2fdc - Revision history

OCA at 09:22, 14 February 2024

2024-02-14T09:22:54Z

← Older revision		Revision as of 09:22, 14 February 2024
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	<StructureSection load='2fdc' size='340' side='right'caption='[[2fdc]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='2fdc' size='340' side='right'caption='[[2fdc]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fdc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~'bacillus_caldotenax' 'bacillus~~ caldotenax']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FDC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fdc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_caldotenax Bacillus caldotenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FDC FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FLQ:N~~-[~~6-(ACETYLAMINO)HEXYL~~]-3~~,6-DIHYDROXY-~~3~~-OXO-3H-SPIRO[2-BENZOFURAN-1,9-XANTHENE]-6-CARBOXAMIDE'>FLQ</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]] 3.3Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;'>~~[~~[1t5l\|1t5l]~~], [~~[1d9x\|1d9x]]~~, ~~[[1d9z\|1d9z~~]~~], [[1yd1\|1yd1]], [[1qoj\|1qoj]]</div></td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLQ:N-[6-(ACETYLAMINO)HEXYL]-3,6-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9-XANTHENE]-6-CARBOXAMIDE'>FLQ</scene></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=1395 'Bacillus caldotenax'])~~</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=2fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdc OCA], [https://pdbe.org/2fdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fdc RCSB], [https://www.ebi.ac.uk/pdbsum/2fdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fdc 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=2fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdc OCA], [https://pdbe.org/2fdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fdc RCSB], [https://www.ebi.ac.uk/pdbsum/2fdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fdc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/UVRB_BACCA UVRB_BACCA]] 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).[HAMAP-Rule:MF_00204]		[https://www.uniprot.org/uniprot/UVRB_BACCA UVRB_BACCA] 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).[HAMAP-Rule:MF_00204]
	== 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=2fdc 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=2fdc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	DNA-damage recognition in the nucleotide excision repair (NER) cascade is a complex process, operating on a wide variety of damages. UvrB is the central component in prokaryotic NER, directly involved in DNA-damage recognition and guiding the DNA through repair synthesis. We report the first structure of a UvrB-double-stranded DNA complex, providing insights into the mechanism by which UvrB binds DNA, leading to formation of the preincision complex. One DNA strand, containing a 3' overhang, threads behind a beta-hairpin motif of UvrB, indicating that this motif inserts between the strands of the double helix, thereby locking down either the damaged or undamaged strand. The nucleotide directly behind the beta-hairpin is flipped out and inserted into a small, highly conserved pocket in UvrB.

	Structural basis for DNA recognition and processing by UvrB.,Truglio JJ, Karakas E, Rhau B, Wang H, DellaVecchia MJ, Van Houten B, Kisker C Nat Struct Mol Biol. 2006 Apr;13(4):360-4. Epub 2006 Mar 12. PMID:16532007<ref>PMID:16532007</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2fdc" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[UvrABC\|UvrABC]]		*[[UvrABC\|UvrABC]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Bacillus caldotenax]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kisker, C]]		[[Category: Kisker C]]
	[[Category: Truglio~~, J J]]~~		[[Category: Truglio JJ]]
	~~[[Category: Dna binding protein-dna complex]]~~
	~~[[Category: Dna repair]]~~
	~~[[Category: Ner]]~~
	~~[[Category: Nucleotide excision repair]]~~
	~~[[Category: Protein-dna complex]]~~
	~~[[Category: Uvra]]~~
	~~[[Category: Uvrb]]~~
	~~[[Category: Uvrc]]~~
	~~[[Category: Uvrd~~]]

OCA at 07:15, 24 February 2021

2021-02-24T07:15:18Z

← Older revision		Revision as of 07:15, 24 February 2021
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	==Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex==		==Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex==
	<StructureSection load='2fdc' size='340' side='right' caption='[[2fdc]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='2fdc' size='340' side='right'caption='[[2fdc]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fdc]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/'bacillus_caldotenax' 'bacillus caldotenax']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2FDC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fdc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/'bacillus_caldotenax' 'bacillus caldotenax']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FDC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLQ:N-[6-(ACETYLAMINO)HEXYL]-3,6-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9-XANTHENE]-6-CARBOXAMIDE'>FLQ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLQ:N-[6-(ACETYLAMINO)HEXYL]-3,6-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9-XANTHENE]-6-CARBOXAMIDE'>FLQ</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5l\|1t5l]], [[1d9x\|1d9x]], [[1d9z\|1d9z]], [[1yd1\|1yd1]], [[1qoj\|1qoj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1t5l\|1t5l]], [[1d9x\|1d9x]], [[1d9z\|1d9z]], [[1yd1\|1yd1]], [[1qoj\|1qoj]]</div></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=1395 'Bacillus caldotenax'])</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=1395 'Bacillus caldotenax'])</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=2fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdc OCA], [~~http~~://pdbe.org/2fdc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2fdc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2fdc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2fdc 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=2fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdc OCA], [https://pdbe.org/2fdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fdc RCSB], [https://www.ebi.ac.uk/pdbsum/2fdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fdc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/UVRB_BACCA UVRB_BACCA]] 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).[HAMAP-Rule:MF_00204]		[[https://www.uniprot.org/uniprot/UVRB_BACCA UVRB_BACCA]] 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).[HAMAP-Rule:MF_00204]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/2fdc_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/2fdc_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>
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	</div>		</div>
	<div class="pdbe-citations 2fdc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2fdc" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[UvrABC\|UvrABC]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus caldotenax]]		[[Category: Bacillus caldotenax]]
			[[Category: Large Structures]]
	[[Category: Kisker, C]]		[[Category: Kisker, C]]
	[[Category: Truglio, J J]]		[[Category: Truglio, J J]]

