1iqu - Revision history

OCA at 07:11, 25 October 2023

OCA — Wed, 25 Oct 2023 07:11:12 GMT

←Older revision		Revision as of 07:11, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='1iqu' size='340' side='right'caption='[[1iqu]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1iqu' size='340' side='right'caption='[[1iqu]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1iqu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IQU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1iqu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IQU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</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]] 2.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1iqr\|1iqr]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Deoxyribodipyrimidine_photo-lyase Deoxyribodipyrimidine photo-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.3 4.1.99.3]~~ </~~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=1iqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iqu OCA], [https://pdbe.org/1iqu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iqu RCSB], [https://www.ebi.ac.uk/pdbsum/1iqu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iqu ProSAT], [https://www.topsan.org/Proteins/RSGI/1iqu 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=1iqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iqu OCA], [https://pdbe.org/1iqu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iqu RCSB], [https://www.ebi.ac.uk/pdbsum/1iqu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iqu ProSAT], [https://www.topsan.org/Proteins/RSGI/1iqu TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PHR_THET8 PHR_THET8]] Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutyl pyrimidine dimers (in cis-syn configuration), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation (By similarity).	+	[https://www.uniprot.org/uniprot/PHR_THET8 PHR_THET8] Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutyl pyrimidine dimers (in cis-syn configuration), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation (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: Flavobacterium thermophilum yoshida and oshima 1971]]
-	[[Category: Deoxyribodipyrimidine photo-lyase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Inoue, Y]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Komori, H]]	+	[[Category: Inoue Y]]
-	[[Category: Kuramitsu, S]]	+	[[Category: Komori H]]
-	[[Category: Masui, R]]	+	[[Category: Kuramitsu S]]
-	[[Category: Miki, K]]	+	[[Category: Masui R]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Miki K]]
-	[[Category: Shibata, T]]	+	[[Category: Shibata T]]
-	[[Category: Yokoyama, S]]	+	[[Category: Yokoyama S]]
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Fad]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Photoreactivating enzyme]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 07:13, 14 April 2021

OCA — Wed, 14 Apr 2021 07:13:22 GMT

←Older revision		Revision as of 07:13, 14 April 2021
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	<StructureSection load='1iqu' size='340' side='right'caption='[[1iqu]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1iqu' size='340' side='right'caption='[[1iqu]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1iqu]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1IQU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1iqu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IQU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iqr\|1iqr]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1iqr\|1iqr]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Deoxyribodipyrimidine_photo-lyase Deoxyribodipyrimidine photo-lyase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.3 4.1.99.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribodipyrimidine_photo-lyase Deoxyribodipyrimidine photo-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.3 4.1.99.3] </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=1iqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iqu OCA], [~~http~~://pdbe.org/1iqu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1iqu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1iqu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1iqu ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1iqu 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=1iqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iqu OCA], [https://pdbe.org/1iqu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iqu RCSB], [https://www.ebi.ac.uk/pdbsum/1iqu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iqu ProSAT], [https://www.topsan.org/Proteins/RSGI/1iqu TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PHR_THET8 PHR_THET8]] Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutyl pyrimidine dimers (in cis-syn configuration), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation (By similarity).	+	[[https://www.uniprot.org/uniprot/PHR_THET8 PHR_THET8]] Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutyl pyrimidine dimers (in cis-syn configuration), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:15, 10 July 2019

OCA — Wed, 10 Jul 2019 07:15:58 GMT

←Older revision		Revision as of 07:15, 10 July 2019
Line 1:		Line 1:

	==Crystal structure of photolyase-thymine complex==		==Crystal structure of photolyase-thymine complex==
-	<StructureSection load='1iqu' size='340' side='right' caption='[[1iqu]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1iqu' size='340' side='right'caption='[[1iqu]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1iqu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IQU FirstGlance]. <br>		<table><tr><td colspan='2'>[[1iqu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IQU FirstGlance]. <br>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iq/1iqu_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iq/1iqu_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 36:		Line 36:
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Deoxyribodipyrimidine photo-lyase]]		[[Category: Deoxyribodipyrimidine photo-lyase]]
		+	[[Category: Large Structures]]
	[[Category: Inoue, Y]]		[[Category: Inoue, Y]]
	[[Category: Komori, H]]		[[Category: Komori, H]]

