2rh6 - Revision history

OCA at 11:57, 30 August 2023

OCA — Wed, 30 Aug 2023 11:57:15 GMT

←Older revision		Revision as of 11:57, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2rh6' size='340' side='right'caption='[[2rh6]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='2rh6' size='340' side='right'caption='[[2rh6]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rh6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Xanac Xanac~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RH6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rh6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_citri_pv._citri_str._306 Xanthomonas citri pv. citri str. 306]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RH6 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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]] 1.45Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2gsu\|2gsu]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=2rh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh6 OCA], [https://pdbe.org/2rh6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rh6 RCSB], [https://www.ebi.ac.uk/pdbsum/2rh6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rh6 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=2rh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh6 OCA], [https://pdbe.org/2rh6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rh6 RCSB], [https://www.ebi.ac.uk/pdbsum/2rh6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rh6 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8PIS1_XANAC Q8PIS1_XANAC]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2rh6 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2rh6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The rapid expansion of the amount of genomic and structural data has provided many examples of enzymes with evolutionarily related active sites that catalyze different reactions. Functional comparisons of these active sites can provide insight into the origins of the enormous catalytic proficiency of enzymes and the evolutionary changes that can lead to different enzyme activities. The alkaline phosphatase (AP) superfamily is an ideal system to use in making such comparisons given the extensive data available on both nonenzymatic and enzymatic phosphoryl transfer reactions. Some superfamily members, such as AP itself, preferentially hydrolyze phosphate monoesters, whereas others, such as nucleotide pyrophosphatase/phosphodiesterase (NPP), preferentially hydrolyze phosphate diesters. We have measured rate constants for NPP-catalyzed hydrolysis of phosphate diesters and monoesters. NPP preferentially catalyzes diester hydrolysis by factors of 10(2)-10(6), depending on the identity of the diester substrate. To identify features of the NPP active site that could lead to preferential phosphate diester hydrolysis, we have determined the structure of NPP in the absence of ligands and in complexes with vanadate and AMP. Comparisons to existing structures of AP reveal bimetallo cores that are structurally indistinguishable, but there are several distinct structural features outside of the conserved bimetallo site. The structural and functional data together suggest that some of these distinct functional groups provide specific substrate binding interactions, whereas others tune the properties of the bimetallo active site itself to discriminate between phosphate diester and monoester substrates.
-
-	Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution.,Zalatan JG, Fenn TD, Brunger AT, Herschlag D Biochemistry. 2006 Aug 15;45(32):9788-803. PMID:16893180<ref>PMID:16893180</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2rh6" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Nucleotide diphosphatase]]~~	+	[[Category: Xanthomonas citri pv. citri str. 306]]
-	~~[[Category: Xanac~~]]	+	[[Category: Brunger AT]]
-	[[Category: Brunger~~, A T~~]]	+	[[Category: Fenn TD]]
-	[[Category: Fenn~~, T D~~]]	+	[[Category: Hershlag D]]
-	[[Category: Hershlag, D]]	+	[[Category: Zalatan JG]]
-	[[Category: Zalatan~~, J G]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:47, 16 March 2022

OCA — Wed, 16 Mar 2022 07:47:50 GMT

←Older revision		Revision as of 07:47, 16 March 2022
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	<StructureSection load='2rh6' size='340' side='right'caption='[[2rh6]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='2rh6' size='340' side='right'caption='[[2rh6]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rh6]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Xanac Xanac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2RH6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rh6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanac Xanac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RH6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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">[[2gsu\|2gsu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2gsu\|2gsu]]</div></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~~://proteopedia.org/fgij/fg.htm?mol=2rh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh6 OCA], [~~http~~://pdbe.org/2rh6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rh6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rh6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rh6 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=2rh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh6 OCA], [https://pdbe.org/2rh6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rh6 RCSB], [https://www.ebi.ac.uk/pdbsum/2rh6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rh6 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:12, 10 June 2020

OCA — Wed, 10 Jun 2020 07:12:16 GMT

←Older revision		Revision as of 07:12, 10 June 2020
Line 1:		Line 1:

	==Structure of Xac NPP for evaluation of refinement methodology==		==Structure of Xac NPP for evaluation of refinement methodology==
-	<StructureSection load='2rh6' size='340' side='right' caption='[[2rh6]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='2rh6' size='340' side='right'caption='[[2rh6]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rh6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanac Xanac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RH6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rh6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanac Xanac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2RH6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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">[[2gsu\|2gsu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsu\|2gsu]]</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=2rh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh6 OCA], [http://pdbe.org/2rh6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rh6 RCSB], [http://www.ebi.ac.uk/pdbsum/2rh6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rh6 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2rh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh6 OCA], [http://pdbe.org/2rh6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rh6 RCSB], [http://www.ebi.ac.uk/pdbsum/2rh6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rh6 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Nucleotide diphosphatase]]		[[Category: Nucleotide diphosphatase]]
	[[Category: Xanac]]		[[Category: Xanac]]

