5u6z - Revision history

OCA at 14:25, 6 March 2024

OCA — Wed, 06 Mar 2024 14:25:29 GMT

←Older revision		Revision as of 14:25, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5u6z' size='340' side='right'caption='[[5u6z]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5u6z' size='340' side='right'caption='[[5u6z]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u6z]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~African_clawed_frog African clawed frog~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U6Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5U6Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u6z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U6Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U6Z FirstGlance]. <br>
-	</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>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.6Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>apex2, apex2-prov ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~8355 African clawed frog])</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>, <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-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </~~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=5u6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u6z OCA], [https://pdbe.org/5u6z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u6z RCSB], [https://www.ebi.ac.uk/pdbsum/5u6z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u6z ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5u6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u6z OCA], [~~http~~://pdbe.org/5u6z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5u6z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5u6z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5u6z ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/Q6DDT4_XENLA Q6DDT4_XENLA]] Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends.[RuleBase:RU362131]	+	[https://www.uniprot.org/uniprot/Q6DDT4_XENLA Q6DDT4_XENLA] Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends.[RuleBase:RU362131]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The Xenopus laevis APE2 (apurinic/apyrimidinic endonuclease 2) nuclease participates in 3'-5' nucleolytic resection of oxidative DNA damage and activation of the ATR-Chk1 DNA damage response (DDR) pathway via ill-defined mechanisms. Here we report that APE2 resection activity is regulated by DNA interactions in its Zf-GRF domain, a region sharing high homology with DDR proteins Topoisomerase 3alpha (TOP3alpha) and NEIL3 (Nei-like DNA glycosylase 3), as well as transcription and RNA regulatory proteins, such as TTF2 (transcription termination factor 2), TFIIS, and RPB9. Biochemical and NMR results establish the nucleic acid-binding activity of the Zf-GRF domain. Moreover, an APE2 Zf-GRF X-ray structure and small-angle X-ray scattering analyses show that the Zf-GRF fold is typified by a crescent-shaped ssDNA binding claw that is flexibly appended to an APE2 endonuclease/exonuclease/phosphatase (EEP) catalytic core. Structure-guided Zf-GRF mutations impact APE2 DNA binding and 3'-5' exonuclease processing, and also prevent efficient APE2-dependent RPA recruitment to damaged chromatin and activation of the ATR-Chk1 DDR pathway in response to oxidative stress in Xenopus egg extracts. Collectively, our data unveil the APE2 Zf-GRF domain as a nucleic acid interaction module in the regulation of a key single-strand break resection function of APE2, and also reveal topologic similarity of the Zf-GRF to the zinc ribbon domains of TFIIS and RPB9.	+
-		+
-	APE2 Zf-GRF facilitates 3'-5' resection of DNA damage following oxidative stress.,Wallace BD, Berman Z, Mueller GA, Lin Y, Chang T, Andres SN, Wojtaszek JL, DeRose EF, Appel CD, London RE, Yan S, Williams RS Proc Natl Acad Sci U S A. 2017 Jan 10;114(2):304-309. doi:, 10.1073/pnas.1610011114. Epub 2016 Dec 27. PMID:28028224<ref>PMID:28028224</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5u6z" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: African clawed frog]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Wallace, B D~~]]	+	[[Category: Xenopus laevis]]
-	[[Category: ~~Williams, R S~~]]	+	[[Category: Wallace BD]]
-	[[Category: ~~3' ap endo/exonuclease]]~~	+	[[Category: Williams RS]]
-	~~[[Category: Dna binding]]~~	+
-	~~[[Category: Grf zinc finger]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 12:28, 23 September 2020

OCA — Wed, 23 Sep 2020 12:28:26 GMT

←Older revision		Revision as of 12:28, 23 September 2020
Line 1:		Line 1:

