1dml - Revision history

OCA at 06:56, 7 February 2024

2024-02-07T06:56:14Z

←Older revision		Revision as of 06:56, 7 February 2024
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	<StructureSection load='1dml' size='340' side='right'caption='[[1dml]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1dml' size='340' side='right'caption='[[1dml]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dml]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Hhv-1 Hhv-~~1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DML OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DML FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dml]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_alphaherpesvirus_1 Human alphaherpesvirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DML OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DML FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>[[1plq\|1plq]]~~, [[~~1axc~~\|~~1axc~~]]~~, [[1b8h\|1b8h]]</div></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]] 2.7Å</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=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [https://pdbe.org/1dml PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [https://www.ebi.ac.uk/pdbsum/1dml PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dml 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=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [https://pdbe.org/1dml PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [https://www.ebi.ac.uk/pdbsum/1dml PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dml ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PAP_HHV11 PAP_HHV11]] Plays an essential role in viral DNA replication by acting as the polymerase accessory subunit. Associates with the viral polymerase to increase its processivity and forms high-affinity direct interactions with DNA. Facilitates the origin-binding protein UL9 loading onto DNA thus increasing its ability to assemble into a functional complex capable of unwinding duplex DNA.<ref>PMID:2173776</ref> [[https://www.uniprot.org/uniprot/DPOL_HHV1A DPOL_HHV1A]] Replicates viral genomic DNA. The replication complex is composed of six viral proteins: the DNA polymerase, processivity factor, primase, primase-associated factor, helicase, and ssDNA-binding protein. Additionally, the polymerase contains an intrinsic ribonuclease H (RNase H) activity that specifically degrades RNA/DNA heteroduplexes or duplex DNA substrates in the 5' to 3' direction. Therefore, it can catalyze the excision of the RNA primers that initiate the synthesis of Okazaki fragments at a replication fork during viral DNA replication (By similarity).	+	[https://www.uniprot.org/uniprot/PAP_HHV11 PAP_HHV11] Plays an essential role in viral DNA replication by acting as the polymerase accessory subunit. Associates with the viral polymerase to increase its processivity and forms high-affinity direct interactions with DNA. Facilitates the origin-binding protein UL9 loading onto DNA thus increasing its ability to assemble into a functional complex capable of unwinding duplex DNA.<ref>PMID:2173776</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 19:
	</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=1dml 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=1dml ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Herpes simplex virus DNA polymerase is a heterodimer composed of a catalytic subunit, Pol, and an unusual processivity subunit, UL42, which, unlike processivity factors such as PCNA, directly binds DNA. The crystal structure of a complex of the C-terminal 36 residues of Pol bound to residues 1-319 of UL42 reveals remarkable similarities between UL42 and PCNA despite contrasting biochemical properties and lack of sequence homology. Moreover, the Pol-UL42 interaction resembles the interaction between the cell cycle regulator p21 and PCNA. The structure and previous data suggest that the UL42 monomer interacts with DNA quite differently than does multimeric toroidal PCNA. The details of the structure lead to a model for the mechanism of UL42, provide the basis for drug design, and allow modeling of other proteins that lack sequence homology with UL42 or PCNA.
-
-	The crystal structure of an unusual processivity factor, herpes simplex virus UL42, bound to the C terminus of its cognate polymerase.,Zuccola HJ, Filman DJ, Coen DM, Hogle JM Mol Cell. 2000 Feb;5(2):267-78. PMID:10882068<ref>PMID:10882068</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1dml" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~DNA-directed DNA polymerase]]~~	+	[[Category: Human alphaherpesvirus 1]]
-	~~[[Category: Hhv-~~1]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Coen~~, D M~~]]	+	[[Category: Coen DM]]
-	[[Category: Filman~~, D J~~]]	+	[[Category: Filman DJ]]
-	[[Category: Hogle~~, J M~~]]	+	[[Category: Hogle JM]]
-	[[Category: Zuccola~~, H J]]~~	+	[[Category: Zuccola HJ]]
-	~~[[Category: Dna binding protein-transferase complex]]~~	+
-	~~[[Category: Dna synthesis]]~~	+
-	~~[[Category: Herpes simplex virus]]~~	+
-	~~[[Category: Pcna]]~~	+
-	~~[[Category: Processivity]]~~	+
-	~~[[Category: Sliding clamp~~]]	+

