1k7k - Revision history

OCA at 07:58, 3 April 2024

OCA — Wed, 03 Apr 2024 07:58:28 GMT

←Older revision		Revision as of 07:58, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='1k7k' size='340' side='right'caption='[[1k7k]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1k7k' size='340' side='right'caption='[[1k7k]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k7k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K7K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k7k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K7K FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 1.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1k7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k7k OCA], [https://pdbe.org/1k7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k7k RCSB], [https://www.ebi.ac.uk/pdbsum/1k7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k7k ProSAT], [https://www.topsan.org/Proteins/MCSG/1k7k TOPSAN]</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=1k7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k7k OCA], [https://pdbe.org/1k7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k7k RCSB], [https://www.ebi.ac.uk/pdbsum/1k7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k7k ProSAT], [https://www.topsan.org/Proteins/MCSG/1k7k TOPSAN]</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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	</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=1k7k 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=1k7k ConSurf].
	<div style="clear:both"></div>		<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.
-
-	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>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1k7k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Edwards, A]]	+	[[Category: Edwards A]]
-	[[Category: Joachimiak, A]]	+	[[Category: Joachimiak A]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Sanishvili R]]
-	[[Category: Sanishvili, R]]	+	[[Category: Savchenko A]]
-	[[Category: Savchenko, A]]	+	[[Category: Skarina T]]
-	[[Category: Skarina, T]]	+
-	~~[[Category: Disordered se-met]]~~	+
-	~~[[Category: His-tag]]~~	+
-	~~[[Category: Large groove]]~~	+
-	~~[[Category: Mad]]~~	+
-	~~[[Category: Mcsg]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Putative ribosomal protein]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 08:46, 21 April 2021

OCA — Wed, 21 Apr 2021 08:46:05 GMT

←Older revision		Revision as of 08:46, 21 April 2021
Line 3:		Line 3:
	<StructureSection load='1k7k' size='340' side='right'caption='[[1k7k]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1k7k' size='340' side='right'caption='[[1k7k]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k7k]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K7K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1K7K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k7k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K7K FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1k7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k7k OCA], [~~http~~://pdbe.org/1k7k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1k7k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1k7k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1k7k ProSAT], [~~http~~://www.topsan.org/Proteins/MCSG/1k7k TOPSAN]</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=1k7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k7k OCA], [https://pdbe.org/1k7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k7k RCSB], [https://www.ebi.ac.uk/pdbsum/1k7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k7k ProSAT], [https://www.topsan.org/Proteins/MCSG/1k7k TOPSAN]</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]]

OCA at 12:57, 17 July 2019

OCA — Wed, 17 Jul 2019 12:57:43 GMT

←Older revision		Revision as of 12:57, 17 July 2019
Line 1:		Line 1:

	==crystal structure of RdgB- inosine triphosphate pyrophosphatase from E. coli==		==crystal structure of RdgB- inosine triphosphate pyrophosphatase from E. coli==
-	<StructureSection load='1k7k' size='340' side='right' caption='[[1k7k]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='1k7k' size='340' side='right'caption='[[1k7k]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1k7k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K7K FirstGlance]. <br>		<table><tr><td colspan='2'>[[1k7k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K7K FirstGlance]. <br>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k7/1k7k_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k7/1k7k_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>
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Edwards, A]]		[[Category: Edwards, A]]
	[[Category: Joachimiak, A]]		[[Category: Joachimiak, A]]

OCA at 07:14, 11 October 2017

OCA — Wed, 11 Oct 2017 07:14:39 GMT

←Older revision		Revision as of 07:14, 11 October 2017
Line 1:		Line 1:
		+
	==crystal structure of RdgB- inosine triphosphate pyrophosphatase from E. coli==		==crystal structure of RdgB- inosine triphosphate pyrophosphatase from E. coli==
	<StructureSection load='1k7k' size='340' side='right' caption='[[1k7k]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1k7k' size='340' side='right' caption='[[1k7k]], [[Resolution\|resolution]] 1.50Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1k7k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K7K FirstGlance]. <br>		<table><tr><td colspan='2'>[[1k7k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K7K FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1k7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k7k OCA], [http://pdbe.org/1k7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k7k RCSB], [http://www.ebi.ac.uk/pdbsum/1k7k PDBsum], [http://www.topsan.org/Proteins/MCSG/1k7k TOPSAN]</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=1k7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k7k OCA], [http://pdbe.org/1k7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k7k RCSB], [http://www.ebi.ac.uk/pdbsum/1k7k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k7k ProSAT], [http://www.topsan.org/Proteins/MCSG/1k7k TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	<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=1k7k ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:35, 11 September 2015