	==Crystal Structure of Xenopus laevis Apex2 C-terminal Znf-GRF Domain==		==Crystal Structure of Xenopus laevis Apex2 C-terminal Znf-GRF Domain==
-	<StructureSection load='5u6z' size='340' side='right' caption='[[5u6z]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5u6z' size='340' side='right'caption='[[5u6z]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u6z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U6Z OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5U6Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u6z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U6Z OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5U6Z 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>, <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=SO4:SULFATE+ION'>SO4</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">apex2, apex2-prov ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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=5u6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u6z OCA], [http://pdbe.org/5u6z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u6z RCSB], [http://www.ebi.ac.uk/pdbsum/5u6z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u6z ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5u6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u6z OCA], [http://pdbe.org/5u6z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u6z RCSB], [http://www.ebi.ac.uk/pdbsum/5u6z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u6z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: African clawed frog]]
		+	[[Category: Large Structures]]
	[[Category: Wallace, B D]]		[[Category: Wallace, B D]]
	[[Category: Williams, R S]]		[[Category: Williams, R S]]

OCA at 16:41, 18 January 2017

OCA — Wed, 18 Jan 2017 16:41:25 GMT

←Older revision		Revision as of 16:41, 18 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5u6z is ~~ON HOLD~~	+	==Crystal Structure of Xenopus laevis Apex2 C-terminal Znf-GRF Domain==
		+	<StructureSection load='5u6z' size='340' side='right' caption='[[5u6z]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5u6z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U6Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U6Z 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>, <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-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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=5u6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u6z OCA], [http://pdbe.org/5u6z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u6z RCSB], [http://www.ebi.ac.uk/pdbsum/5u6z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u6z ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q6DDT4_XENLA Q6DDT4_XENLA]] Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends.[RuleBase:RU362131]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Xenopus laevis APE2 (apurinic/apyrimidinic endonuclease 2) nuclease participates in 3'-5' nucleolytic resection of oxidative DNA damage and activation of the ATR-Chk1 DNA damage response (DDR) pathway via ill-defined mechanisms. Here we report that APE2 resection activity is regulated by DNA interactions in its Zf-GRF domain, a region sharing high homology with DDR proteins Topoisomerase 3alpha (TOP3alpha) and NEIL3 (Nei-like DNA glycosylase 3), as well as transcription and RNA regulatory proteins, such as TTF2 (transcription termination factor 2), TFIIS, and RPB9. Biochemical and NMR results establish the nucleic acid-binding activity of the Zf-GRF domain. Moreover, an APE2 Zf-GRF X-ray structure and small-angle X-ray scattering analyses show that the Zf-GRF fold is typified by a crescent-shaped ssDNA binding claw that is flexibly appended to an APE2 endonuclease/exonuclease/phosphatase (EEP) catalytic core. Structure-guided Zf-GRF mutations impact APE2 DNA binding and 3'-5' exonuclease processing, and also prevent efficient APE2-dependent RPA recruitment to damaged chromatin and activation of the ATR-Chk1 DDR pathway in response to oxidative stress in Xenopus egg extracts. Collectively, our data unveil the APE2 Zf-GRF domain as a nucleic acid interaction module in the regulation of a key single-strand break resection function of APE2, and also reveal topologic similarity of the Zf-GRF to the zinc ribbon domains of TFIIS and RPB9.

-	~~Authors~~:	+	APE2 Zf-GRF facilitates 3'-5' resection of DNA damage following oxidative stress.,Wallace BD, Berman Z, Mueller GA, Lin Y, Chang T, Andres SN, Wojtaszek JL, DeRose EF, Appel CD, London RE, Yan S, Williams RS Proc Natl Acad Sci U S A. 2017 Jan 10;114(2):304-309. doi:, 10.1073/pnas.1610011114. Epub 2016 Dec 27. PMID:28028224<ref>PMID:28028224</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5u6z" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Wallace, B D]]
		+	[[Category: Williams, R S]]
		+	[[Category: 3' ap endo/exonuclease]]
		+	[[Category: Dna binding]]
		+	[[Category: Grf zinc finger]]
		+	[[Category: Lyase]]

OCA: Protected "5u6z" [edit=sysop:move=sysop]

OCA — Thu, 22 Dec 2016 20:28:52 GMT

Protected "5u6z" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:28, 22 December 2016

OCA: New page: '''Unreleased structure''' The entry 5u6z is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 22 Dec 2016 20:28:51 GMT

New page: '''Unreleased structure''' The entry 5u6z is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5u6z is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]