OCA at 06:30, 11 August 2021

2021-08-11T06:30:57Z

←Older revision		Revision as of 06:30, 11 August 2021
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	<StructureSection load='1dml' size='340' side='right'caption='[[1dml]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1dml' size='340' side='right'caption='[[1dml]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dml]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Hhv-1 Hhv-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DML OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1DML FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dml]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Hhv-1 Hhv-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DML OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DML FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1plq\|1plq]], [[1axc\|1axc]], [[1b8h\|1b8h]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1plq\|1plq]], [[1axc\|1axc]], [[1b8h\|1b8h]]</div></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=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [~~http~~://pdbe.org/1dml PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1dml PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1dml 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=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [https://pdbe.org/1dml PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [https://www.ebi.ac.uk/pdbsum/1dml PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dml ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PAP_HHV11 PAP_HHV11]] Plays an essential role in viral DNA replication by acting as the polymerase accessory subunit. Associates with the viral polymerase to increase its processivity and forms high-affinity direct interactions with DNA. Facilitates the origin-binding protein UL9 loading onto DNA thus increasing its ability to assemble into a functional complex capable of unwinding duplex DNA.<ref>PMID:2173776</ref> [[~~http~~://www.uniprot.org/uniprot/DPOL_HHV1A DPOL_HHV1A]] Replicates viral genomic DNA. The replication complex is composed of six viral proteins: the DNA polymerase, processivity factor, primase, primase-associated factor, helicase, and ssDNA-binding protein. Additionally, the polymerase contains an intrinsic ribonuclease H (RNase H) activity that specifically degrades RNA/DNA heteroduplexes or duplex DNA substrates in the 5' to 3' direction. Therefore, it can catalyze the excision of the RNA primers that initiate the synthesis of Okazaki fragments at a replication fork during viral DNA replication (By similarity).	+	[[https://www.uniprot.org/uniprot/PAP_HHV11 PAP_HHV11]] Plays an essential role in viral DNA replication by acting as the polymerase accessory subunit. Associates with the viral polymerase to increase its processivity and forms high-affinity direct interactions with DNA. Facilitates the origin-binding protein UL9 loading onto DNA thus increasing its ability to assemble into a functional complex capable of unwinding duplex DNA.<ref>PMID:2173776</ref> [[https://www.uniprot.org/uniprot/DPOL_HHV1A DPOL_HHV1A]] Replicates viral genomic DNA. The replication complex is composed of six viral proteins: the DNA polymerase, processivity factor, primase, primase-associated factor, helicase, and ssDNA-binding protein. Additionally, the polymerase contains an intrinsic ribonuclease H (RNase H) activity that specifically degrades RNA/DNA heteroduplexes or duplex DNA substrates in the 5' to 3' direction. Therefore, it can catalyze the excision of the RNA primers that initiate the synthesis of Okazaki fragments at a replication fork during viral DNA replication (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:01, 6 November 2019

2019-11-06T09:01:40Z

←Older revision		Revision as of 09:01, 6 November 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C-TERMINUS OF HSV POL==		==CRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C-TERMINUS OF HSV POL==
-	<StructureSection load='1dml' size='340' side='right' caption='[[1dml]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='1dml' size='340' side='right'caption='[[1dml]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dml]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Hhv-1 Hhv-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DML FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dml]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Hhv-1 Hhv-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DML FirstGlance]. <br>
Line 35:		Line 35:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Hhv-1]]		[[Category: Hhv-1]]
		+	[[Category: Large Structures]]
	[[Category: Coen, D M]]		[[Category: Coen, D M]]
	[[Category: Filman, D J]]		[[Category: Filman, D J]]

