3wup - Revision history

OCA at 19:22, 29 May 2024

2024-05-29T19:22:25Z

← Older revision		Revision as of 19:22, 29 May 2024
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	==Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta==		==Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta==
	<StructureSection load='3wup' size='340' side='right'caption='[[3wup]]' scene=''>		<StructureSection load='3wup' size='340' side='right'caption='[[3wup]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WUP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3wup]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WUP FirstGlance]. <br>
	</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=3wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wup OCA], [https://pdbe.org/3wup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wup RCSB], [https://www.ebi.ac.uk/pdbsum/3wup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wup ProSAT]</span></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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=3wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wup OCA], [https://pdbe.org/3wup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wup RCSB], [https://www.ebi.ac.uk/pdbsum/3wup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wup ProSAT]</span></td></tr>
	</table>		</table>
			== Disease ==
			[https://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN] Defects in POLH are the cause of xeroderma pigmentosum variant type (XPV) [MIM:[https://omim.org/entry/278750 278750]; also designated as XP-V. Xeroderma pigmentosum (XP) is an autosomal recessive disease due to deficient nucleotide excision repair. It is characterized by hypersensitivity of the skin to sunlight, followed by high incidence of skin cancer and frequent neurologic abnormalities. XPV shows normal nucleotide excision repair, but an exaggerated delay in recovery of replicative DNA synthesis. Most XPV patients do not develop clinical symptoms and skin neoplasias until a later age. Clinical manifestations are limited to photo-induced deterioration of the skin and eyes.<ref>PMID:10385124</ref> <ref>PMID:10398605</ref> <ref>PMID:11032022</ref> <ref>PMID:11121129</ref> <ref>PMID:11773631</ref>
			== Function ==
			[https://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Plays an important role in the repair of UV-induced pyrimidine dimers. Depending on the context, it inserts the correct base, but causes frequent base transitions and transversions. May play a role in hypermutation at immunoglobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity. Targets POLI to replication foci.<ref>PMID:10385124</ref> <ref>PMID:11743006</ref> <ref>PMID:11376341</ref> <ref>PMID:14630940</ref> <ref>PMID:14734526</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The ubiquitin-binding zinc finger (UBZ) is a type of zinc-coordinating beta-beta-alpha fold domain found mainly in proteins involved in DNA repair and transcriptional regulation. Here we report the crystal structure of the UBZ domain of Y-family DNA polymerase (pol) eta and the crystal structure of the complex between the UBZ domain of Werner helicase-interacting protein 1 (WRNIP1) and ubiquitin, crystallized using the green fluorescent protein fusion technique. In contrast to the pol eta UBZ, which has been proposed to bind ubiquitin via its C-terminal alpha helix, ubiquitin binds to a novel surface of WRNIP1 UBZ composed of the first beta strand and the C-terminal alpha helix. In addition, we report the structure of the tandem UBZ domains of Tax1-binding protein 1 (TAX1BP1) and show that the second UBZ of TAX1BP1 binds ubiquitin, presumably in a manner similar to that of WRNIP1 UBZ. We propose that UBZ domains can be divided into at least two different types in terms of the ubiquitin-binding surfaces: the pol eta type and the WRNIP1 type. This article is protected by copyright. All rights reserved.

			A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1.,Suzuki N, Rohaim A, Kato R, Dikic I, Wakatsuki S, Kawasaki M FEBS J. 2016 Apr 8. doi: 10.1111/febs.13734. PMID:27062441<ref>PMID:27062441</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 3wup" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kawasaki S]]		[[Category: Kawasaki S]]
	[[Category: Suzuki N]]		[[Category: Suzuki N]]
	[[Category: Wakatsuki S]]		[[Category: Wakatsuki S]]

