
 <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>
+== Function ==
+[https://www.uniprot.org/uniprot/Q92UV8_RHIME Q92UV8_RHIME]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Ensifer meliloti]]
 [[Category: Large Structures]]
-[[Category: Nucleotide diphosphatase]]
+[[Category: Sinorhizobium meliloti 1021]]
-[[Category: Agarwal, V]]
+[[Category: Agarwal V]]
-[[Category: Nair, S K]]
+[[Category: Nair SK]]
-[[Category: Alkaline phosphatase superfamily]]
-[[Category: Hydrolase]]
-[[Category: Transition state mimic]]

3t00: Difference between revisions

Latest revision as of 10:17, 13 August 2026

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

Structural highlights

Function

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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