OCA at 11:32, 5 September 2018

OCA — Wed, 05 Sep 2018 11:32:43 GMT

←Older revision		Revision as of 11:32, 5 September 2018
Line 1:		Line 1:
		+
	==Structure of Xac NPP for evaluation of refinement methodology==		==Structure of Xac NPP for evaluation of refinement methodology==
	<StructureSection load='2rh6' size='340' side='right' caption='[[2rh6]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='2rh6' size='340' side='right' caption='[[2rh6]], [[Resolution\|resolution]] 1.45Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsu\|2gsu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsu\|2gsu]]</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=2rh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh6 OCA], [http://pdbe.org/2rh6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rh6 RCSB], [http://www.ebi.ac.uk/pdbsum/2rh6 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=2rh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh6 OCA], [http://pdbe.org/2rh6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rh6 RCSB], [http://www.ebi.ac.uk/pdbsum/2rh6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rh6 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rh/2rh6_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rh/2rh6_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 09:54, 7 February 2016

OCA — Sun, 07 Feb 2016 09:54:38 GMT

←Older revision		Revision as of 09:54, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='2rh6' size='340' side='right' caption='[[2rh6]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='2rh6' size='340' side='right' caption='[[2rh6]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rh6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Xanthomonas_citri Xanthomonas citri~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RH6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rh6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanac Xanac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RH6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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">[[2gsu\|2gsu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsu\|2gsu]]</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=2rh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rh6 RCSB], [http://www.ebi.ac.uk/pdbsum/2rh6 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=2rh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh6 OCA], [http://pdbe.org/2rh6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rh6 RCSB], [http://www.ebi.ac.uk/pdbsum/2rh6 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2rh6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 2rh6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Nucleotide diphosphatase]]		[[Category: Nucleotide diphosphatase]]
-	[[Category: ~~Xanthomonas citri~~]]	+	[[Category: Xanac]]
	[[Category: Brunger, A T]]		[[Category: Brunger, A T]]
	[[Category: Fenn, T D]]		[[Category: Fenn, T D]]

OCA at 18:41, 19 January 2015

OCA — Mon, 19 Jan 2015 18:41:14 GMT

←Older revision		Revision as of 18:41, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rh6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanthomonas_citri Xanthomonas citri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RH6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rh6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanthomonas_citri Xanthomonas citri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RH6 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsu\|2gsu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsu\|2gsu]]</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=2rh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rh6 RCSB], [http://www.ebi.ac.uk/pdbsum/2rh6 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=2rh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rh6 RCSB], [http://www.ebi.ac.uk/pdbsum/2rh6 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	[[Category: Nucleotide diphosphatase]]		[[Category: Nucleotide diphosphatase]]
	[[Category: Xanthomonas citri]]		[[Category: Xanthomonas citri]]
-	[[Category: Brunger, A T.]]	+	[[Category: Brunger, A T]]
-	[[Category: Fenn, T D.]]	+	[[Category: Fenn, T D]]
-	[[Category: Hershlag, D.]]	+	[[Category: Hershlag, D]]
-	[[Category: Zalatan, J G.]]	+	[[Category: Zalatan, J G]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 20:21, 30 September 2014

OCA — Tue, 30 Sep 2014 20:21:19 GMT

←Older revision		Revision as of 20:21, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2rh6.~~png~~\|~~left~~\|200px]]	+	==Structure of Xac NPP for evaluation of refinement methodology==
		+	<StructureSection load='2rh6' size='340' side='right' caption='[[2rh6]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2rh6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanthomonas_citri Xanthomonas citri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RH6 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gsu\|2gsu]]</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=2rh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rh6 RCSB], [http://www.ebi.ac.uk/pdbsum/2rh6 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rh/2rh6_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The rapid expansion of the amount of genomic and structural data has provided many examples of enzymes with evolutionarily related active sites that catalyze different reactions. Functional comparisons of these active sites can provide insight into the origins of the enormous catalytic proficiency of enzymes and the evolutionary changes that can lead to different enzyme activities. The alkaline phosphatase (AP) superfamily is an ideal system to use in making such comparisons given the extensive data available on both nonenzymatic and enzymatic phosphoryl transfer reactions. Some superfamily members, such as AP itself, preferentially hydrolyze phosphate monoesters, whereas others, such as nucleotide pyrophosphatase/phosphodiesterase (NPP), preferentially hydrolyze phosphate diesters. We have measured rate constants for NPP-catalyzed hydrolysis of phosphate diesters and monoesters. NPP preferentially catalyzes diester hydrolysis by factors of 10(2)-10(6), depending on the identity of the diester substrate. To identify features of the NPP active site that could lead to preferential phosphate diester hydrolysis, we have determined the structure of NPP in the absence of ligands and in complexes with vanadate and AMP. Comparisons to existing structures of AP reveal bimetallo cores that are structurally indistinguishable, but there are several distinct structural features outside of the conserved bimetallo site. The structural and functional data together suggest that some of these distinct functional groups provide specific substrate binding interactions, whereas others tune the properties of the bimetallo active site itself to discriminate between phosphate diester and monoester substrates.