OCA at 10:36, 31 August 2022

2022-08-31T10:36:22Z

← Older revision		Revision as of 10:36, 31 August 2022
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	==Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta==		==Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta==
	<StructureSection load='3wup' size='340' side='right'caption='[[3wup]]~~, [[Resolution\|resolution]] 1.60Å~~' scene=''>		<StructureSection load='3wup' size='340' side='right'caption='[[3wup]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[3wup]] is a 1 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WUP FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WUP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</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=3wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wup OCA], [https://pdbe.org/3wup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wup RCSB], [https://www.ebi.ac.uk/pdbsum/3wup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wup ProSAT]</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'>[https://proteopedia.org/fgij/fg.htm?mol=3wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wup OCA], [https://pdbe.org/3wup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wup RCSB], [https://www.ebi.ac.uk/pdbsum/3wup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wup ProSAT]</span></td></tr>
	</table>		</table>
	~~== Disease ==~~
	[[https://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] Defects in POLH are the cause of xeroderma pigmentosum variant type (XPV) [MIM:[https://omim.org/entry/278750 278750]]; also designated as XP-V. Xeroderma pigmentosum (XP) is an autosomal recessive disease due to deficient nucleotide excision repair. It is characterized by hypersensitivity of the skin to sunlight, followed by high incidence of skin cancer and frequent neurologic abnormalities. XPV shows normal nucleotide excision repair, but an exaggerated delay in recovery of replicative DNA synthesis. Most XPV patients do not develop clinical symptoms and skin neoplasias until a later age. Clinical manifestations are limited to photo-induced deterioration of the skin and eyes.<ref>PMID:10385124</ref> <ref>PMID:10398605</ref> <ref>PMID:11032022</ref> <ref>PMID:11121129</ref> <ref>PMID:11773631</ref>
	~~== Function ==~~
	[[https://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Plays an important role in the repair of UV-induced pyrimidine dimers. Depending on the context, it inserts the correct base, but causes frequent base transitions and transversions. May play a role in hypermutation at immunoglobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity. Targets POLI to replication foci.<ref>PMID:10385124</ref> <ref>PMID:11743006</ref> <ref>PMID:11376341</ref> <ref>PMID:14630940</ref> <ref>PMID:14734526</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The ubiquitin-binding zinc finger (UBZ) is a type of zinc-coordinating beta-beta-alpha fold domain found mainly in proteins involved in DNA repair and transcriptional regulation. Here we report the crystal structure of the UBZ domain of Y-family DNA polymerase (pol) eta and the crystal structure of the complex between the UBZ domain of Werner helicase-interacting protein 1 (WRNIP1) and ubiquitin, crystallized using the green fluorescent protein fusion technique. In contrast to the pol eta UBZ, which has been proposed to bind ubiquitin via its C-terminal alpha helix, ubiquitin binds to a novel surface of WRNIP1 UBZ composed of the first beta strand and the C-terminal alpha helix. In addition, we report the structure of the tandem UBZ domains of Tax1-binding protein 1 (TAX1BP1) and show that the second UBZ of TAX1BP1 binds ubiquitin, presumably in a manner similar to that of WRNIP1 UBZ. We propose that UBZ domains can be divided into at least two different types in terms of the ubiquitin-binding surfaces: the pol eta type and the WRNIP1 type. This article is protected by copyright. All rights reserved.

	A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1.,Suzuki N, Rohaim A, Kato R, Dikic I, Wakatsuki S, Kawasaki M FEBS J. 2016 Apr 8. doi: 10.1111/febs.13734. PMID:27062441<ref>PMID:27062441</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3wup" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: DNA-directed DNA polymerase]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kawasaki, S]]		[[Category: Kawasaki S]]
	[[Category: Suzuki, N]]		[[Category: Suzuki N]]
	[[Category: Wakatsuki, S]]		[[Category: Wakatsuki S]]
	~~[[Category: Transferase]]~~
	~~[[Category: Ubiquitin and ubiquitin-binding domain]]~~
	~~[[Category: Ubiquitin-binding zinc finger]]~~
	~~[[Category: Zinc finger~~]]