OCA at 09:46, 4 October 2017

OCA — Wed, 04 Oct 2017 09:46:27 GMT

←Older revision		Revision as of 09:46, 4 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of photolyase-thymine complex==		==Crystal structure of photolyase-thymine complex==
	<StructureSection load='1iqu' size='340' side='right' caption='[[1iqu]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1iqu' size='340' side='right' caption='[[1iqu]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iqr\|1iqr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iqr\|1iqr]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribodipyrimidine_photo-lyase Deoxyribodipyrimidine photo-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.3 4.1.99.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribodipyrimidine_photo-lyase Deoxyribodipyrimidine photo-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.3 4.1.99.3] </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=1iqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iqu OCA], [http://pdbe.org/1iqu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iqu RCSB], [http://www.ebi.ac.uk/pdbsum/1iqu PDBsum], [http://www.topsan.org/Proteins/RSGI/1iqu 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=1iqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iqu OCA], [http://pdbe.org/1iqu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iqu RCSB], [http://www.ebi.ac.uk/pdbsum/1iqu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1iqu ProSAT], [http://www.topsan.org/Proteins/RSGI/1iqu TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=1iqu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 40:		Line 41:
	[[Category: Masui, R]]		[[Category: Masui, R]]
	[[Category: Miki, K]]		[[Category: Miki, K]]
		+	[[Category: Structural genomic]]
	[[Category: Shibata, T]]		[[Category: Shibata, T]]
	[[Category: Yokoyama, S]]		[[Category: Yokoyama, S]]
Line 47:		Line 49:
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Photoreactivating enzyme]]		[[Category: Photoreactivating enzyme]]
-	[[Category: Structural genomic]]
	[[Category: Rsgi]]		[[Category: Rsgi]]

OCA at 00:04, 12 September 2015

OCA — Sat, 12 Sep 2015 00:04:46 GMT

←Older revision		Revision as of 00:04, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='1iqu' size='340' side='right' caption='[[1iqu]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1iqu' size='340' side='right' caption='[[1iqu]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1iqu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IQU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1iqu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IQU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iqr\|1iqr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iqr\|1iqr]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribodipyrimidine_photo-lyase Deoxyribodipyrimidine photo-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.3 4.1.99.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribodipyrimidine_photo-lyase Deoxyribodipyrimidine photo-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.3 4.1.99.3] </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=1iqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iqu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iqu RCSB], [http://www.ebi.ac.uk/pdbsum/1iqu PDBsum], [http://www.topsan.org/Proteins/RSGI/1iqu 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=1iqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iqu OCA], [http://pdbe.org/1iqu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iqu RCSB], [http://www.ebi.ac.uk/pdbsum/1iqu PDBsum], [http://www.topsan.org/Proteins/RSGI/1iqu TOPSAN]</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 1iqu" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Deoxyribodipyrimidine photo-lyase]]		[[Category: Deoxyribodipyrimidine photo-lyase]]
-	[[Category: Thermus thermophilus]]
	[[Category: Inoue, Y]]		[[Category: Inoue, Y]]
	[[Category: Komori, H]]		[[Category: Komori, H]]

OCA at 21:11, 25 December 2014

OCA — Thu, 25 Dec 2014 21:11:11 GMT

←Older revision		Revision as of 21:11, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1iqu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IQU FirstGlance]. <br>		<table><tr><td colspan='2'>[[1iqu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IQU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iqr\|1iqr]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iqr\|1iqr]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribodipyrimidine_photo-lyase Deoxyribodipyrimidine photo-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.3 4.1.99.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribodipyrimidine_photo-lyase Deoxyribodipyrimidine photo-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.3 4.1.99.3] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1iqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iqu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iqu RCSB], [http://www.ebi.ac.uk/pdbsum/1iqu PDBsum], [http://www.topsan.org/Proteins/RSGI/1iqu 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=1iqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iqu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iqu RCSB], [http://www.ebi.ac.uk/pdbsum/1iqu PDBsum], [http://www.topsan.org/Proteins/RSGI/1iqu TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PHR_THET8 PHR_THET8]] Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutyl pyrimidine dimers (in cis-syn configuration), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Deoxyribodipyrimidine photo-lyase]]		[[Category: Deoxyribodipyrimidine photo-lyase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Inoue, Y.]]	+	[[Category: Inoue, Y]]
-	[[Category: Komori, H.]]	+	[[Category: Komori, H]]
-	[[Category: Kuramitsu, S.]]	+	[[Category: Kuramitsu, S]]
-	[[Category: Masui, R.]]	+	[[Category: Masui, R]]
-	[[Category: Miki, K.]]	+	[[Category: Miki, K]]
-	[[Category: Shibata, T.]]	+	[[Category: Shibata, T]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Dna repair]]		[[Category: Dna repair]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
Line 44:		Line 46:
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Photoreactivating enzyme]]		[[Category: Photoreactivating enzyme]]
-	[[Category: Riken structural genomics/proteomics initiative]]
-	[[Category: Rsgi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
		+	[[Category: Rsgi]]