OCA — Fri, 11 Sep 2015 21:35:45 GMT

←Older revision		Revision as of 21:35, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1k7k' size='340' side='right' caption='[[1k7k]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1k7k' size='340' side='right' caption='[[1k7k]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k7k]] 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=1K7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K7K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k7k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K7K FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1k7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k7k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k7k RCSB], [http://www.ebi.ac.uk/pdbsum/1k7k PDBsum], [http://www.topsan.org/Proteins/MCSG/1k7k TOPSAN]</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=1k7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k7k OCA], [http://pdbe.org/1k7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k7k RCSB], [http://www.ebi.ac.uk/pdbsum/1k7k PDBsum], [http://www.topsan.org/Proteins/MCSG/1k7k TOPSAN]</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 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 1k7k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Edwards, A]]		[[Category: Edwards, A]]
	[[Category: Joachimiak, A]]		[[Category: Joachimiak, A]]

OCA at 20:00, 25 December 2014

OCA — Thu, 25 Dec 2014 20:00:01 GMT

←Older revision		Revision as of 20:00, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1k7k]] 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=1K7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K7K FirstGlance]. <br>		<table><tr><td colspan='2'>[[1k7k]] 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=1K7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K7K FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1k7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k7k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k7k RCSB], [http://www.ebi.ac.uk/pdbsum/1k7k PDBsum], [http://www.topsan.org/Proteins/MCSG/1k7k TOPSAN]</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=1k7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k7k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k7k RCSB], [http://www.ebi.ac.uk/pdbsum/1k7k PDBsum], [http://www.topsan.org/Proteins/MCSG/1k7k TOPSAN]</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 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Edwards, A.]]	+	[[Category: Edwards, A]]
-	[[Category: Joachimiak, A.]]	+	[[Category: Joachimiak, A]]
-	[[Category: ~~MCSG, Midwest Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sanishvili, R.]]	+	[[Category: Sanishvili, R]]
-	[[Category: Savchenko, A.]]	+	[[Category: Savchenko, A]]
-	[[Category: Skarina, T.]]	+	[[Category: Skarina, T]]
	[[Category: Disordered se-met]]		[[Category: Disordered se-met]]
	[[Category: His-tag]]		[[Category: His-tag]]
Line 40:		Line 42:
	[[Category: Mad]]		[[Category: Mad]]
	[[Category: Mcsg]]		[[Category: Mcsg]]
-	[[Category: ~~Midwest center for structural genomic]]~~	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category:~~ Protein structure initiative]]	+
-	~~[[Category: Psi~~]]	+
	[[Category: Putative ribosomal protein]]		[[Category: Putative ribosomal protein]]
-	[[Category: Structural genomic]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 09:56, 28 September 2014

OCA — Sun, 28 Sep 2014 09:56:04 GMT

←Older revision		Revision as of 09:56, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1k7k.~~png\|left~~\|200px]]	+	==crystal structure of RdgB- inosine triphosphate pyrophosphatase from E. coli==
		+	<StructureSection load='1k7k' size='340' side='right' caption='[[1k7k]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1k7k]] 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=1K7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K7K FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1k7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k7k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k7k RCSB], [http://www.ebi.ac.uk/pdbsum/1k7k PDBsum], [http://www.topsan.org/Proteins/MCSG/1k7k TOPSAN]</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/k7/1k7k_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_1k7k\| PDB=1k7k \| 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>

-	~~===crystal structure~~ of ~~RdgB- inosine triphosphate pyrophosphatase from E~~. ~~coli===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17976651}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1k7k]] 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=1K7K OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017976651<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Edwards, A.]]		[[Category: Edwards, A.]]

OCA: Protected "1k7k" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 19:33:56 GMT

Protected "1k7k" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:33, 5 December 2012

OCA at 19:33, 5 December 2012

OCA — Wed, 05 Dec 2012 19:33:51 GMT

←Older revision		Revision as of 19:33, 5 December 2012
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-	{{Seed}}
	[[Image:1k7k.png\|left\|200px]]		[[Image:1k7k.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1k7k", 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_1k7k\| PDB=1k7k \| SCENE= }}		{{STRUCTURE_1k7k\| PDB=1k7k \| SCENE= }}

	===crystal structure of RdgB- inosine triphosphate pyrophosphatase from E. coli===		===crystal structure of RdgB- inosine triphosphate pyrophosphatase from E. coli===

-
-	<!--
-	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==
-	~~1K7K~~ 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=1K7K OCA].	+	[[1k7k]] 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=1K7K 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: Edwards, A.]]		[[Category: Edwards, A.]]
Line 42:		Line 30:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Unknown function]]		[[Category: Unknown function]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:28:26 2009''

OCA at 03:28, 18 February 2009

OCA — Wed, 18 Feb 2009 03:28:27 GMT

←Older revision		Revision as of 03:28, 18 February 2009
Line 23:		Line 23:

	==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: Edwards, A.]]		[[Category: Edwards, A.]]
Line 43:		Line 43:
	[[Category: Unknown function]]		[[Category: Unknown function]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri Jan 2 09~~:13:21 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:28:26 2009''