2d7d - Revision history

OCA at 08:24, 25 October 2023

2023-10-25T08:24:45Z

← Older revision		Revision as of 08:24, 25 October 2023
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	<StructureSection load='2d7d' size='340' side='right'caption='[[2d7d]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2d7d' size='340' side='right'caption='[[2d7d]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d7d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D7D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d7d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D7D FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADP:ADENOSINE~~-~~5-DIPHOSPHATE'>ADP</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]] 2.1Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~uvrB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=1423 "Vibrio subtilis" Ehrenberg 1835])~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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=2d7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7d OCA], [https://pdbe.org/2d7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d7d RCSB], [https://www.ebi.ac.uk/pdbsum/2d7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d7d 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=2d7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7d OCA], [https://pdbe.org/2d7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d7d RCSB], [https://www.ebi.ac.uk/pdbsum/2d7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d7d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/UVRB_BACSU UVRB_BACSU]] The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage (By similarity).		[https://www.uniprot.org/uniprot/UVRB_BACSU UVRB_BACSU] The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage (By similarity).
	== 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: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]		[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Barrett~~, T E]]~~		[[Category: Barrett TE]]
	~~[[Category: Helicase]]~~
	~~[[Category: Hydrolase-dna complex]]~~
	~~[[Category: Protein-dna-adp ternary complex~~]]

OCA at 11:55, 3 February 2021

2021-02-03T11:55:02Z

← Older revision		Revision as of 11:55, 3 February 2021
Line 1:		Line 1:

	==Structural insights into the cryptic DNA dependent ATP-ase activity of UvrB==		==Structural insights into the cryptic DNA dependent ATP-ase activity of UvrB==
	<StructureSection load='2d7d' size='340' side='right' caption='[[2d7d]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2d7d' size='340' side='right'caption='[[2d7d]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d7d]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2D7D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d7d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D7D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uvrB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uvrB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=2d7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7d OCA], [~~http~~://pdbe.org/2d7d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2d7d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2d7d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2d7d 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=2d7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7d OCA], [https://pdbe.org/2d7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d7d RCSB], [https://www.ebi.ac.uk/pdbsum/2d7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d7d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/UVRB_BACSU UVRB_BACSU]] The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage (By similarity).		[[https://www.uniprot.org/uniprot/UVRB_BACSU UVRB_BACSU]] The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Vibrio subtilis ehrenberg 1835]]		[[Category: Vibrio subtilis ehrenberg 1835]]
			[[Category: Large Structures]]
	[[Category: Barrett, T E]]		[[Category: Barrett, T E]]
	[[Category: Helicase]]		[[Category: Helicase]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]
	[[Category: Protein-dna-adp ternary complex]]		[[Category: Protein-dna-adp ternary complex]]

OCA at 06:25, 30 May 2018

2018-05-30T06:25:43Z

← Older revision		Revision as of 06:25, 30 May 2018
Line 1:		Line 1:

	==Structural insights into the cryptic DNA dependent ATP-ase activity of UvrB==		==Structural insights into the cryptic DNA dependent ATP-ase activity of UvrB==
	<StructureSection load='2d7d' size='340' side='right' caption='[[2d7d]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2d7d' size='340' side='right' caption='[[2d7d]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d7d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"~~bacillus_globigii~~"~~_migula_1900~~ "~~bacillus globigii~~" ~~migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D7D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d7d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D7D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uvrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "~~Bacillus globigii~~" ~~Migula 1900~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uvrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=2d7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7d OCA], [http://pdbe.org/2d7d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d7d RCSB], [http://www.ebi.ac.uk/pdbsum/2d7d 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=2d7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7d OCA], [http://pdbe.org/2d7d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d7d RCSB], [http://www.ebi.ac.uk/pdbsum/2d7d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d7d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d7/2d7d_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d7/2d7d_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=2d7d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus globigii migula 1900~~]]		[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: Barrett, T E]]		[[Category: Barrett, T E]]
	[[Category: Helicase]]		[[Category: Helicase]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]
	[[Category: Protein-dna-adp ternary complex]]		[[Category: Protein-dna-adp ternary complex]]