OCA at 12:06, 28 September 2014

OCA — Sun, 28 Sep 2014 12:06:21 GMT

←Older revision		Revision as of 12:06, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1iqu.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of photolyase-thymine complex==
		+	<StructureSection load='1iqu' size='340' side='right' caption='[[1iqu]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1iqu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IQU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iqr\|1iqr]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribodipyrimidine_photo-lyase Deoxyribodipyrimidine photo-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.3 4.1.99.3] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1iqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iqu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iqu RCSB], [http://www.ebi.ac.uk/pdbsum/1iqu PDBsum], [http://www.topsan.org/Proteins/RSGI/1iqu 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/iq/1iqu_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 photolyase is a pyrimidine-dimer repair enzyme that uses visible light. Photolyase generally contains two chromophore cofactors. One is a catalytic cofactor directly contributing to the repair of a pyrimidine-dimer. The other is a light-harvesting cofactor, which absorbs visible light and transfers energy to the catalytic cofactor. Photolyases are classified according to their second cofactor into either a folate- or deazaflavin-type. The native structures of both types of photolyases have already been determined, but the mechanism of substrate recognition remains largely unclear because of the lack of structural information regarding the photolyase-substrate complex. Photolyase from Thermus thermophilus, the first thermostable class I photolyase found, is favorable for function analysis, but even the type of the second cofactor has not been identified. Here, we report the crystal structures of T. thermophilus photolyase in both forms of the native enzyme and the complex along with a part of its substrate, thymine. A structural comparison with other photolyases suggests that T. thermophilus photolyase has structural features allowing for thermostability and that its light-harvesting cofactor binding site bears a close resemblance to a deazaflavin-type photolyase. One thymine base is found at the hole, a putative substrate-binding site near the catalytic cofactor in the complex form. This structural data for the photolyase-thymine complex allow us to propose a detailed model for the pyrimidine-dimer recognition mechanism.

-	~~{{STRUCTURE_1iqu\| PDB=1iqu \| SCENE= }}~~	+	Crystal structure of thermostable DNA photolyase: pyrimidine-dimer recognition mechanism.,Komori H, Masui R, Kuramitsu S, Yokoyama S, Shibata T, Inoue Y, Miki K Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13560-5. Epub 2001 Nov 13. PMID:11707580<ref>PMID:11707580</ref>

-	~~===Crystal structure~~ of ~~photolyase-thymine complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11707580}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1iqu]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus Thermus thermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1IQU OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:011707580<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Deoxyribodipyrimidine photo-lyase]]		[[Category: Deoxyribodipyrimidine photo-lyase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

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

OCA — Wed, 28 Nov 2012 14:59:07 GMT

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

←Older revision

Revision as of 14:59, 28 November 2012

OCA at 14:59, 28 November 2012

OCA — Wed, 28 Nov 2012 14:59:04 GMT

←Older revision		Revision as of 14:59, 28 November 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1iqu.png\|left\|200px]]		[[Image:1iqu.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1iqu", 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_1iqu\| PDB=1iqu \| SCENE= }}		{{STRUCTURE_1iqu\| PDB=1iqu \| SCENE= }}

	===Crystal structure of photolyase-thymine complex===		===Crystal structure of photolyase-thymine complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11707580}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11707580 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11707580}}		{{ABSTRACT_PUBMED_11707580}}

	==About this Structure==		==About this Structure==
-	~~1IQU~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQU OCA].	+	[[1iqu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQU OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11707580~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011707580</ref><references group="xtra"/>
	[[Category: Deoxyribodipyrimidine photo-lyase]]		[[Category: Deoxyribodipyrimidine photo-lyase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
Line 41:		Line 29:
	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Sep 3 16:21:39 2009''

OCA at 13:21, 3 September 2009

OCA — Thu, 03 Sep 2009 13:21:41 GMT

←Older revision		Revision as of 13:21, 3 September 2009
Line 10:		Line 10:
	{{STRUCTURE_1iqu\| PDB=1iqu \| SCENE= }}		{{STRUCTURE_1iqu\| PDB=1iqu \| SCENE= }}

-	===~~crystal~~ structure of photolyase-thymine complex===	+	===Crystal structure of photolyase-thymine complex===


Line 31:		Line 31:
	[[Category: Masui, R.]]		[[Category: Masui, R.]]
	[[Category: Miki, K.]]		[[Category: Miki, K.]]
-	[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
	[[Category: Shibata, T.]]		[[Category: Shibata, T.]]
	[[Category: Yokoyama, S.]]		[[Category: Yokoyama, S.]]
Line 37:		Line 36:
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
	[[Category: Fad]]		[[Category: Fad]]
		+	[[Category: Lyase]]
	[[Category: Photoreactivating enzyme]]		[[Category: Photoreactivating enzyme]]
	[[Category: Riken structural genomics/proteomics initiative]]		[[Category: Riken structural genomics/proteomics initiative]]
Line 42:		Line 42:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Feb 18 07~~:43:32 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Sep 3 16:21:39 2009''