2fcc - Revision history

OCA at 09:24, 30 August 2023

OCA — Wed, 30 Aug 2023 09:24:48 GMT

←Older revision		Revision as of 09:24, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2fcc' size='340' side='right'caption='[[2fcc]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2fcc' size='340' side='right'caption='[[2fcc]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2fcc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bpt4 Bpt4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FCC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2fcc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FCC FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.3Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">denV ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </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=2fcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcc OCA], [https://pdbe.org/2fcc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fcc RCSB], [https://www.ebi.ac.uk/pdbsum/2fcc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fcc 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=2fcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcc OCA], [https://pdbe.org/2fcc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fcc RCSB], [https://www.ebi.ac.uk/pdbsum/2fcc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fcc ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/END5_BPT4 END5_BPT4]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]		*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
Line 37:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt4~~]]	+	[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dodson~~, M L~~]]	+	[[Category: Dodson ML]]
-	[[Category: Fernandes~~, A S~~]]	+	[[Category: Fernandes AS]]
-	[[Category: Golan, G]]	+	[[Category: Golan G]]
-	[[Category: Grollman~~, A P~~]]	+	[[Category: Grollman AP]]
-	[[Category: Lloyd~~, R S~~]]	+	[[Category: Lloyd RS]]
-	[[Category: McCullough~~, A K~~]]	+	[[Category: McCullough AK]]
-	[[Category: Shoham, G]]	+	[[Category: Shoham G]]
-	[[Category: Zharkov~~, D O]]~~	+	[[Category: Zharkov DO]]
-	~~[[Category: Covalent intermediate]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Enzyme-dna complex]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pyrimidine dimer]]~~	+
-	~~[[Category: T4-pdg~~]]	+

OCA at 07:14, 24 February 2021

OCA — Wed, 24 Feb 2021 07:14:44 GMT

←Older revision		Revision as of 07:14, 24 February 2021
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	==Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site==		==Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site==
-	<StructureSection load='2fcc' size='340' side='right' caption='[[2fcc]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='2fcc' size='340' side='right'caption='[[2fcc]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2fcc]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2FCC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2fcc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FCC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">denV ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">denV ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </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=2fcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcc OCA], [~~http~~://pdbe.org/2fcc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2fcc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2fcc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2fcc 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=2fcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcc OCA], [https://pdbe.org/2fcc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fcc RCSB], [https://www.ebi.ac.uk/pdbsum/2fcc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fcc ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]	+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
-	*[[Endonuclease\|Endonuclease]]	+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Dodson, M L]]		[[Category: Dodson, M L]]
	[[Category: Fernandes, A S]]		[[Category: Fernandes, A S]]

OCA at 08:33, 14 June 2018

OCA — Thu, 14 Jun 2018 08:33:21 GMT

←Older revision		Revision as of 08:33, 14 June 2018
Line 1:		Line 1:
		+
	==Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site==		==Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site==
	<StructureSection load='2fcc' size='340' side='right' caption='[[2fcc]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2fcc' size='340' side='right' caption='[[2fcc]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">denV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">denV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </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=2fcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcc OCA], [http://pdbe.org/2fcc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fcc RCSB], [http://www.ebi.ac.uk/pdbsum/2fcc 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=2fcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcc OCA], [http://pdbe.org/2fcc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fcc RCSB], [http://www.ebi.ac.uk/pdbsum/2fcc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2fcc ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fc/2fcc_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fc/2fcc_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>

OCA at 04:17, 10 February 2016

OCA — Wed, 10 Feb 2016 04:17:03 GMT

←Older revision		Revision as of 04:17, 10 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2fcc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:18, 11 September 2015

OCA — Fri, 11 Sep 2015 05:18:07 GMT

←Older revision		Revision as of 05:18, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2fcc' size='340' side='right' caption='[[2fcc]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2fcc' size='340' side='right' caption='[[2fcc]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2fcc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_t4 Enterobacteria phage t4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FCC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2fcc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FCC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">denV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 ~~Enterobacteria phage T4~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">denV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </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=2fcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fcc RCSB], [http://www.ebi.ac.uk/pdbsum/2fcc 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=2fcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcc OCA], [http://pdbe.org/2fcc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fcc RCSB], [http://www.ebi.ac.uk/pdbsum/2fcc PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2fcc" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage t4~~]]	+	[[Category: Bpt4]]
	[[Category: Dodson, M L]]		[[Category: Dodson, M L]]
	[[Category: Fernandes, A S]]		[[Category: Fernandes, A S]]

OCA at 11:44, 25 December 2014

OCA — Thu, 25 Dec 2014 11:44:21 GMT

←Older revision		Revision as of 11:44, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fcc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FCC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fcc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FCC FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">denV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">denV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </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=2fcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fcc RCSB], [http://www.ebi.ac.uk/pdbsum/2fcc 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=2fcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fcc RCSB], [http://www.ebi.ac.uk/pdbsum/2fcc PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
-	[[Category: Dodson, M L.]]	+	[[Category: Dodson, M L]]
-	[[Category: Fernandes, A S.]]	+	[[Category: Fernandes, A S]]
-	[[Category: Golan, G.]]	+	[[Category: Golan, G]]
-	[[Category: Grollman, A P.]]	+	[[Category: Grollman, A P]]
-	[[Category: Lloyd, R S.]]	+	[[Category: Lloyd, R S]]
-	[[Category: McCullough, A K.]]	+	[[Category: McCullough, A K]]
-	[[Category: Shoham, G.]]	+	[[Category: Shoham, G]]
-	[[Category: Zharkov, D O.]]	+	[[Category: Zharkov, D O]]
	[[Category: Covalent intermediate]]		[[Category: Covalent intermediate]]
	[[Category: Dna repair]]		[[Category: Dna repair]]