-	~~{{STRUCTURE_2rh6\| PDB=2rh6 \| SCENE= }}~~	+	Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution.,Zalatan JG, Fenn TD, Brunger AT, Herschlag D Biochemistry. 2006 Aug 15;45(32):9788-803. PMID:16893180<ref>PMID:16893180</ref>

-	~~===Structure~~ of ~~Xac NPP for evaluation of refinement methodology===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16893180}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2rh6]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Xanthomonas_citri Xanthomonas citri]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016893180<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Nucleotide diphosphatase]]		[[Category: Nucleotide diphosphatase]]
	[[Category: Xanthomonas citri]]		[[Category: Xanthomonas citri]]

OCA: Protected "2rh6" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 20:32:08 GMT

Protected "2rh6" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:32, 7 January 2013

OCA at 20:32, 7 January 2013

OCA — Mon, 07 Jan 2013 20:32:07 GMT

←Older revision		Revision as of 20:32, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2rh6.png\|left\|200px]]		[[Image:2rh6.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2rh6", 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_2rh6\| PDB=2rh6 \| SCENE= }}		{{STRUCTURE_2rh6\| PDB=2rh6 \| SCENE= }}

	===Structure of Xac NPP for evaluation of refinement methodology===		===Structure of Xac NPP for evaluation of refinement methodology===

		+	{{ABSTRACT_PUBMED_16893180}}

	==About this Structure==		==About this Structure==
-	~~2RH6~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Xanthomonas_axonopodis_pv._citri~~ Xanthomonas ~~axonopodis pv.~~ citri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA].	+	[[2rh6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanthomonas_citri Xanthomonas citri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16893180~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016893180</ref><references group="xtra"/>
	[[Category: Nucleotide diphosphatase]]		[[Category: Nucleotide diphosphatase]]
-	[[Category: Xanthomonas ~~axonopodis pv.~~ citri]]	+	[[Category: Xanthomonas citri]]
	[[Category: Brunger, A T.]]		[[Category: Brunger, A T.]]
	[[Category: Fenn, T D.]]		[[Category: Fenn, T D.]]
Line 25:		Line 19:
	[[Category: Zalatan, J G.]]		[[Category: Zalatan, J G.]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:01:23 2009''

OCA at 11:01, 16 February 2009

OCA — Mon, 16 Feb 2009 11:01:25 GMT

←Older revision		Revision as of 11:01, 16 February 2009
Line 1:		Line 1:
-	[[Image:2rh6.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2rh6.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2rh6\| PDB=2rh6 \| SCENE= }}		{{STRUCTURE_2rh6\| PDB=2rh6 \| SCENE= }}

-	~~'''~~Structure of Xac NPP for evaluation of refinement methodology~~'''~~	+	===Structure of Xac NPP for evaluation of refinement methodology===

-
-	==Overview==
-	The rapid expansion of the amount of genomic and structural data has provided many examples of enzymes with evolutionarily related active sites that catalyze different reactions. Functional comparisons of these active sites can provide insight into the origins of the enormous catalytic proficiency of enzymes and the evolutionary changes that can lead to different enzyme activities. The alkaline phosphatase (AP) superfamily is an ideal system to use in making such comparisons given the extensive data available on both nonenzymatic and enzymatic phosphoryl transfer reactions. Some superfamily members, such as AP itself, preferentially hydrolyze phosphate monoesters, whereas others, such as nucleotide pyrophosphatase/phosphodiesterase (NPP), preferentially hydrolyze phosphate diesters. We have measured rate constants for NPP-catalyzed hydrolysis of phosphate diesters and monoesters. NPP preferentially catalyzes diester hydrolysis by factors of 10(2)-10(6), depending on the identity of the diester substrate. To identify features of the NPP active site that could lead to preferential phosphate diester hydrolysis, we have determined the structure of NPP in the absence of ligands and in complexes with vanadate and AMP. Comparisons to existing structures of AP reveal bimetallo cores that are structurally indistinguishable, but there are several distinct structural features outside of the conserved bimetallo site. The structural and functional data together suggest that some of these distinct functional groups provide specific substrate binding interactions, whereas others tune the properties of the bimetallo active site itself to discriminate between phosphate diester and monoester substrates.

	==About this Structure==		==About this Structure==
-	2RH6 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Xanthomonas_axonopodis_pv._citri Xanthomonas axonopodis pv. citri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA].	+	2RH6 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Xanthomonas_axonopodis_pv._citri Xanthomonas axonopodis pv. citri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH6 OCA].

	==Reference==		==Reference==
-	Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution., Zalatan JG, Fenn TD, Brunger AT, Herschlag D, Biochemistry. 2006 Aug 15;45(32):9788-803. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16893180 16893180]~~	+	<ref group="xtra">PMID:16893180</ref><references group="xtra"/>
	[[Category: Nucleotide diphosphatase]]		[[Category: Nucleotide diphosphatase]]
-	[[Category: Single protein]]
	[[Category: Xanthomonas axonopodis pv. citri]]		[[Category: Xanthomonas axonopodis pv. citri]]
	[[Category: Brunger, A T.]]		[[Category: Brunger, A T.]]
Line 28:		Line 25:
	[[Category: Zalatan, J G.]]		[[Category: Zalatan, J G.]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4~~ 16:54:~~19 2008~~''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:01:23 2009''