OCA at 07:48, 13 December 2017

2017-12-13T07:48:03Z

←Older revision		Revision as of 07:48, 13 December 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C-TERMINUS OF HSV POL==		==CRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C-TERMINUS OF HSV POL==
	<StructureSection load='1dml' size='340' side='right' caption='[[1dml]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1dml' size='340' side='right' caption='[[1dml]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1plq\|1plq]], [[1axc\|1axc]], [[1b8h\|1b8h]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1plq\|1plq]], [[1axc\|1axc]], [[1b8h\|1b8h]]</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=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [http://pdbe.org/1dml PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [http://www.ebi.ac.uk/pdbsum/1dml 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=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [http://pdbe.org/1dml PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [http://www.ebi.ac.uk/pdbsum/1dml PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dml ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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/dm/1dml_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dm/1dml_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 01:40, 7 February 2016

2016-02-07T01:40:43Z

←Older revision		Revision as of 01:40, 7 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=1dml ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:26, 9 September 2015

2015-09-09T20:26:30Z

←Older revision		Revision as of 20:26, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1dml' size='340' side='right' caption='[[1dml]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1dml' size='340' side='right' caption='[[1dml]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dml]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Human_herpesvirus_1 Human herpesvirus~~ 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DML FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dml]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Hhv-1 Hhv-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DML FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1plq\|1plq]], [[1axc\|1axc]], [[1b8h\|1b8h]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1plq\|1plq]], [[1axc\|1axc]], [[1b8h\|1b8h]]</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=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [http://www.ebi.ac.uk/pdbsum/1dml 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=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [http://pdbe.org/1dml PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [http://www.ebi.ac.uk/pdbsum/1dml PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~VPAP_HHV11 VPAP_HHV11~~]] Plays an essential role in viral DNA replication by acting as the polymerase accessory subunit. Associates with the viral polymerase to increase its processivity and forms high-affinity direct interactions with DNA. Facilitates the origin-binding protein UL9 loading onto DNA thus increasing its ability to assemble into a functional complex capable of unwinding duplex DNA.<ref>PMID:2173776</ref> [[http://www.uniprot.org/uniprot/DPOL_HHV1A DPOL_HHV1A]] Replicates viral genomic DNA. The replication complex is composed of six viral proteins: the DNA polymerase, processivity factor, primase, primase-associated factor, helicase, and ssDNA-binding protein. Additionally, the polymerase contains an intrinsic ribonuclease H (RNase H) activity that specifically degrades RNA/DNA heteroduplexes or duplex DNA substrates in the 5' to 3' direction. Therefore, it can catalyze the excision of the RNA primers that initiate the synthesis of Okazaki fragments at a replication fork during viral DNA replication (By similarity).	+	[[http://www.uniprot.org/uniprot/PAP_HHV11 PAP_HHV11]] Plays an essential role in viral DNA replication by acting as the polymerase accessory subunit. Associates with the viral polymerase to increase its processivity and forms high-affinity direct interactions with DNA. Facilitates the origin-binding protein UL9 loading onto DNA thus increasing its ability to assemble into a functional complex capable of unwinding duplex DNA.<ref>PMID:2173776</ref> [[http://www.uniprot.org/uniprot/DPOL_HHV1A DPOL_HHV1A]] Replicates viral genomic DNA. The replication complex is composed of six viral proteins: the DNA polymerase, processivity factor, primase, primase-associated factor, helicase, and ssDNA-binding protein. Additionally, the polymerase contains an intrinsic ribonuclease H (RNase H) activity that specifically degrades RNA/DNA heteroduplexes or duplex DNA substrates in the 5' to 3' direction. Therefore, it can catalyze the excision of the RNA primers that initiate the synthesis of Okazaki fragments at a replication fork during viral DNA replication (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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 1dml" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: ~~Human herpesvirus~~ 1]]	+	[[Category: Hhv-1]]
	[[Category: Coen, D M]]		[[Category: Coen, D M]]
	[[Category: Filman, D J]]		[[Category: Filman, D J]]