OCA at 04:59, 25 August 2022

2022-08-25T04:59:27Z

← Older revision		Revision as of 04:59, 25 August 2022
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	<StructureSection load='3wup' size='340' side='right'caption='[[3wup]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3wup' size='340' side='right'caption='[[3wup]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3wup]] is a 1 chain structure ~~with sequence from [https://en.wikipedia.org/wiki/Human Human]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WUP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3wup]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WUP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLH, RAD30, RAD30A, XPV ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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='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=3wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wup OCA], [https://pdbe.org/3wup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wup RCSB], [https://www.ebi.ac.uk/pdbsum/3wup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wup 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=3wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wup OCA], [https://pdbe.org/3wup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wup RCSB], [https://www.ebi.ac.uk/pdbsum/3wup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wup ProSAT]</span></td></tr>
Line 27:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	~~[[Category: Human]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kawasaki, S]]		[[Category: Kawasaki, S]]

OCA at 05:32, 10 August 2022

2022-08-10T05:32:08Z

← Older revision		Revision as of 05:32, 10 August 2022
Line 1:		Line 1:

	==Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta==		==Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta==
	<StructureSection load='3wup' size='340' side='right' caption='[[3wup]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3wup' size='340' side='right'caption='[[3wup]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3wup]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WUP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3wup]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WUP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLH, RAD30, RAD30A, XPV ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLH, RAD30, RAD30A, XPV ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wup OCA], [~~http~~://pdbe.org/3wup PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3wup RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3wup PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3wup 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=3wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wup OCA], [https://pdbe.org/3wup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wup RCSB], [https://www.ebi.ac.uk/pdbsum/3wup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wup ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
	[[~~http~~://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] Defects in POLH are the cause of xeroderma pigmentosum variant type (XPV) [MIM:[~~http~~://omim.org/entry/278750 278750]]; also designated as XP-V. Xeroderma pigmentosum (XP) is an autosomal recessive disease due to deficient nucleotide excision repair. It is characterized by hypersensitivity of the skin to sunlight, followed by high incidence of skin cancer and frequent neurologic abnormalities. XPV shows normal nucleotide excision repair, but an exaggerated delay in recovery of replicative DNA synthesis. Most XPV patients do not develop clinical symptoms and skin neoplasias until a later age. Clinical manifestations are limited to photo-induced deterioration of the skin and eyes.<ref>PMID:10385124</ref> <ref>PMID:10398605</ref> <ref>PMID:11032022</ref> <ref>PMID:11121129</ref> <ref>PMID:11773631</ref>		[[https://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] Defects in POLH are the cause of xeroderma pigmentosum variant type (XPV) [MIM:[https://omim.org/entry/278750 278750]]; also designated as XP-V. Xeroderma pigmentosum (XP) is an autosomal recessive disease due to deficient nucleotide excision repair. It is characterized by hypersensitivity of the skin to sunlight, followed by high incidence of skin cancer and frequent neurologic abnormalities. XPV shows normal nucleotide excision repair, but an exaggerated delay in recovery of replicative DNA synthesis. Most XPV patients do not develop clinical symptoms and skin neoplasias until a later age. Clinical manifestations are limited to photo-induced deterioration of the skin and eyes.<ref>PMID:10385124</ref> <ref>PMID:10398605</ref> <ref>PMID:11032022</ref> <ref>PMID:11121129</ref> <ref>PMID:11773631</ref>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Plays an important role in the repair of UV-induced pyrimidine dimers. Depending on the context, it inserts the correct base, but causes frequent base transitions and transversions. May play a role in hypermutation at immunoglobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity. Targets POLI to replication foci.<ref>PMID:10385124</ref> <ref>PMID:11743006</ref> <ref>PMID:11376341</ref> <ref>PMID:14630940</ref> <ref>PMID:14734526</ref>		[[https://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Plays an important role in the repair of UV-induced pyrimidine dimers. Depending on the context, it inserts the correct base, but causes frequent base transitions and transversions. May play a role in hypermutation at immunoglobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity. Targets POLI to replication foci.<ref>PMID:10385124</ref> <ref>PMID:11743006</ref> <ref>PMID:11376341</ref> <ref>PMID:14630940</ref> <ref>PMID:14734526</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 28:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Kawasaki, S]]		[[Category: Kawasaki, S]]
	[[Category: Suzuki, N]]		[[Category: Suzuki, N]]

