5nnh - Revision history

OCA at 13:12, 15 November 2023

OCA — Wed, 15 Nov 2023 13:12:40 GMT

←Older revision		Revision as of 13:12, 15 November 2023
Line 3:		Line 3:
	<StructureSection load='5nnh' size='340' side='right'caption='[[5nnh]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5nnh' size='340' side='right'caption='[[5nnh]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nnh]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Hhv-8 Hhv-~~8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NNH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NNH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nnh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_gammaherpesvirus_8 Human gammaherpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NNH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NNH FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><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]] 2.2Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5nn7\|5nn7]]~~, [[~~5nnu~~\|~~5nnu~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ORF46 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~37296 HHV-8])</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=5nnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nnh OCA], [https://pdbe.org/5nnh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nnh RCSB], [https://www.ebi.ac.uk/pdbsum/5nnh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nnh ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27]~~ </~~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=5nnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nnh OCA], [~~http~~://pdbe.org/5nnh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5nnh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5nnh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5nnh ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~Q76RG8_HHV8 Q76RG8_HHV8]~~] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or deamination of cytosines. Therefore may reduce deleterious uracil incorporation into the viral genome, particularly in terminally differentiated cells which lack DNA repair enzymes.[HAMAP-Rule:MF_04046]	+	[https://www.uniprot.org/uniprot/UNG_HHV8P UNG_HHV8P] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or deamination of cytosines. Therefore may reduce deleterious uracil incorporation into the viral genome, particularly in terminally differentiated cells which lack DNA repair enzymes.[HAMAP-Rule:MF_04046]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hhv-~~8]]	+	[[Category: Human gammaherpesvirus 8]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Uracil-DNA glycosylase]]~~	+	[[Category: Bagneris C]]
-	[[Category: Bagneris, C]]	+	[[Category: Barrett T]]
-	[[Category: Barrett, T]]	+	[[Category: Cole AR]]
-	[[Category: Cole~~, A R~~]]	+	[[Category: Earl C]]
-	[[Category: Earl, C]]	+	[[Category: Savva R]]
-	[[Category: Savva, R]]	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Uracil-dna glycosylase~~]]	+

OCA at 05:51, 10 October 2019

OCA — Thu, 10 Oct 2019 05:51:31 GMT

←Older revision		Revision as of 05:51, 10 October 2019
Line 1:		Line 1:

	==KSHV uracil-DNA glycosylase, apo form==		==KSHV uracil-DNA glycosylase, apo form==
-	<StructureSection load='5nnh' size='340' side='right' caption='[[5nnh]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5nnh' size='340' side='right'caption='[[5nnh]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5nnh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hhv-8 Hhv-8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NNH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NNH FirstGlance]. <br>		<table><tr><td colspan='2'>[[5nnh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hhv-8 Hhv-8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NNH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NNH FirstGlance]. <br>
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]	+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Hhv-8]]		[[Category: Hhv-8]]
		+	[[Category: Large Structures]]
	[[Category: Uracil-DNA glycosylase]]		[[Category: Uracil-DNA glycosylase]]
	[[Category: Bagneris, C]]		[[Category: Bagneris, C]]

OCA at 05:47, 16 May 2018

OCA — Wed, 16 May 2018 05:47:28 GMT

←Older revision		Revision as of 05:47, 16 May 2018
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5nnh" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5nnh" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA glycosylase\|DNA glycosylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:07, 11 April 2018

OCA — Wed, 11 Apr 2018 14:07:27 GMT

←Older revision		Revision as of 14:07, 11 April 2018
Line 3:		Line 3:
	<StructureSection load='5nnh' size='340' side='right' caption='[[5nnh]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5nnh' size='340' side='right' caption='[[5nnh]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nnh]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NNH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NNH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nnh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hhv-8 Hhv-8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NNH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NNH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5nn7\|5nn7]], [[5nnu\|5nnu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5nn7\|5nn7]], [[5nnu\|5nnu]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ORF46 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37296 HHV-8])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27] </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=5nnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nnh OCA], [http://pdbe.org/5nnh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nnh RCSB], [http://www.ebi.ac.uk/pdbsum/5nnh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nnh ProSAT]</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=5nnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nnh OCA], [http://pdbe.org/5nnh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nnh RCSB], [http://www.ebi.ac.uk/pdbsum/5nnh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nnh ProSAT]</span></td></tr>
Line 11:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/Q76RG8_HHV8 Q76RG8_HHV8]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or deamination of cytosines. Therefore may reduce deleterious uracil incorporation into the viral genome, particularly in terminally differentiated cells which lack DNA repair enzymes.[HAMAP-Rule:MF_04046]		[[http://www.uniprot.org/uniprot/Q76RG8_HHV8 Q76RG8_HHV8]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or deamination of cytosines. Therefore may reduce deleterious uracil incorporation into the viral genome, particularly in terminally differentiated cells which lack DNA repair enzymes.[HAMAP-Rule:MF_04046]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Efficient gamma-herpesvirus lytic phase replication requires a virally encoded UNG-type uracil-DNA glycosylase as a structural element of the viral replisome. Uniquely, gamma-herpesvirus UNGs carry a seven or eight residue insertion of variable sequence in the otherwise highly conserved minor-groove DNA binding loop. In Epstein-Barr Virus [HHV-4] UNG, this motif forms a disc-shaped loop structure of unclear significance. To ascertain the biological role of the loop insertion, we determined the crystal structure of Kaposi's sarcoma-associated herpesvirus [HHV-8] UNG (kUNG) in its product complex with a uracil-containing dsDNA, as well as two structures of kUNG in its apo state. We find the disc-like conformation is conserved, but only when the kUNG DNA-binding cleft is occupied. Surprisingly, kUNG uses this structure to flip the orphaned partner base of the substrate deoxyuridine out of the DNA duplex while retaining canonical UNG deoxyuridine-flipping and catalysis. The orphan base is stably posed in the DNA major groove which, due to DNA backbone manipulation by kUNG, is more open than in other UNG-dsDNA structures. Mutagenesis suggests a model in which the kUNG loop is pinned outside the DNA-binding cleft until DNA docking promotes rigid structuring of the loop and duplex nucleotide flipping, a novel observation for UNGs.
		+
		+	A structurally conserved motif in gamma-herpesvirus uracil-DNA glycosylases elicits duplex nucleotide-flipping.,Earl C, Bagneris C, Zeman K, Cole A, Barrett T, Savva R Nucleic Acids Res. 2018 Mar 27. pii: 4955253. doi: 10.1093/nar/gky217. PMID:29596604<ref>PMID:29596604</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5nnh" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Hhv-8]]
	[[Category: Uracil-DNA glycosylase]]		[[Category: Uracil-DNA glycosylase]]
	[[Category: Bagneris, C]]		[[Category: Bagneris, C]]

