2pyu - Revision history

OCA at 11:13, 30 August 2023

OCA — Wed, 30 Aug 2023 11:13:04 GMT

←Older revision		Revision as of 11:13, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2pyu' size='340' side='right'caption='[[2pyu]], [[Resolution\|resolution]] 2.02Å' scene=''>		<StructureSection load='2pyu' size='340' side='right'caption='[[2pyu]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pyu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PYU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pyu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PYU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</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]] 2.02Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1k7k\|1k7k]], [[2q16\|2q16]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>yggV ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~83333 ECOLI])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] </~~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=2pyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyu OCA], [https://pdbe.org/2pyu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pyu RCSB], [https://www.ebi.ac.uk/pdbsum/2pyu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyu 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=2pyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyu OCA], [https://pdbe.org/2pyu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pyu RCSB], [https://www.ebi.ac.uk/pdbsum/2pyu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~RDGB_ECOLI RDGB_ECOLI]~~] Pyrophosphatase that ~~hydrolyzes~~ the non-canonical purine nucleotides ~~deoxyinosine triphosphate~~ (dITP) and ~~xanthosine triphosphate~~ (~~XTP~~) ~~as well as~~ 2'-deoxy-N-6-hydroxylaminopurine ~~triposphate~~ (dHAPTP) ~~to their respective monophosphate derivatives~~. ~~Probably excludes~~ non-canonical ~~purines~~ from ~~DNA precursor~~ pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions.[HAMAP-Rule:MF_01405]<ref>PMID:17090528</ref>	+	[https://www.uniprot.org/uniprot/IXTPA_ECOLI IXTPA_ECOLI] Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP (PubMed:12297000, PubMed:17976651). Can also efficiently hydrolyze 2'-deoxy-N-6-hydroxylaminopurine triphosphate (dHAPTP) (PubMed:17090528). Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA/RNA and avoiding chromosomal lesions (PubMed:12297000, PubMed:12730170, PubMed:17090528). To a much lesser extent, is also able to hydrolyze GTP, dGTP and dUTP, but shows very low activity toward the canonical nucleotides dATP, dCTP and dTTP and toward 8-oxo-dGTP, purine deoxyribose triphosphate, 2-aminopurine deoxyribose triphosphate and 2,6-diaminopurine deoxyribose triphosphate (PubMed:12297000, PubMed:17090528).[HAMAP-Rule:MF_01405]<ref>PMID:12297000</ref> <ref>PMID:12730170</ref> <ref>PMID:17090528</ref> <ref>PMID:17976651</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Nucleoside-triphosphate diphosphatase]]~~	+	[[Category: Proudfoot M]]
-	[[Category: Proudfoot, M]]	+	[[Category: Savchenko A]]
-	[[Category: Savchenko, A]]	+	[[Category: Singer AU]]
-	[[Category: Singer~~, A U~~]]	+	[[Category: Skarina T]]
-	[[Category: Skarina, T]]	+	[[Category: Yakunin AF]]
-	[[Category: Yakunin~~, A F]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Itp pyrophosphatase x-ray structure enzyme mechanism product~~]]	+

OCA at 15:36, 17 June 2021

OCA — Thu, 17 Jun 2021 15:36:33 GMT

←Older revision		Revision as of 15:36, 17 June 2021
Line 1:		Line 1:

	==Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP==		==Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP==
-	<StructureSection load='2pyu' size='340' side='right' caption='[[2pyu]], [[Resolution\|resolution]] 2.02Å' scene=''>	+	<StructureSection load='2pyu' size='340' side='right'caption='[[2pyu]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pyu]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PYU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pyu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PYU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1k7k\|1k7k]], [[2q16\|2q16]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1k7k\|1k7k]], [[2q16\|2q16]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yggV ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yggV ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] </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=2pyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyu OCA], [~~http~~://pdbe.org/2pyu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pyu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pyu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyu 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=2pyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyu OCA], [https://pdbe.org/2pyu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pyu RCSB], [https://www.ebi.ac.uk/pdbsum/2pyu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RDGB_ECOLI RDGB_ECOLI]] Pyrophosphatase that hydrolyzes the non-canonical purine nucleotides deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) to their respective monophosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions.[HAMAP-Rule:MF_01405]<ref>PMID:17090528</ref>	+	[[https://www.uniprot.org/uniprot/RDGB_ECOLI RDGB_ECOLI]] Pyrophosphatase that hydrolyzes the non-canonical purine nucleotides deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) to their respective monophosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions.[HAMAP-Rule:MF_01405]<ref>PMID:17090528</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Nucleoside-triphosphate diphosphatase]]		[[Category: Nucleoside-triphosphate diphosphatase]]
	[[Category: Proudfoot, M]]		[[Category: Proudfoot, M]]