OCA at 09:05, 21 February 2019

2019-02-21T09:05:35Z

← Older revision		Revision as of 09:05, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='3wup' size='340' side='right' caption='[[3wup]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3wup' size='340' side='right' caption='[[3wup]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3wup]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WUP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3wup]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WUP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLH, RAD30, RAD30A, XPV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wup OCA], [http://pdbe.org/3wup PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wup RCSB], [http://www.ebi.ac.uk/pdbsum/3wup 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=3wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wup OCA], [http://pdbe.org/3wup PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wup RCSB], [http://www.ebi.ac.uk/pdbsum/3wup PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wup ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 26:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
			[[Category: Human]]
	[[Category: Kawasaki, S]]		[[Category: Kawasaki, S]]
	[[Category: Suzuki, N]]		[[Category: Suzuki, N]]

OCA at 07:39, 1 June 2016

2016-06-01T07:39:40Z

← Older revision		Revision as of 07:39, 1 June 2016
Line 1:		Line 1:

	==Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta==		==Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta==
	<StructureSection load='3wup' size='340' side='right' caption='[[3wup]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3wup' size='340' side='right' caption='[[3wup]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=3wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wup OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wup RCSB], [http://www.ebi.ac.uk/pdbsum/3wup 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=3wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wup OCA], [http://pdbe.org/3wup PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wup RCSB], [http://www.ebi.ac.uk/pdbsum/3wup PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 11:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Plays an important role in the repair of UV-induced pyrimidine dimers. Depending on the context, it inserts the correct base, but causes frequent base transitions and transversions. May play a role in hypermutation at immunoglobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity. Targets POLI to replication foci.<ref>PMID:10385124</ref> <ref>PMID:11743006</ref> <ref>PMID:11376341</ref> <ref>PMID:14630940</ref> <ref>PMID:14734526</ref>		[[http://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Plays an important role in the repair of UV-induced pyrimidine dimers. Depending on the context, it inserts the correct base, but causes frequent base transitions and transversions. May play a role in hypermutation at immunoglobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity. Targets POLI to replication foci.<ref>PMID:10385124</ref> <ref>PMID:11743006</ref> <ref>PMID:11376341</ref> <ref>PMID:14630940</ref> <ref>PMID:14734526</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The ubiquitin-binding zinc finger (UBZ) is a type of zinc-coordinating beta-beta-alpha fold domain found mainly in proteins involved in DNA repair and transcriptional regulation. Here we report the crystal structure of the UBZ domain of Y-family DNA polymerase (pol) eta and the crystal structure of the complex between the UBZ domain of Werner helicase-interacting protein 1 (WRNIP1) and ubiquitin, crystallized using the green fluorescent protein fusion technique. In contrast to the pol eta UBZ, which has been proposed to bind ubiquitin via its C-terminal alpha helix, ubiquitin binds to a novel surface of WRNIP1 UBZ composed of the first beta strand and the C-terminal alpha helix. In addition, we report the structure of the tandem UBZ domains of Tax1-binding protein 1 (TAX1BP1) and show that the second UBZ of TAX1BP1 binds ubiquitin, presumably in a manner similar to that of WRNIP1 UBZ. We propose that UBZ domains can be divided into at least two different types in terms of the ubiquitin-binding surfaces: the pol eta type and the WRNIP1 type. This article is protected by copyright. All rights reserved.

