3t02 - Revision history

OCA at 13:13, 14 March 2024

OCA — Thu, 14 Mar 2024 13:13:26 GMT

←Older revision		Revision as of 13:13, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3t02' size='340' side='right'caption='[[3t02]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3t02' size='340' side='right'caption='[[3t02]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t02]] 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=3T02 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T02 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t02]] 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=3T02 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T02 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PAE:PHOSPHONOACETIC+ACID'>PAE</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]] 2Å</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]], [[3t00\|3t00]], [[3t01\|3t01]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PAE:PHOSPHONOACETIC+ACID'>PAE</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=3t02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t02 OCA], [https://pdbe.org/3t02 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t02 RCSB], [https://www.ebi.ac.uk/pdbsum/3t02 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t02 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=3t02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t02 OCA], [https://pdbe.org/3t02 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t02 RCSB], [https://www.ebi.ac.uk/pdbsum/3t02 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t02 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q92UV8_RHIME Q92UV8_RHIME]
-	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<ref>PMID:22035792<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3t02" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Ensifer meliloti]]
	[[Category: Large Structures]]		[[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~~]]	+

OCA at 08:17, 29 June 2022

OCA — Wed, 29 Jun 2022 08:17:52 GMT

←Older revision		Revision as of 08:17, 29 June 2022
Line 1:		Line 1:

	==Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoacetate==		==Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoacetate==
-	<StructureSection load='3t02' size='340' side='right' caption='[[3t02]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3t02' size='340' side='right'caption='[[3t02]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t02]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ensifer_meliloti Ensifer meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T02 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3T02 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t02]] 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=3T02 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T02 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PAE:PHOSPHONOACETIC+ACID'>PAE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PAE:PHOSPHONOACETIC+ACID'>PAE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3szy\|3szy]], [[3szz\|3szz]], [[3t00\|3t00]], [[3t01\|3t01]]</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]], [[3t00\|3t00]], [[3t01\|3t01]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phnA, RB0978, SM_b21538 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266834 Ensifer meliloti])</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'>[~~http~~://en.wikipedia.org/wiki/Nucleotide_diphosphatase Nucleotide diphosphatase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.9 3.6.1.9] </span></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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3t02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t02 OCA], [~~http~~://pdbe.org/3t02 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3t02 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3t02 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3t02 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=3t02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t02 OCA], [https://pdbe.org/3t02 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t02 RCSB], [https://www.ebi.ac.uk/pdbsum/3t02 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t02 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Ensifer meliloti]]		[[Category: Ensifer meliloti]]
		+	[[Category: Large Structures]]
	[[Category: Nucleotide diphosphatase]]		[[Category: Nucleotide diphosphatase]]
	[[Category: Agarwal, V]]		[[Category: Agarwal, V]]

OCA at 13:23, 11 August 2016

OCA — Thu, 11 Aug 2016 13:23:10 GMT

←Older revision		Revision as of 13:23, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoacetate==		==Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoacetate==
	<StructureSection load='3t02' size='340' side='right' caption='[[3t02]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3t02' size='340' side='right' caption='[[3t02]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t02]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sinorhizobium_meliloti Sinorhizobium~~ meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T02 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t02]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ensifer_meliloti Ensifer meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T02 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PAE:PHOSPHONOACETIC+ACID'>PAE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PAE:PHOSPHONOACETIC+ACID'>PAE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3szy\|3szy]], [[3szz\|3szz]], [[3t00\|3t00]], [[3t01\|3t01]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3szy\|3szy]], [[3szz\|3szz]], [[3t00\|3t00]], [[3t01\|3t01]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phnA, RB0978, SM_b21538 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~382 Sinorhizobium~~ meliloti])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phnA, RB0978, SM_b21538 ([http://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'>[http://en.wikipedia.org/wiki/Nucleotide_diphosphatase Nucleotide diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.9 3.6.1.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleotide_diphosphatase Nucleotide diphosphatase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3t02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t02 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t02 RCSB], [http://www.ebi.ac.uk/pdbsum/3t02 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3t02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t02 OCA], [http://pdbe.org/3t02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3t02 RCSB], [http://www.ebi.ac.uk/pdbsum/3t02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3t02 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3t02" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ensifer meliloti]]
	[[Category: Nucleotide diphosphatase]]		[[Category: Nucleotide diphosphatase]]
-	[[Category: Sinorhizobium meliloti]]
	[[Category: Agarwal, V]]		[[Category: Agarwal, V]]
	[[Category: Nair, S K]]		[[Category: Nair, S K]]
	[[Category: Alkaline phosphatase superfamily]]		[[Category: Alkaline phosphatase superfamily]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 10:20, 4 January 2015