OCA at 08:42, 29 August 2018

OCA — Wed, 29 Aug 2018 08:42:33 GMT

←Older revision		Revision as of 08:42, 29 August 2018
Line 1:		Line 1:
		+
	==Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP==		==Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP==
	<StructureSection load='2pyu' size='340' side='right' caption='[[2pyu]], [[Resolution\|resolution]] 2.02Å' scene=''>		<StructureSection load='2pyu' size='340' side='right' caption='[[2pyu]], [[Resolution\|resolution]] 2.02Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yggV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yggV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] </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=2pyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyu OCA], [http://pdbe.org/2pyu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pyu RCSB], [http://www.ebi.ac.uk/pdbsum/2pyu 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=2pyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyu OCA], [http://pdbe.org/2pyu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pyu RCSB], [http://www.ebi.ac.uk/pdbsum/2pyu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2pyu_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2pyu_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>
	</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=2pyu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:48, 12 September 2015

OCA — Sat, 12 Sep 2015 00:48:14 GMT

←Older revision		Revision as of 00:48, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='2pyu' size='340' side='right' caption='[[2pyu]], [[Resolution\|resolution]] 2.02Å' scene=''>		<StructureSection load='2pyu' size='340' side='right' caption='[[2pyu]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pyu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia coli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PYU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pyu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PYU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1k7k\|1k7k]], [[2q16\|2q16]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1k7k\|1k7k]], [[2q16\|2q16]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yggV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562 Escherichia coli~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yggV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] </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=2pyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pyu RCSB], [http://www.ebi.ac.uk/pdbsum/2pyu 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=2pyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyu OCA], [http://pdbe.org/2pyu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pyu RCSB], [http://www.ebi.ac.uk/pdbsum/2pyu PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~HAM1_ECOLI HAM1_ECOLI~~]] Pyrophosphatase that hydrolyzes the non-canonical purine nucleotides deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) to their respective monophosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions.<ref>PMID:17090528</ref>	+	[[http://www.uniprot.org/uniprot/RDGB_ECOLI RDGB_ECOLI]] Pyrophosphatase that hydrolyzes the non-canonical purine nucleotides deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) to their respective monophosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions.[HAMAP-Rule:MF_01405]<ref>PMID:17090528</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	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 2pyu" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecoli]]
	[[Category: Nucleoside-triphosphate diphosphatase]]		[[Category: Nucleoside-triphosphate diphosphatase]]
	[[Category: Proudfoot, M]]		[[Category: Proudfoot, M]]

OCA at 21:36, 25 December 2014

OCA — Thu, 25 Dec 2014 21:36:25 GMT

←Older revision		Revision as of 21:36, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pyu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PYU FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pyu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PYU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1k7k\|1k7k]], [[2q16\|2q16]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1k7k\|1k7k]], [[2q16\|2q16]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yggV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yggV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] </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=2pyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pyu RCSB], [http://www.ebi.ac.uk/pdbsum/2pyu 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=2pyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pyu RCSB], [http://www.ebi.ac.uk/pdbsum/2pyu PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HAM1_ECOLI HAM1_ECOLI]] Pyrophosphatase that hydrolyzes the non-canonical purine nucleotides deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) to their respective monophosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions.<ref>PMID:17090528</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Nucleoside-triphosphate diphosphatase]]		[[Category: Nucleoside-triphosphate diphosphatase]]
-	[[Category: Proudfoot, M.]]	+	[[Category: Proudfoot, M]]
-	[[Category: Savchenko, A.]]	+	[[Category: Savchenko, A]]
-	[[Category: Singer, A U.]]	+	[[Category: Singer, A U]]
-	[[Category: Skarina, T.]]	+	[[Category: Skarina, T]]
-	[[Category: Yakunin, A F.]]	+	[[Category: Yakunin, A F]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Itp pyrophosphatase x-ray structure enzyme mechanism product]]		[[Category: Itp pyrophosphatase x-ray structure enzyme mechanism product]]

OCA at 18:52, 30 September 2014

OCA — Tue, 30 Sep 2014 18:52:21 GMT

←Older revision		Revision as of 18:52, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2pyu.~~png~~\|~~left~~\|200px]]	+	==Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP==
		+	<StructureSection load='2pyu' size='340' side='right' caption='[[2pyu]], [[Resolution\|resolution]] 2.02Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2pyu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PYU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1k7k\|1k7k]], [[2q16\|2q16]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yggV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] </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=2pyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pyu RCSB], [http://www.ebi.ac.uk/pdbsum/2pyu 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/py/2pyu_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 ==
		+	Inosine triphosphate pyrophosphatases, which are ubiquitous house-cleaning enzymes, hydrolyze noncanonical nucleoside triphosphates (inosine triphosphate (ITP) and xanthosine triphosphate (XTP)) and prevent the incorporation of hypoxanthine or xanthine into nascent DNA or RNA. Here we present the 1.5-A-resolution crystal structure of the inosine triphosphate pyrophosphatase RdgB from Escherichia coli in a free state and in complex with a substrate (ITP+Ca(2+)) or a product (inosine monophosphate (IMP)). ITP binding to RdgB induced a large displacement of the alpha1 helix, closing the enzyme active site. This positions the conserved Lys13 close to the bridging oxygen between the alpha- and beta-phosphates of the substrate, weakening the P(alpha)-O bond. On the other side of the substrate, the conserved Asp69 is proposed to act as a base coordinating the catalytic water molecule. Our data provide insight into the molecular mechanisms of the substrate selectivity and catalysis of RdgB and other ITPases.