OCA at 01:32, 12 September 2015

2015-09-12T01:32:01Z

← Older revision		Revision as of 01:32, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='2d7d' size='340' side='right' caption='[[2d7d]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2d7d' size='340' side='right' caption='[[2d7d]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d7d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D7D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d7d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D7D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uvrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uvrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=2d7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d7d RCSB], [http://www.ebi.ac.uk/pdbsum/2d7d 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=2d7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7d OCA], [http://pdbe.org/2d7d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d7d RCSB], [http://www.ebi.ac.uk/pdbsum/2d7d PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 2d7d" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Bacillus ~~subtilis~~]]		[[Category: Bacillus globigii migula 1900]]
	[[Category: Barrett, T E]]		[[Category: Barrett, T E]]
	[[Category: Helicase]]		[[Category: Helicase]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]
	[[Category: Protein-dna-adp ternary complex]]		[[Category: Protein-dna-adp ternary complex]]

OCA at 22:01, 25 December 2014

2014-12-25T22:01:59Z

← Older revision		Revision as of 22:01, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d7d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D7D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d7d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D7D FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uvrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uvrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=2d7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d7d RCSB], [http://www.ebi.ac.uk/pdbsum/2d7d 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=2d7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d7d RCSB], [http://www.ebi.ac.uk/pdbsum/2d7d PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/UVRB_BACSU UVRB_BACSU]] The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Barrett, T E.]]		[[Category: Barrett, T E]]
	[[Category: Helicase]]		[[Category: Helicase]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]
	[[Category: Protein-dna-adp ternary complex]]		[[Category: Protein-dna-adp ternary complex]]

OCA at 01:47, 30 September 2014

2014-09-30T01:47:31Z

← Older revision		Revision as of 01:47, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2d7d~~.~~png~~\|~~left~~\|~~200px~~]]		==Structural insights into the cryptic DNA dependent ATP-ase activity of UvrB==
			<StructureSection load='2d7d' size='340' side='right' caption='[[2d7d]], [[Resolution\|resolution]] 2.10Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2d7d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D7D FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene><br>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uvrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=2d7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d7d RCSB], [http://www.ebi.ac.uk/pdbsum/2d7d 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/d7/2d7d_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The UvrABC pathway is a ubiquitously occurring mechanism targeted towards the repair of bulky base damage. Key to this process is UvrB, a DNA-dependent limited helicase that acts as a lesion recognition element whilst part of a tracking complex involving UvrA, and as a DNA-binding platform required for the presentation of damage to UvrC for subsequent processing. We have been able to determine the structure of a ternary complex involving UvrB* (a C-terminal truncation of full-length UvrB), a polythymine trinucleotide and ADP. This structure has highlighted the roles of key conserved residues in DNA binding distinct from those of the beta-hairpin, where most of the attention in previous studies has been focussed. We are also the first to report the structural basis underlying conformational re-modelling of the beta-hairpin that is absolutely required for DNA binding and how this event results in an ATPase primed for catalysis. Our data provide the first insights at the molecular level into the transformation of UvrB into an active helicase.

	~~{{STRUCTURE_2d7d\| PDB=2d7d \| SCENE= }}~~		Structural insights into the cryptic DNA-dependent ATPase activity of UvrB.,Eryilmaz J, Ceschini S, Ryan J, Geddes S, Waters TR, Barrett TE J Mol Biol. 2006 Mar 17;357(1):62-72. Epub 2006 Jan 6. PMID:16426634<ref>PMID:16426634</ref>

	~~===Structural insights into~~ the ~~cryptic DNA dependent ATP-ase activity~~ of ~~UvrB===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

	~~{{ABSTRACT_PUBMED_16426634}}~~		==See Also==
			*[[UvrABC\|UvrABC]]
	==~~About this Structure~~==		== References ==
	[[~~2d7d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis~~]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA~~].		<references/>
			__TOC__
	==~~Reference~~==		</StructureSection>
	<~~ref group="xtra">PMID:016426634<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Barrett, T E.]]		[[Category: Barrett, T E.]]