OCA at 07:36, 18 October 2017

2017-10-18T07:36:55Z

← Older revision		Revision as of 07:36, 18 October 2017
Line 1:		Line 1:

	==Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex==		==Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex==
	<StructureSection load='2fdc' size='340' side='right' caption='[[2fdc]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='2fdc' size='340' side='right' caption='[[2fdc]], [[Resolution\|resolution]] 3.30Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5l\|1t5l]], [[1d9x\|1d9x]], [[1d9z\|1d9z]], [[1yd1\|1yd1]], [[1qoj\|1qoj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5l\|1t5l]], [[1d9x\|1d9x]], [[1d9z\|1d9z]], [[1yd1\|1yd1]], [[1qoj\|1qoj]]</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=1395 'Bacillus caldotenax'])</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=1395 'Bacillus caldotenax'])</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=2fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdc OCA], [http://pdbe.org/2fdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fdc RCSB], [http://www.ebi.ac.uk/pdbsum/2fdc 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=2fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdc OCA], [http://pdbe.org/2fdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fdc RCSB], [http://www.ebi.ac.uk/pdbsum/2fdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2fdc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 2fdc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2fdc" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[UvrABC\|UvrABC]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:35, 7 February 2016

2016-02-07T06:35:59Z

← Older revision		Revision as of 06:35, 7 February 2016
Line 18:		Line 18:
	<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=2fdc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:47, 9 September 2015

2015-09-09T22:47:40Z

← Older revision		Revision as of 22:47, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='2fdc' size='340' side='right' caption='[[2fdc]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='2fdc' size='340' side='right' caption='[[2fdc]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_caldotenax Bacillus~~ caldotenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FDC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/'bacillus_caldotenax' 'bacillus caldotenax']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FDC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLQ:N-[6-(ACETYLAMINO)HEXYL]-3,6-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9-XANTHENE]-6-CARBOXAMIDE'>FLQ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLQ:N-[6-(ACETYLAMINO)HEXYL]-3,6-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9-XANTHENE]-6-CARBOXAMIDE'>FLQ</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5l\|1t5l]], [[1d9x\|1d9x]], [[1d9z\|1d9z]], [[1yd1\|1yd1]], [[1qoj\|1qoj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5l\|1t5l]], [[1d9x\|1d9x]], [[1d9z\|1d9z]], [[1yd1\|1yd1]], [[1qoj\|1qoj]]</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=1395 Bacillus caldotenax])</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=1395 'Bacillus caldotenax'])</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=2fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fdc RCSB], [http://www.ebi.ac.uk/pdbsum/2fdc 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=2fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdc OCA], [http://pdbe.org/2fdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fdc RCSB], [http://www.ebi.ac.uk/pdbsum/2fdc PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2fdc" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 08:40, 24 December 2014

2014-12-24T08:40:45Z

← Older revision		Revision as of 08:40, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_caldotenax Bacillus caldotenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FDC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_caldotenax Bacillus caldotenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FDC FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLQ:N-[6-(ACETYLAMINO)HEXYL]-3,6-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9-XANTHENE]-6-CARBOXAMIDE'>FLQ</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLQ:N-[6-(ACETYLAMINO)HEXYL]-3,6-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9-XANTHENE]-6-CARBOXAMIDE'>FLQ</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5l\|1t5l]], [[1d9x\|1d9x]], [[1d9z\|1d9z]], [[1yd1\|1yd1]], [[1qoj\|1qoj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5l\|1t5l]], [[1d9x\|1d9x]], [[1d9z\|1d9z]], [[1yd1\|1yd1]], [[1qoj\|1qoj]]</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=1395 Bacillus caldotenax])</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=1395 Bacillus caldotenax])</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=2fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fdc RCSB], [http://www.ebi.ac.uk/pdbsum/2fdc 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=2fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fdc RCSB], [http://www.ebi.ac.uk/pdbsum/2fdc PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/UVRB_BACCA UVRB_BACCA]] 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).[HAMAP-Rule:MF_00204]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus caldotenax]]		[[Category: Bacillus caldotenax]]
	[[Category: Kisker, C.]]		[[Category: Kisker, C]]
	[[Category: Truglio, J J.]]		[[Category: Truglio, J J]]
	[[Category: Dna binding protein-dna complex]]		[[Category: Dna binding protein-dna complex]]
	[[Category: Dna repair]]		[[Category: Dna repair]]

