2py5 - Revision history

OCA at 11:12, 30 August 2023

2023-08-30T11:12:04Z

← Older revision		Revision as of 11:12, 30 August 2023
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	<StructureSection load='2py5' size='340' side='right'caption='[[2py5]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2py5' size='340' side='right'caption='[[2py5]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2py5]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bpph2 Bpph2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PY5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2py5]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_virus_phi29 Bacillus virus phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PY5 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1~~,~~2-ETHANEDIOL'>EDO</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]] 1.6Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em~~;~~'>[[2pyj\|2pyj]], [[2pyl\|2pyl]], [[2pzs\|2pzs]]</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>2, gp2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 BPPH2])</td></tr>~~
	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase]~~, ~~with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7]~~ </~~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=2py5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py5 OCA], [https://pdbe.org/2py5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2py5 RCSB], [https://www.ebi.ac.uk/pdbsum/2py5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2py5 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=2py5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py5 OCA], [https://pdbe.org/2py5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2py5 RCSB], [https://www.ebi.ac.uk/pdbsum/2py5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2py5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/DPOL_BPPH2 DPOL_BPPH2]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction.		[https://www.uniprot.org/uniprot/DPOL_BPPH2 DPOL_BPPH2] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 2py5" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2py5" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bpph2]]~~		[[Category: Bacillus virus phi29]]
	~~[[Category: DNA-directed DNA polymerase~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Berman~~, A J~~]]		[[Category: Berman AJ]]
	[[Category: Blanco, L]]		[[Category: Blanco L]]
	[[Category: Goodman~~, J L~~]]		[[Category: Goodman JL]]
	[[Category: Kamtekar, S]]		[[Category: Kamtekar S]]
	[[Category: Lazaro~~, J M~~]]		[[Category: Lazaro JM]]
	[[Category: Salas, M]]		[[Category: Salas M]]
	[[Category: Steitz~~, T A~~]]		[[Category: Steitz TA]]
	[[Category: Vega, M ~~de]]~~		[[Category: De Vega M]]
	~~[[Category: Protein-dna complex]]~~
	~~[[Category: Replication]]~~
	~~[[Category: Transferase-dna complex~~]]

OCA at 15:36, 17 June 2021

2021-06-17T15:36:02Z

← Older revision		Revision as of 15:36, 17 June 2021
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	==Phi29 DNA polymerase complexed with single-stranded DNA==		==Phi29 DNA polymerase complexed with single-stranded DNA==
	<StructureSection load='2py5' size='340' side='right' caption='[[2py5]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2py5' size='340' side='right'caption='[[2py5]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2py5]] is a 7 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bpph2 Bpph2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PY5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2py5]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpph2 Bpph2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PY5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pyj\|2pyj]], [[2pyl\|2pyl]], [[2pzs\|2pzs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2pyj\|2pyj]], [[2pyl\|2pyl]], [[2pzs\|2pzs]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">2, gp2 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 BPPH2])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">2, gp2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 BPPH2])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=2py5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py5 OCA], [~~http~~://pdbe.org/2py5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2py5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2py5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2py5 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=2py5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py5 OCA], [https://pdbe.org/2py5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2py5 RCSB], [https://www.ebi.ac.uk/pdbsum/2py5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2py5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/DPOL_BPPH2 DPOL_BPPH2]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction.		[[https://www.uniprot.org/uniprot/DPOL_BPPH2 DPOL_BPPH2]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 2py5" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2py5" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 40:		Line 37:
	[[Category: Bpph2]]		[[Category: Bpph2]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
			[[Category: Large Structures]]
	[[Category: Berman, A J]]		[[Category: Berman, A J]]
	[[Category: Blanco, L]]		[[Category: Blanco, L]]

OCA at 08:14, 29 August 2018

2018-08-29T08:14:13Z

← Older revision		Revision as of 08:14, 29 August 2018
Line 1:		Line 1:

	==Phi29 DNA polymerase complexed with single-stranded DNA==		==Phi29 DNA polymerase complexed with single-stranded DNA==
	<StructureSection load='2py5' size='340' side='right' caption='[[2py5]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2py5' size='340' side='right' caption='[[2py5]], [[Resolution\|resolution]] 1.60Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">2, gp2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 BPPH2])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">2, gp2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 BPPH2])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=2py5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py5 OCA], [http://pdbe.org/2py5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2py5 RCSB], [http://www.ebi.ac.uk/pdbsum/2py5 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=2py5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py5 OCA], [http://pdbe.org/2py5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2py5 RCSB], [http://www.ebi.ac.uk/pdbsum/2py5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2py5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2py5_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2py5_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2py5 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:24, 11 September 2015

2015-09-11T07:24:56Z

← Older revision		Revision as of 07:24, 11 September 2015
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	<StructureSection load='2py5' size='340' side='right' caption='[[2py5]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2py5' size='340' side='right' caption='[[2py5]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2py5]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_phage_phi29 Bacillus phage phi29~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PY5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2py5]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpph2 Bpph2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PY5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pyj\|2pyj]], [[2pyl\|2pyl]], [[2pzs\|2pzs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pyj\|2pyj]], [[2pyl\|2pyl]], [[2pzs\|2pzs]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">2, gp2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 ~~Bacillus phage phi29~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">2, gp2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 BPPH2])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=2py5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2py5 RCSB], [http://www.ebi.ac.uk/pdbsum/2py5 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=2py5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py5 OCA], [http://pdbe.org/2py5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2py5 RCSB], [http://www.ebi.ac.uk/pdbsum/2py5 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2py5" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus phage phi29~~]]		[[Category: Bpph2]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Berman, A J]]		[[Category: Berman, A J]]

OCA at 13:11, 25 December 2014

2014-12-25T13:11:32Z

← Older revision		Revision as of 13:11, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2py5]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_phage_phi29 Bacillus phage phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PY5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2py5]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_phage_phi29 Bacillus phage phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PY5 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pyj\|2pyj]], [[2pyl\|2pyl]], [[2pzs\|2pzs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pyj\|2pyj]], [[2pyl\|2pyl]], [[2pzs\|2pzs]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">2, gp2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 Bacillus phage phi29])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">2, gp2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 Bacillus phage phi29])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=2py5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2py5 RCSB], [http://www.ebi.ac.uk/pdbsum/2py5 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=2py5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2py5 RCSB], [http://www.ebi.ac.uk/pdbsum/2py5 PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/DPOL_BPPH2 DPOL_BPPH2]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Bacillus phage phi29]]		[[Category: Bacillus phage phi29]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Berman, A J.]]		[[Category: Berman, A J]]
	[[Category: Blanco, L.]]		[[Category: Blanco, L]]
	[[Category: Goodman, J L.]]		[[Category: Goodman, J L]]
	[[Category: Kamtekar, S.]]		[[Category: Kamtekar, S]]
	[[Category: Lazaro, J M.]]		[[Category: Lazaro, J M]]
	[[Category: Salas, M.]]		[[Category: Salas, M]]
	[[Category: Steitz, T A.]]		[[Category: Steitz, T A]]
	[[Category: Vega, M de.]]		[[Category: Vega, M de]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
	[[Category: Replication]]		[[Category: Replication]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 06:13, 29 September 2014

2014-09-29T06:13:59Z

← Older revision		Revision as of 06:13, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2py5~~.~~png~~\|~~left~~\|~~200px~~]]		==Phi29 DNA polymerase complexed with single-stranded DNA==
			<StructureSection load='2py5' size='340' side='right' caption='[[2py5]], [[Resolution\|resolution]] 1.60Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2py5]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_phage_phi29 Bacillus phage phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PY5 FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pyj\|2pyj]], [[2pyl\|2pyl]], [[2pzs\|2pzs]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">2, gp2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 Bacillus phage phi29])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=2py5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2py5 RCSB], [http://www.ebi.ac.uk/pdbsum/2py5 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/py/2py5_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 ==
			Replicative DNA polymerases (DNAPs) move along template DNA in a processive manner. The structural basis of the mechanism of translocation has been better studied in the A-family of polymerases than in the B-family of replicative polymerases. To address this issue, we have determined the X-ray crystal structures of phi29 DNAP, a member of the protein-primed subgroup of the B-family of polymerases, complexed with primer-template DNA in the presence or absence of the incoming nucleoside triphosphate, the pre- and post-translocated states, respectively. Comparison of these structures reveals a mechanism of translocation that appears to be facilitated by the coordinated movement of two conserved tyrosine residues into the insertion site. This differs from the mechanism employed by the A-family polymerases, in which a conserved tyrosine moves into the templating and insertion sites during the translocation step. Polymerases from the two families also interact with downstream single-stranded template DNA in very different ways.

