1u5w - Revision history

OCA at 08:44, 14 February 2024

OCA — Wed, 14 Feb 2024 08:44:13 GMT

←Older revision		Revision as of 08:44, 14 February 2024
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	<StructureSection load='1u5w' size='340' side='right'caption='[[1u5w]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1u5w' size='340' side='right'caption='[[1u5w]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u5w]] is a 8 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=1U5W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1U5W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u5w]] is a 8 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=1U5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U5W FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.3Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>yjjX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1u5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u5w OCA], [~~http~~://pdbe.org/1u5w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1u5w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1u5w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1u5w ProSAT], [~~http~~://www.topsan.org/Proteins/BSGI/1u5w 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=1u5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u5w OCA], [https://pdbe.org/1u5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u5w RCSB], [https://www.ebi.ac.uk/pdbsum/1u5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u5w ProSAT], [https://www.topsan.org/Proteins/BSGI/1u5w TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NCPP_ECOLI NCPP_ECOLI]] Phosphatase that hydrolyzes non-canonical purine nucleotides such as XTP and ITP to their respective diphosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions. ITP is the best substrate, followed by XTP, GDP or dITP. Also implicated in the resistance against the thiamine metabolism inhibitors bacimethrin and CF3-HMP.<ref>PMID:16216582</ref>	+	[https://www.uniprot.org/uniprot/NCPP_ECOLI NCPP_ECOLI] Phosphatase that hydrolyzes non-canonical purine nucleotides such as XTP and ITP to their respective diphosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions. ITP is the best substrate, followed by XTP, GDP or dITP. Also implicated in the resistance against the thiamine metabolism inhibitors bacimethrin and CF3-HMP.<ref>PMID:16216582</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=1u5w 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=1u5w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Inosine triphosphate (ITP) and xanthosine triphosphate (XTP) are formed upon deamination of ATP and GTP as a result of exposure to chemical mutagens and oxidative damage. Nucleic acid synthesis requires safeguard mechanisms to minimize undesired lethal incorporation of ITP and XTP. Here, we present the crystal structure of YjjX, a protein of hitherto unknown function. The three-dimensional fold of YjjX is similar to those of Mj0226 from Methanococcus janschii, which possesses nucleotidase activity, and of Maf from Bacillus subtilis, which can bind nucleotides. Biochemical analyses of YjjX revealed it to exhibit specific phosphatase activity for inosine and xanthosine triphosphates and have a possible interaction with elongation factor Tu. The enzymatic activity of YjjX as an inosine/xanthosine triphosphatase provides evidence for a plausible protection mechanism by clearing the noncanonical nucleotides from the cell during oxidative stress in E. coli.
-
-	Identification of an ITPase/XTPase in Escherichia coli by structural and biochemical analysis.,Zheng J, Singh VK, Jia Z Structure. 2005 Oct;13(10):1511-20. PMID:16216582<ref>PMID:16216582</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1u5w" 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: Structural genomic]]~~	+	[[Category: Jia Z]]
-	[[Category: Jia, Z]]	+	[[Category: Singh VK]]
-	[[Category: Singh~~, V K~~]]	+	[[Category: Zheng J]]
-	[[Category: Zheng, J]]	+
-	~~[[Category: Layers alpha/beta/alpha protein]]~~	+
-	~~[[Category: Bsgi]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 07:22, 30 December 2020

OCA — Wed, 30 Dec 2020 07:22:38 GMT

←Older revision		Revision as of 07:22, 30 December 2020
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	==Crystal structure of hypothetical protein yjjX from Escherichia coli==		==Crystal structure of hypothetical protein yjjX from Escherichia coli==
-	<StructureSection load='1u5w' size='340' side='right' caption='[[1u5w]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='1u5w' size='340' side='right'caption='[[1u5w]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u5w]] is a 8 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=1U5W OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1U5W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u5w]] is a 8 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=1U5W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1U5W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yjjX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yjjX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1u5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u5w OCA], [http://pdbe.org/1u5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u5w RCSB], [http://www.ebi.ac.uk/pdbsum/1u5w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u5w ProSAT], [http://www.topsan.org/Proteins/BSGI/1u5w TOPSAN]</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=1u5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u5w OCA], [http://pdbe.org/1u5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u5w RCSB], [http://www.ebi.ac.uk/pdbsum/1u5w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u5w ProSAT], [http://www.topsan.org/Proteins/BSGI/1u5w TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u5/1u5w_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u5/1u5w_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 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Jia, Z]]		[[Category: Jia, Z]]