OCA at 09:20, 3 October 2014

2014-10-03T09:20:39Z

← Older revision		Revision as of 09:20, 3 October 2014
Line 1:		Line 1:
	~~{{STRUCTURE_2fdc\| PDB=2fdc \| SCENE= }}~~		==Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex==
	===Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex===		<StructureSection load='2fdc' size='340' side='right' caption='[[2fdc]], [[Resolution\|resolution]] 3.30Å' scene=''>
	~~{{ABSTRACT_PUBMED_16532007}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[2fdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_caldotenax Bacillus caldotenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FDC FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLQ:N-[6-(ACETYLAMINO)HEXYL]-3,6-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9-XANTHENE]-6-CARBOXAMIDE'>FLQ</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5l\|1t5l]], [[1d9x\|1d9x]], [[1d9z\|1d9z]], [[1yd1\|1yd1]], [[1qoj\|1qoj]]</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=1395 Bacillus caldotenax])</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=2fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fdc RCSB], [http://www.ebi.ac.uk/pdbsum/2fdc 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/fd/2fdc_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 ==
			DNA-damage recognition in the nucleotide excision repair (NER) cascade is a complex process, operating on a wide variety of damages. UvrB is the central component in prokaryotic NER, directly involved in DNA-damage recognition and guiding the DNA through repair synthesis. We report the first structure of a UvrB-double-stranded DNA complex, providing insights into the mechanism by which UvrB binds DNA, leading to formation of the preincision complex. One DNA strand, containing a 3' overhang, threads behind a beta-hairpin motif of UvrB, indicating that this motif inserts between the strands of the double helix, thereby locking down either the damaged or undamaged strand. The nucleotide directly behind the beta-hairpin is flipped out and inserted into a small, highly conserved pocket in UvrB.

	~~==Function==~~		Structural basis for DNA recognition and processing by UvrB.,Truglio JJ, Karakas E, Rhau B, Wang H, DellaVecchia MJ, Van Houten B, Kisker C Nat Struct Mol Biol. 2006 Apr;13(4):360-4. Epub 2006 Mar 12. PMID:16532007<ref>PMID:16532007</ref>
	~~[[http://www.uniprot.org/uniprot/UVRB_BACCA UVRB_BACCA]] 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).[HAMAP-Rule~~:~~MF_00204]~~

	~~==About this Structure==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[2fdc]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_caldotenax Bacillus caldotenax]~~. ~~Full crystallographic information is available from [http:/~~/~~oca.weizmann.ac.il/oca-bin/ocashort?id=2FDC OCA].~~		</div>

	==See Also==		==See Also==
	*[[UvrABC\|UvrABC]]		*[[UvrABC\|UvrABC]]
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:016532007</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
			</StructureSection>
	[[Category: Bacillus caldotenax]]		[[Category: Bacillus caldotenax]]
	[[Category: Kisker, C.]]		[[Category: Kisker, C.]]

OCA at 08:38, 23 April 2014

2014-04-23T08:38:22Z

← Older revision		Revision as of 08:38, 23 April 2014
Line 1:		Line 1:
	~~[[Image:2fdc.png\|left\|200px]]~~

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2fdc", 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_2fdc\| PDB=2fdc \| SCENE= }}		{{STRUCTURE_2fdc\| PDB=2fdc \| SCENE= }}

	===Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex===		===Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex===
			{{ABSTRACT_PUBMED_16532007}}

			==Function==
	~~<!--~~		[[http://www.uniprot.org/uniprot/UVRB_BACCA UVRB_BACCA]] 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).[HAMAP-Rule:MF_00204]
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16532007}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov~~), ~~where 16532007~~ is the ~~PubMed ID number~~.
	-->
	~~{{ABSTRACT_PUBMED_16532007}}~~

	==About this Structure==		==About this Structure==
	[[2fdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_caldotenax Bacillus caldotenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDC OCA].		[[2fdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_caldotenax Bacillus caldotenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDC OCA].

			==See Also==
			*[[UvrABC\|UvrABC]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:016532007</ref><~~ref~~ group="xtra"~~>PMID:018578568<~~/~~ref~~><references ~~group="xtra"~~/>		<ref group="xtra">PMID:016532007</ref><references group="xtra"/><references/>
	[[Category: Bacillus caldotenax]]		[[Category: Bacillus caldotenax]]
	[[Category: Kisker, C.]]		[[Category: Kisker, C.]]

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

2012-06-10T15:54:51Z

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

← Older revision	Revision as of 15:54, 10 June 2012
(No difference)