	~~{{STRUCTURE_2py5\| PDB=2py5 \| SCENE= }}~~		Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases.,Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA EMBO J. 2007 Jul 25;26(14):3494-505. Epub 2007 Jul 5. PMID:17611604<ref>PMID:17611604</ref>

	~~===Phi29 DNA polymerase complexed with single-stranded DNA===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17611604}}~~

	~~==About this Structure==~~
	~~[[2py5]] is~~ a ~~7 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Bacillus_phage_phi29 Bacillus phage phi29]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann.ac.il/oca-bin~~/~~ocashort?id=2PY5 OCA].~~

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:017611604<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Bacillus phage phi29]]		[[Category: Bacillus phage phi29]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]

OCA at 17:04, 20 October 2012

2012-10-20T17:04:52Z

← Older revision		Revision as of 17:04, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2py5]] is a 7 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacillus_phage_phi29 Bacillus phage phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA].		[[2py5]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_phage_phi29 Bacillus phage phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA].

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

OCA: Protected "2py5" [edit=sysop:move=sysop]

2012-07-26T23:46:13Z

Protected "2py5" [edit=sysop:move=sysop]

← Older revision	Revision as of 23:46, 26 July 2012
(No difference)

OCA at 23:46, 26 July 2012

2012-07-26T23:46:12Z

← Older revision		Revision as of 23:46, 26 July 2012
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	~~{{Seed}}~~
	[[Image:2py5.png\|left\|200px]]		[[Image:2py5.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2py5", 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_2py5\| PDB=2py5 \| SCENE= }}		{{STRUCTURE_2py5\| PDB=2py5 \| SCENE= }}

	===Phi29 DNA polymerase complexed with single-stranded DNA===		===Phi29 DNA polymerase complexed with single-stranded DNA===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17611604}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17611604 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17611604}}		{{ABSTRACT_PUBMED_17611604}}

	==About this Structure==		==About this Structure==
	~~2PY5~~ is a 7 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Bacillus_phage_phi29 Bacillus phage phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA].		[[2py5]] is a 7 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_phage_phi29 Bacillus phage phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA].

			==See Also==
			*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17611604~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017611604</ref><references group="xtra"/>
	[[Category: Bacillus phage phi29]]		[[Category: Bacillus phage phi29]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
Line 35:		Line 26:
	[[Category: Vega, M de.]]		[[Category: Vega, M de.]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
			[[Category: Replication]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 17:05:08 2009''~~		[[Category: Transferase-dna complex]]

OCA at 15:05, 17 February 2009

2009-02-17T15:05:10Z

← Older revision		Revision as of 15:05, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2PY5 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Bacillus_phage_phi29 Bacillus phage phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA].		2PY5 is a 7 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_phage_phi29 Bacillus phage phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA].

	==Reference==		==Reference==
	Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases., Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA, EMBO J. 2007 Jul 25;26(14):3494-505. Epub 2007 Jul 5. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~17611604 17611604]~~		<ref group="xtra">PMID:17611604</ref><references group="xtra"/>
	[[Category: Bacillus phage phi29]]		[[Category: Bacillus phage phi29]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	~~[[Category: Single protein]]~~
	[[Category: Berman, A J.]]		[[Category: Berman, A J.]]
	[[Category: Blanco, L.]]		[[Category: Blanco, L.]]
Line 37:		Line 36:
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 23~~:55:~~29 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:05:08 2009''