			A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1.,Suzuki N, Rohaim A, Kato R, Dikic I, Wakatsuki S, Kawasaki M FEBS J. 2016 Apr 8. doi: 10.1111/febs.13734. PMID:27062441<ref>PMID:27062441</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 3wup" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:20, 17 June 2015

2015-06-17T15:20:04Z

← Older revision		Revision as of 15:20, 17 June 2015
Line 1:		Line 1:
	'''~~Unreleased structure~~'''		==Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta==
			<StructureSection load='3wup' size='340' side='right' caption='[[3wup]], [[Resolution\|resolution]] 1.60Å' scene=''>
	~~The entry~~ 3wup is ~~ON HOLD until Paper Publication~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[3wup]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WUP FirstGlance]. <br>
	~~Authors~~: ~~Suzuki~~, N., ~~Wakatsuki~~, S., ~~Kawasaki, S~~.		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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>
	~~Description~~: ~~Crystal Structure~~ of ~~the Ubiquitin~~-~~Binding Zinc Finger~~ (~~UBZ~~) ~~Domain~~ of the ~~Human~~ DNA ~~Polymerase Eta~~		<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=3wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wup OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wup RCSB], [http://www.ebi.ac.uk/pdbsum/3wup PDBsum]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			== Disease ==
			[[http://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] Defects in POLH are the cause of xeroderma pigmentosum variant type (XPV) [MIM:[http://omim.org/entry/278750 278750]]; also designated as XP-V. Xeroderma pigmentosum (XP) is an autosomal recessive disease due to deficient nucleotide excision repair. It is characterized by hypersensitivity of the skin to sunlight, followed by high incidence of skin cancer and frequent neurologic abnormalities. XPV shows normal nucleotide excision repair, but an exaggerated delay in recovery of replicative DNA synthesis. Most XPV patients do not develop clinical symptoms and skin neoplasias until a later age. Clinical manifestations are limited to photo-induced deterioration of the skin and eyes.<ref>PMID:10385124</ref> <ref>PMID:10398605</ref> <ref>PMID:11032022</ref> <ref>PMID:11121129</ref> <ref>PMID:11773631</ref>
			== Function ==
			[[http://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Plays an important role in the repair of UV-induced pyrimidine dimers. Depending on the context, it inserts the correct base, but causes frequent base transitions and transversions. May play a role in hypermutation at immunoglobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity. Targets POLI to replication foci.<ref>PMID:10385124</ref> <ref>PMID:11743006</ref> <ref>PMID:11376341</ref> <ref>PMID:14630940</ref> <ref>PMID:14734526</ref>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: DNA-directed DNA polymerase]]
	[[Category: Kawasaki, S]]		[[Category: Kawasaki, S]]
			[[Category: Suzuki, N]]
	[[Category: Wakatsuki, S]]		[[Category: Wakatsuki, S]]
	[[Category: ~~Suzuki, N~~]]		[[Category: Transferase]]
			[[Category: Ubiquitin and ubiquitin-binding domain]]
			[[Category: Ubiquitin-binding zinc finger]]
			[[Category: Zinc finger]]

OCA at 12:59, 24 December 2014

2014-12-24T12:59:07Z

← Older revision		Revision as of 12:59, 24 December 2014
Line 6:		Line 6:

	Description: Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta		Description: Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta
			[[Category: Unreleased Structures]]
			[[Category: Kawasaki, S]]
			[[Category: Wakatsuki, S]]
			[[Category: Suzuki, N]]

OCA at 07:21, 21 May 2014

2014-05-21T07:21:19Z

← Older revision		Revision as of 07:21, 21 May 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 3wup is ON HOLD		The entry 3wup is ON HOLD until Paper Publication

	Authors: Suzuki, N., Wakatsuki, S., Kawasaki, S.		Authors: Suzuki, N., Wakatsuki, S., Kawasaki, S.

	Description: Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta		Description: Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta

OCA: Protected "3wup" [edit=sysop:move=sysop]

2014-05-07T07:17:42Z

Protected "3wup" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:17, 7 May 2014
(No difference)