OCA at 08:35, 12 October 2017

OCA — Thu, 12 Oct 2017 08:35:03 GMT

←Older revision		Revision as of 08:35, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of hypothetical protein yjjX from Escherichia coli==		==Crystal structure of hypothetical protein yjjX from Escherichia coli==
	<StructureSection load='1u5w' size='340' side='right' caption='[[1u5w]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1u5w' size='340' side='right' caption='[[1u5w]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yjjX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yjjX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1u5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u5w OCA], [http://pdbe.org/1u5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u5w RCSB], [http://www.ebi.ac.uk/pdbsum/1u5w PDBsum], [http://www.topsan.org/Proteins/BSGI/1u5w 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=1u5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u5w OCA], [http://pdbe.org/1u5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u5w RCSB], [http://www.ebi.ac.uk/pdbsum/1u5w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u5w ProSAT], [http://www.topsan.org/Proteins/BSGI/1u5w TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 02:57, 10 February 2016

OCA — Wed, 10 Feb 2016 02:57:22 GMT

←Older revision		Revision as of 02:57, 10 February 2016
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	<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=1u5w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:42, 11 September 2015

OCA — Fri, 11 Sep 2015 04:42:01 GMT

←Older revision		Revision as of 04:42, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1u5w' size='340' side='right' caption='[[1u5w]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1u5w' size='340' side='right' caption='[[1u5w]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u5w]] is a 8 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=1U5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U5W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u5w]] is a 8 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=1U5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U5W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yjjX ([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">yjjX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1u5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u5w RCSB], [http://www.ebi.ac.uk/pdbsum/1u5w PDBsum], [http://www.topsan.org/Proteins/BSGI/1u5w 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=1u5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u5w OCA], [http://pdbe.org/1u5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u5w RCSB], [http://www.ebi.ac.uk/pdbsum/1u5w PDBsum], [http://www.topsan.org/Proteins/BSGI/1u5w TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~YJJX_ECOLI YJJX_ECOLI~~]] Phosphatase that hydrolyzes non-canonical purine nucleotides such as XTP and ITP to their respective diphosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions. ITP is the best substrate, followed by XTP, GDP or dITP. Also implicated in the resistance against the thiamine metabolism inhibitors bacimethrin and CF3-HMP.<ref>PMID:16216582</ref>	+	[[http://www.uniprot.org/uniprot/NCPP_ECOLI NCPP_ECOLI]] Phosphatase that hydrolyzes non-canonical purine nucleotides such as XTP and ITP to their respective diphosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions. ITP is the best substrate, followed by XTP, GDP or dITP. Also implicated in the resistance against the thiamine metabolism inhibitors bacimethrin and CF3-HMP.<ref>PMID:16216582</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 27:
	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 1u5w" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Jia, Z]]		[[Category: Jia, Z]]

OCA at 11:19, 25 December 2014

OCA — Thu, 25 Dec 2014 11:19:00 GMT

←Older revision		Revision as of 11:19, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1u5w]] is a 8 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=1U5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U5W FirstGlance]. <br>		<table><tr><td colspan='2'>[[1u5w]] is a 8 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=1U5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U5W FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yjjX ([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">yjjX ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1u5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u5w RCSB], [http://www.ebi.ac.uk/pdbsum/1u5w PDBsum], [http://www.topsan.org/Proteins/BSGI/1u5w 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=1u5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u5w RCSB], [http://www.ebi.ac.uk/pdbsum/1u5w PDBsum], [http://www.topsan.org/Proteins/BSGI/1u5w TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/YJJX_ECOLI YJJX_ECOLI]] Phosphatase that hydrolyzes non-canonical purine nucleotides such as XTP and ITP to their respective diphosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions. ITP is the best substrate, followed by XTP, GDP or dITP. Also implicated in the resistance against the thiamine metabolism inhibitors bacimethrin and CF3-HMP.<ref>PMID:16216582</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: BSGI, Montreal-Kingston Bacterial Structural Genomics Initiative.]]
-	[[Category: Jia, Z.]]
-	[[Category: Singh, V K.]]
-	[[Category: Zheng, J.]]
-	[[Category: 3 layers alpha/beta/alpha protein]]
-	[[Category: Bsgi]]
-	[[Category: Montreal-kingston bacterial structural genomics initiative]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
		+	[[Category: Jia, Z]]
		+	[[Category: Singh, V K]]
		+	[[Category: Zheng, J]]
		+	[[Category: Layers alpha/beta/alpha protein]]
		+	[[Category: Bsgi]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 18:30, 29 September 2014