OCA — Sun, 04 Jan 2015 10:20:52 GMT

←Older revision		Revision as of 10:20, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3t02]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T02 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3t02]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T02 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PAE:PHOSPHONOACETIC+ACID'>PAE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PAE:PHOSPHONOACETIC+ACID'>PAE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3szy\|3szy]], [[3szz\|3szz]], [[3t00\|3t00]], [[3t01\|3t01]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3szy\|3szy]], [[3szz\|3szz]], [[3t00\|3t00]], [[3t01\|3t01]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phnA, RB0978, SM_b21538 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 Sinorhizobium meliloti])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phnA, RB0978, SM_b21538 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 Sinorhizobium meliloti])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleotide_diphosphatase Nucleotide diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.9 3.6.1.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleotide_diphosphatase Nucleotide diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.9 3.6.1.9] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3t02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t02 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t02 RCSB], [http://www.ebi.ac.uk/pdbsum/3t02 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3t02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t02 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t02 RCSB], [http://www.ebi.ac.uk/pdbsum/3t02 PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 15:
	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>		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>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 23:		Line 23:
	[[Category: Nucleotide diphosphatase]]		[[Category: Nucleotide diphosphatase]]
	[[Category: Sinorhizobium meliloti]]		[[Category: Sinorhizobium meliloti]]
-	[[Category: Agarwal, V.]]	+	[[Category: Agarwal, V]]
-	[[Category: Nair, S K.]]	+	[[Category: Nair, S K]]
	[[Category: Alkaline phosphatase superfamily]]		[[Category: Alkaline phosphatase superfamily]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 05:48, 5 June 2014

OCA — Thu, 05 Jun 2014 05:48:59 GMT

←Older revision		Revision as of 05:48, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3t02.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoacetate==
		+	<StructureSection load='3t02' size='340' side='right' caption='[[3t02]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3t02]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T02 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PAE:PHOSPHONOACETIC+ACID'>PAE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3szy\|3szy]], [[3szz\|3szz]], [[3t00\|3t00]], [[3t01\|3t01]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phnA, RB0978, SM_b21538 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 Sinorhizobium meliloti])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleotide_diphosphatase Nucleotide diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.9 3.6.1.9] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3t02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t02 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t02 RCSB], [http://www.ebi.ac.uk/pdbsum/3t02 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== 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<ref>PMID:22035792</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3t02"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_3t02\| PDB=3t02 \| SCENE= }}~~	+

-	~~===Crystal Structure~~ of ~~Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoacetate===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22035792}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22035792 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22035792}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3t02]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T02 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022035792<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Nucleotide diphosphatase]]		[[Category: Nucleotide diphosphatase]]
	[[Category: Sinorhizobium meliloti]]		[[Category: Sinorhizobium meliloti]]

OCA at 10:56, 9 November 2011

OCA — Wed, 09 Nov 2011 10:56:00 GMT

←Older revision		Revision as of 10:56, 9 November 2011
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-	[[Image:3t02.~~jpg~~\|left\|200px]]	+	[[Image:3t02.png\|left\|200px]]

	<!--		<!--
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	===Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoacetate===		===Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoacetate===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22035792}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22035792 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22035792}}

	==About this Structure==		==About this Structure==
	[[3t02]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T02 OCA].		[[3t02]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T02 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022035792</ref><references group="xtra"/>
	[[Category: Nucleotide diphosphatase]]		[[Category: Nucleotide diphosphatase]]
	[[Category: Sinorhizobium meliloti]]		[[Category: Sinorhizobium meliloti]]

OCA at 09:05, 3 August 2011

OCA — Wed, 03 Aug 2011 09:05:37 GMT

←Older revision		Revision as of 09:05, 3 August 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3t02.jpg\|left\|200px]]

-	The ~~entry 3t02~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3t02", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3t02\| PDB=3t02 \| SCENE= }}

-	~~Authors: Agarwal, V., Nair, S.K.~~	+	===Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoacetate===

-	~~Description: Crystal~~ Structure ~~of Phosphonoacetate hydrolase~~ from Sinorhizobium meliloti ~~1021 in complex with Phosphonoacetate~~	+
		+	==About this Structure==
		+	[[3t02]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T02 OCA].
		+	[[Category: Nucleotide diphosphatase]]
		+	[[Category: Sinorhizobium meliloti]]
		+	[[Category: Agarwal, V.]]
		+	[[Category: Nair, S K.]]
		+	[[Category: Alkaline phosphatase superfamily]]
		+	[[Category: Hydrolase]]

OCA: Protected "3t02" [edit=sysop:move=sysop]

OCA — Wed, 27 Jul 2011 05:46:35 GMT

Protected "3t02" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:46, 27 July 2011

OCA: New page: '''Unreleased structure''' The entry 3t02 is ON HOLD Authors: Agarwal, V., Nair, S.K. Description: Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in c...

OCA — Wed, 27 Jul 2011 05:46:34 GMT

New page: '''Unreleased structure''' The entry 3t02 is ON HOLD Authors: Agarwal, V., Nair, S.K. Description: Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in c...

New page

'''Unreleased structure'''

The entry 3t02 is ON HOLD

Authors: Agarwal, V., Nair, S.K.

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