OCA at 06:42, 24 December 2014

2014-12-24T06:42:38Z

←Older revision		Revision as of 06:42, 24 December 2014
Line 7:		Line 7:
	<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=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [http://www.ebi.ac.uk/pdbsum/1dml 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=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [http://www.ebi.ac.uk/pdbsum/1dml PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VPAP_HHV11 VPAP_HHV11]] Plays an essential role in viral DNA replication by acting as the polymerase accessory subunit. Associates with the viral polymerase to increase its processivity and forms high-affinity direct interactions with DNA. Facilitates the origin-binding protein UL9 loading onto DNA thus increasing its ability to assemble into a functional complex capable of unwinding duplex DNA.<ref>PMID:2173776</ref> [[http://www.uniprot.org/uniprot/DPOL_HHV1A DPOL_HHV1A]] Replicates viral genomic DNA. The replication complex is composed of six viral proteins: the DNA polymerase, processivity factor, primase, primase-associated factor, helicase, and ssDNA-binding protein. Additionally, the polymerase contains an intrinsic ribonuclease H (RNase H) activity that specifically degrades RNA/DNA heteroduplexes or duplex DNA substrates in the 5' to 3' direction. Therefore, it can catalyze the excision of the RNA primers that initiate the synthesis of Okazaki fragments at a replication fork during viral DNA replication (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 18:13, 22 December 2014

2014-12-22T18:13:23Z

←Older revision		Revision as of 18:13, 22 December 2014
Line 31:		Line 31:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Human herpesvirus 1]]		[[Category: Human herpesvirus 1]]
-	[[Category: Coen, D M.]]	+	[[Category: Coen, D M]]
-	[[Category: Filman, D J.]]	+	[[Category: Filman, D J]]
-	[[Category: Hogle, J M.]]	+	[[Category: Hogle, J M]]
-	[[Category: Zuccola, H J.]]	+	[[Category: Zuccola, H J]]
	[[Category: Dna binding protein-transferase complex]]		[[Category: Dna binding protein-transferase complex]]
	[[Category: Dna synthesis]]		[[Category: Dna synthesis]]

OCA at 05:46, 10 October 2014

2014-10-10T05:46:52Z

←Older revision		Revision as of 05:46, 10 October 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dml]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_1 Human herpesvirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DML FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dml]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_1 Human herpesvirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DML FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1plq\|1plq]], [[1axc\|1axc]], [[1b8h\|1b8h]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1plq\|1plq]], [[1axc\|1axc]], [[1b8h\|1b8h]]</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=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [http://www.ebi.ac.uk/pdbsum/1dml 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=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [http://www.ebi.ac.uk/pdbsum/1dml PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:30, 4 September 2014

2014-09-04T06:30:32Z

←Older revision		Revision as of 06:30, 4 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1dml.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C-TERMINUS OF HSV POL==
		+	<StructureSection load='1dml' size='340' side='right' caption='[[1dml]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1dml]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_1 Human herpesvirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DML FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1plq\|1plq]], [[1axc\|1axc]], [[1b8h\|1b8h]]</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=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [http://www.ebi.ac.uk/pdbsum/1dml 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/dm/1dml_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 ==
		+	Herpes simplex virus DNA polymerase is a heterodimer composed of a catalytic subunit, Pol, and an unusual processivity subunit, UL42, which, unlike processivity factors such as PCNA, directly binds DNA. The crystal structure of a complex of the C-terminal 36 residues of Pol bound to residues 1-319 of UL42 reveals remarkable similarities between UL42 and PCNA despite contrasting biochemical properties and lack of sequence homology. Moreover, the Pol-UL42 interaction resembles the interaction between the cell cycle regulator p21 and PCNA. The structure and previous data suggest that the UL42 monomer interacts with DNA quite differently than does multimeric toroidal PCNA. The details of the structure lead to a model for the mechanism of UL42, provide the basis for drug design, and allow modeling of other proteins that lack sequence homology with UL42 or PCNA.

-	~~{{STRUCTURE_1dml\| PDB=1dml \| SCENE= }}~~	+	The crystal structure of an unusual processivity factor, herpes simplex virus UL42, bound to the C terminus of its cognate polymerase.,Zuccola HJ, Filman DJ, Coen DM, Hogle JM Mol Cell. 2000 Feb;5(2):267-78. PMID:10882068<ref>PMID:10882068</ref>

-	~~===CRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C-TERMINUS OF HSV POL===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10882068}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1dml]] is~~ a ~~8 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Human_herpesvirus_1 Human herpesvirus 1]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1DML OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010882068<~~/~~ref~~><~~ref group="xtra">PMID:015048824</ref><references group="xtra"~~/>	+
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Human herpesvirus 1]]		[[Category: Human herpesvirus 1]]