OCA — Mon, 29 Sep 2014 18:30:08 GMT

←Older revision		Revision as of 18:30, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1u5w.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of hypothetical protein yjjX from Escherichia coli==
		+	<StructureSection load='1u5w' size='340' side='right' caption='[[1u5w]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1u5w]] is a 8 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=1U5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U5W FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yjjX ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1u5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u5w RCSB], [http://www.ebi.ac.uk/pdbsum/1u5w PDBsum], [http://www.topsan.org/Proteins/BSGI/1u5w 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/u5/1u5w_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 (ITP) and xanthosine triphosphate (XTP) are formed upon deamination of ATP and GTP as a result of exposure to chemical mutagens and oxidative damage. Nucleic acid synthesis requires safeguard mechanisms to minimize undesired lethal incorporation of ITP and XTP. Here, we present the crystal structure of YjjX, a protein of hitherto unknown function. The three-dimensional fold of YjjX is similar to those of Mj0226 from Methanococcus janschii, which possesses nucleotidase activity, and of Maf from Bacillus subtilis, which can bind nucleotides. Biochemical analyses of YjjX revealed it to exhibit specific phosphatase activity for inosine and xanthosine triphosphates and have a possible interaction with elongation factor Tu. The enzymatic activity of YjjX as an inosine/xanthosine triphosphatase provides evidence for a plausible protection mechanism by clearing the noncanonical nucleotides from the cell during oxidative stress in E. coli.

-	~~{{STRUCTURE_1u5w\| PDB=1u5w \| SCENE= }}~~	+	Identification of an ITPase/XTPase in Escherichia coli by structural and biochemical analysis.,Zheng J, Singh VK, Jia Z Structure. 2005 Oct;13(10):1511-20. PMID:16216582<ref>PMID:16216582</ref>

-	~~===Crystal structure~~ of ~~hypothetical protein yjjX from Escherichia coli===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16216582}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1u5w]] is a 8 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=1U5W OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016216582<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: BSGI, Montreal-Kingston Bacterial Structural Genomics Initiative.]]		[[Category: BSGI, Montreal-Kingston Bacterial Structural Genomics Initiative.]]

OCA: Protected "1u5w" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 11:09:02 GMT

Protected "1u5w" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:09, 5 January 2013

OCA at 11:09, 5 January 2013

OCA — Sat, 05 Jan 2013 11:09:00 GMT

←Older revision		Revision as of 11:09, 5 January 2013
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-	{{Seed}}
	[[Image:1u5w.png\|left\|200px]]		[[Image:1u5w.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1u5w", 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_1u5w\| PDB=1u5w \| SCENE= }}		{{STRUCTURE_1u5w\| PDB=1u5w \| SCENE= }}

	===Crystal structure of hypothetical protein yjjX from Escherichia coli===		===Crystal structure of hypothetical protein yjjX from Escherichia coli===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16216582}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16216582 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16216582}}		{{ABSTRACT_PUBMED_16216582}}

	==About this Structure==		==About this Structure==
-	~~1U5W~~ is a 8 ~~chains~~ structure ~~of sequences~~ 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=1U5W OCA].	+	[[1u5w]] is a 8 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=1U5W OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16216582~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016216582</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: BSGI, Montreal-Kingston Bacterial Structural Genomics Initiative.]]		[[Category: BSGI, Montreal-Kingston Bacterial Structural Genomics Initiative.]]
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	[[Category: Montreal-kingston bacterial structural genomics initiative]]		[[Category: Montreal-kingston bacterial structural genomics initiative]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-		+	[[Category: Unknown function]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 14:51:57 2009''~~	+

OCA at 12:51, 17 February 2009

OCA — Tue, 17 Feb 2009 12:51:59 GMT

←Older revision		Revision as of 12:51, 17 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
-	~~Identification of an ITPase/XTPase in Escherichia coli by structural and biochemical analysis., Zheng J, Singh VK, Jia Z, Structure. 2005 Oct;13(10):1511-20.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16216582 16216582]~~	+	<ref group="xtra">PMID:16216582</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: BSGI, Montreal-Kingston Bacterial Structural Genomics Initiative.]]		[[Category: BSGI, Montreal-Kingston Bacterial Structural Genomics Initiative.]]
Line 34:		Line 34:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov 16 10~~:00:~~08 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 14:51:57 2009''