OCA at 07:30, 21 March 2018

OCA — Wed, 21 Mar 2018 07:30:32 GMT

←Older revision		Revision as of 07:30, 21 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5nnh ~~is ON HOLD until Paper Publication~~	+	==KSHV uracil-DNA glycosylase, apo form==
-		+	<StructureSection load='5nnh' size='340' side='right' caption='[[5nnh]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~Authors~~: ~~Earl, C~~.~~, Bagneris, C~~.~~, Cole, A~~.R.~~, Barrett, T~~.~~, Savva, R~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5nnh]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NNH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NNH FirstGlance]. <br>
-	~~Description~~: Uracil-DNA glycosylase	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5nn7\|5nn7]], [[5nnu\|5nnu]]</td></tr>
-	[~~[Category~~: ~~Cole~~, A.R]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27] </span></td></tr>
-	[[~~Category~~: ~~Savva, R~~]]	+	<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=5nnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nnh OCA], [http://pdbe.org/5nnh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nnh RCSB], [http://www.ebi.ac.uk/pdbsum/5nnh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nnh ProSAT]</span></td></tr>
-	[[Category: ~~Earl, C~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q76RG8_HHV8 Q76RG8_HHV8]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or deamination of cytosines. Therefore may reduce deleterious uracil incorporation into the viral genome, particularly in terminally differentiated cells which lack DNA repair enzymes.[HAMAP-Rule:MF_04046]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Uracil-DNA glycosylase]]
	[[Category: Bagneris, C]]		[[Category: Bagneris, C]]
	[[Category: Barrett, T]]		[[Category: Barrett, T]]
		+	[[Category: Cole, A R]]
		+	[[Category: Earl, C]]
		+	[[Category: Savva, R]]
		+	[[Category: Hydrolase]]
		+	[[Category: Uracil-dna glycosylase]]

OCA at 09:44, 24 May 2017

OCA — Wed, 24 May 2017 09:44:47 GMT

←Older revision		Revision as of 09:44, 24 May 2017
Line 3:		Line 3:
	The entry 5nnh is ON HOLD until Paper Publication		The entry 5nnh is ON HOLD until Paper Publication

-	Authors: Earl, C., Bagneris, C., Barrett, T., Savva, R.	+	Authors: Earl, C., Bagneris, C., Cole, A.R., Barrett, T., Savva, R.

	Description: Uracil-DNA glycosylase		Description: Uracil-DNA glycosylase
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Cole, A.R]]
	[[Category: Savva, R]]		[[Category: Savva, R]]
	[[Category: Earl, C]]		[[Category: Earl, C]]
	[[Category: Bagneris, C]]		[[Category: Bagneris, C]]
	[[Category: Barrett, T]]		[[Category: Barrett, T]]

OCA: Protected "5nnh" [edit=sysop:move=sysop]

OCA — Wed, 19 Apr 2017 09:41:34 GMT

Protected "5nnh" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:41, 19 April 2017

OCA: New page: '''Unreleased structure''' The entry 5nnh is ON HOLD until Paper Publication Authors: Earl, C., Bagneris, C., Barrett, T., Savva, R. Description: Uracil-DNA glycosylase [[Category: Unr...

OCA — Wed, 19 Apr 2017 09:41:33 GMT

New page: '''Unreleased structure''' The entry 5nnh is ON HOLD until Paper Publication Authors: Earl, C., Bagneris, C., Barrett, T., Savva, R. Description: Uracil-DNA glycosylase [[Category: Unr...

New page

'''Unreleased structure'''

The entry 5nnh is ON HOLD until Paper Publication

Authors: Earl, C., Bagneris, C., Barrett, T., Savva, R.

Description: Uracil-DNA glycosylase
[[Category: Unreleased Structures]]
[[Category: Savva, R]]
[[Category: Earl, C]]
[[Category: Bagneris, C]]
[[Category: Barrett, T]]