OCA: Protected "2d7d" [edit=sysop:move=sysop]

2013-01-06T11:02:06Z

Protected "2d7d" [edit=sysop:move=sysop]

← Older revision	Revision as of 11:02, 6 January 2013
(No difference)

OCA at 11:02, 6 January 2013

2013-01-06T11:02:03Z

← Older revision		Revision as of 11:02, 6 January 2013
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	~~{{Seed}}~~
	[[Image:2d7d.png\|left\|200px]]		[[Image:2d7d.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2d7d", 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_2d7d\| PDB=2d7d \| SCENE= }}		{{STRUCTURE_2d7d\| PDB=2d7d \| SCENE= }}

	===Structural insights into the cryptic DNA dependent ATP-ase activity of UvrB===		===Structural insights into the cryptic DNA dependent ATP-ase activity of UvrB===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16426634}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16426634 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16426634}}		{{ABSTRACT_PUBMED_16426634}}

	==About this Structure==		==About this Structure==
	~~2D7D~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA].		[[2d7d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16426634~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016426634</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Barrett, T E.]]		[[Category: Barrett, T E.]]
	[[Category: Helicase]]		[[Category: Helicase]]
			[[Category: Hydrolase-dna complex]]
	[[Category: Protein-dna-adp ternary complex]]		[[Category: Protein-dna-adp ternary complex]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:13:47 2009''~~

OCA at 07:13, 18 February 2009

2009-02-18T07:13:48Z

← Older revision		Revision as of 07:13, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2D7D is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA].		2D7D is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7D OCA].

	==Reference==		==Reference==
	~~Structural insights into the cryptic DNA-dependent ATPase activity of UvrB., Eryilmaz J, Ceschini S, Ryan J, Geddes S, Waters TR, Barrett TE, J Mol Biol. 2006 Mar 17;357(1):62-72. Epub 2006 Jan 6.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16426634 16426634]~~		<ref group="xtra">PMID:16426634</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	~~[[Category: Protein complex]]~~
	[[Category: Barrett, T E.]]		[[Category: Barrett, T E.]]
	[[Category: Helicase]]		[[Category: Helicase]]
	[[Category: Protein-dna-adp ternary complex]]		[[Category: Protein-dna-adp ternary complex]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 15~~:27:~~53 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:13:47 2009''

OCA at 12:27, 29 July 2008

2008-07-29T12:27:55Z

← Older revision		Revision as of 12:27, 29 July 2008
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	[[Image:2d7d.~~gif~~\|left\|200px]]		{{Seed}}
			[[Image:2d7d.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2d7d\| PDB=2d7d \| SCENE= }}		{{STRUCTURE_2d7d\| PDB=2d7d \| SCENE= }}

	~~'''~~Structural insights into the cryptic DNA dependent ATP-ase activity of UvrB~~'''~~		===Structural insights into the cryptic DNA dependent ATP-ase activity of UvrB===


	~~==Overview==~~		<!--
	The ~~UvrABC pathway is a ubiquitously occurring mechanism targeted towards the repair of bulky base damage. Key to~~ this ~~process is UvrB~~, ~~a DNA-dependent limited helicase that acts as a lesion recognition element whilst part of a tracking complex involving UvrA~~, ~~and as a DNA-binding platform required for~~ the ~~presentation of damage~~ to ~~UvrC for subsequent processing. We have been able to determine~~ the structure of a ternary complex involving UvrB* (~~a C-terminal truncation of full-length UvrB~~)~~, a polythymine trinucleotide and ADP. This structure has highlighted the roles of key conserved residues in DNA binding distinct from those of the beta-hairpin~~, where ~~most of~~ the ~~attention in previous studies has been focussed~~. ~~We are also the first to report the structural basis underlying conformational re~~-~~modelling of the beta~~-hairpin that is absolutely required for DNA binding and how this event results in an ATPase primed for catalysis. Our data provide the first insights at the molecular level into the transformation of UvrB into an active helicase.		The line below this paragraph, {{ABSTRACT_PUBMED_16426634}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 16426634 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_16426634}}

	==About this Structure==		==About this Structure==
Line 25:		Line 29:
	[[Category: Helicase]]		[[Category: Helicase]]
	[[Category: Protein-dna-adp ternary complex]]		[[Category: Protein-dna-adp ternary complex]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 23~~:48:06 2008''
			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 15:27:53 2008''