OCA at 08:49, 3 October 2014

OCA — Fri, 03 Oct 2014 08:49:56 GMT

←Older revision		Revision as of 08:49, 3 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2fcc.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site==
		+	<StructureSection load='2fcc' size='340' side='right' caption='[[2fcc]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2fcc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FCC FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">denV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </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=2fcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fcc RCSB], [http://www.ebi.ac.uk/pdbsum/2fcc 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/fc/2fcc_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 base excision repair (BER) pathway for ultraviolet light (UV)-induced cyclobutane pyrimidine dimers is initiated by DNA glycosylases that also possess abasic (AP) site lyase activity. The prototypical enzyme known to catalyze these reactions is the T4 pyrimidine dimer glycosylase (T4-Pdg). The fundamental chemical reactions and the critical amino acids that lead to both glycosyl and phosphodiester bond scission are known. Catalysis proceeds via a protonated imine covalent intermediate between the alpha-amino group of the N-terminal threonine residue and the C1' of the deoxyribose sugar of the 5' pyrimidine at the dimer site. This covalent complex can be trapped as an irreversible, reduced cross-linked DNA-protein complex by incubation with a strong reducing agent. This active site trapping reaction is equally efficient on DNA substrates containing pyrimidine dimers or AP sites. Herein, we report the co-crystal structure of T4-Pdg as a reduced covalent complex with an AP site-containing duplex oligodeoxynucleotide. This high-resolution structure reveals essential precatalytic and catalytic features, including flipping of the nucleotide opposite the AP site, a sharp kink (approximately 66 degrees ) in the DNA at the dimer site and the covalent bond linking the enzyme to the DNA. Superposition of this structure with a previously published co-crystal structure of a catalytically incompetent mutant of T4-Pdg with cyclobutane dimer-containing DNA reveals new insights into the structural requirements and the mechanisms involved in DNA bending, nucleotide flipping and catalytic reaction.

-	~~{{STRUCTURE_2fcc\| PDB=2fcc \| SCENE= }}~~	+	Structure of T4 pyrimidine dimer glycosylase in a reduced imine covalent complex with abasic site-containing DNA.,Golan G, Zharkov DO, Grollman AP, Dodson ML, McCullough AK, Lloyd RS, Shoham G J Mol Biol. 2006 Sep 15;362(2):241-58. Epub 2006 Jul 7. PMID:16916523<ref>PMID:16916523</ref>

-	~~===Crystal Structure~~ of ~~T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16916523}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2fcc]] is a 6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA].~~	+

	==See Also==		==See Also==
-	*[[DNA ~~glycosylate~~\|DNA ~~glycosylate~~]]	+	*[[DNA glycosylase\|DNA glycosylase]]
-		+	*[[Endonuclease\|Endonuclease]]
-	==~~Reference~~==	+	== References ==
-	<~~ref group="xtra">PMID:016916523<~~/~~ref~~><~~references group="xtra"~~/>	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Dodson, M L.]]		[[Category: Dodson, M L.]]

OCA at 16:18, 20 October 2012

OCA — Sat, 20 Oct 2012 16:18:10 GMT

←Older revision		Revision as of 16:18, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2fcc]] is a 6 chain structure ~~of [[DNA glycosylate]]~~ with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA].	+	[[2fcc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA].

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

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

OCA — Thu, 26 Jul 2012 21:14:01 GMT

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

←Older revision

Revision as of 21:14, 26 July 2012

OCA at 21:13, 26 July 2012

OCA — Thu, 26 Jul 2012 21:13:59 GMT

←Older revision		Revision as of 21:13, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2fcc.png\|left\|200px]]		[[Image:2fcc.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2fcc", 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_2fcc\| PDB=2fcc \| SCENE= }}		{{STRUCTURE_2fcc\| PDB=2fcc \| SCENE= }}

	===Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site===		===Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16916523}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16916523 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16916523}}		{{ABSTRACT_PUBMED_16916523}}

	==About this Structure==		==About this Structure==
-	~~2FCC~~ is a 6 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA].	+	[[2fcc]] is a 6 chain structure of [[DNA glycosylate]] with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA].
		+
		+	==See Also==
		+	*[[DNA glycosylate\|DNA glycosylate]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16916523~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016916523</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Dodson, M L.]]		[[Category: Dodson, M L.]]
Line 37:		Line 28:
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
	[[Category: Enzyme-dna complex]]		[[Category: Enzyme-dna complex]]
		+	[[Category: Hydrolase]]
	[[Category: Pyrimidine dimer]]		[[Category: Pyrimidine dimer]]
	[[Category: T4-pdg]]		[[Category: T4-pdg]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:21:50 2009''