-	~~{{STRUCTURE_2pyu\| PDB=2pyu \| SCENE= }}~~	+	Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli.,Savchenko A, Proudfoot M, Skarina T, Singer A, Litvinova O, Sanishvili R, Brown G, Chirgadze N, Yakunin AF J Mol Biol. 2007 Dec 7;374(4):1091-103. Epub 2007 Oct 11. PMID:17976651<ref>PMID:17976651</ref>

-	~~===Structure~~ of the E. ~~coli inosine triphosphate pyrophosphatase RgdB in complex with IMP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17976651}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2pyu]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYU OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017976651<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Nucleoside-triphosphate diphosphatase]]		[[Category: Nucleoside-triphosphate diphosphatase]]

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

OCA — Mon, 07 Jan 2013 21:32:48 GMT

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

←Older revision

Revision as of 21:32, 7 January 2013

OCA at 21:32, 7 January 2013

OCA — Mon, 07 Jan 2013 21:32:45 GMT

←Older revision		Revision as of 21:32, 7 January 2013
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-	{{Seed}}
	[[Image:2pyu.png\|left\|200px]]		[[Image:2pyu.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2pyu", 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_2pyu\| PDB=2pyu \| SCENE= }}		{{STRUCTURE_2pyu\| PDB=2pyu \| SCENE= }}

	===Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP===		===Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17976651}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17976651 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17976651}}		{{ABSTRACT_PUBMED_17976651}}

	==About this Structure==		==About this Structure==
-	~~2PYU~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYU OCA].	+	[[2pyu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYU OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17976651~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017976651</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Nucleoside-triphosphate diphosphatase]]		[[Category: Nucleoside-triphosphate diphosphatase]]
Line 33:		Line 21:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Itp pyrophosphatase x-ray structure enzyme mechanism product]]		[[Category: Itp pyrophosphatase x-ray structure enzyme mechanism product]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:34:28 2009''

OCA at 06:34, 18 February 2009

OCA — Wed, 18 Feb 2009 06:34:32 GMT

←Older revision		Revision as of 06:34, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2PYU is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYU OCA].	+	2PYU is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYU OCA].

	==Reference==		==Reference==
-	Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli., Savchenko A, Proudfoot M, Skarina T, Singer A, Litvinova O, Sanishvili R, Brown G, Chirgadze N, Yakunin AF, J Mol Biol. 2007 Dec 7;374(4):1091-103. Epub 2007 Oct 11. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17976651 17976651]~~	+	<ref group="xtra">PMID:17976651</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Nucleoside-triphosphate diphosphatase]]		[[Category: Nucleoside-triphosphate diphosphatase]]
-	[[Category: Single protein]]
	[[Category: Proudfoot, M.]]		[[Category: Proudfoot, M.]]
	[[Category: Savchenko, A.]]		[[Category: Savchenko, A.]]
Line 35:		Line 34:
	[[Category: Itp pyrophosphatase x-ray structure enzyme mechanism product]]		[[Category: Itp pyrophosphatase x-ray structure enzyme mechanism product]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 14~~:49:~~49 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:34:28 2009''

OCA at 11:49, 29 July 2008

OCA — Tue, 29 Jul 2008 11:49:54 GMT

←Older revision		Revision as of 11:49, 29 July 2008
Line 1:		Line 1:
-	[[Image:2pyu.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2pyu.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2pyu\| PDB=2pyu \| SCENE= }}		{{STRUCTURE_2pyu\| PDB=2pyu \| SCENE= }}

-	~~'''~~Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP~~'''~~	+	===Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP===


-	~~==Overview==~~	+	<!--
-	~~Inosine triphosphate pyrophosphatases~~, ~~which are ubiquitous house-cleaning enzymes~~, ~~hydrolyze noncanonical nucleoside triphosphates (inosine triphosphate (ITP) and xanthosine triphosphate (XTP)) and prevent~~ the ~~incorporation of hypoxanthine or xanthine into nascent DNA or RNA. Here we present~~ the ~~1.5-A-resolution crystal structure of the inosine triphosphate pyrophosphatase RdgB from Escherichia coli in a free state and in complex with a substrate~~ (~~ITP+Ca(2+)) or a product (inosine monophosphate (IMP))~~. ~~ITP binding to RdgB induced a large displacement of the alpha1 helix, closing the enzyme active site~~. ~~This positions the conserved Lys13 close to the bridging oxygen between the alpha- and beta-phosphates of the substrate, weakening the P(alpha~~)~~-O bond. On the other side of the substrate~~, ~~the conserved Asp69~~ is ~~proposed to act as a base coordinating~~ the ~~catalytic water molecule. Our data provide insight into the molecular mechanisms of the substrate selectivity and catalysis of RdgB and other ITPases~~.	+	The line below this paragraph, {{ABSTRACT_PUBMED_17976651}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17976651 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17976651}}

	==About this Structure==		==About this Structure==
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	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Itp pyrophosphatase x-ray structure enzyme mechanism product]]		[[Category: Itp pyrophosphatase x-ray structure enzyme mechanism product]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4~~ 14:02:15 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 14:49:49 2008''