5y7g - Revision history

OCA at 08:23, 22 November 2023

OCA — Wed, 22 Nov 2023 08:23:57 GMT

←Older revision		Revision as of 08:23, 22 November 2023
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	<StructureSection load='5y7g' size='340' side='right'caption='[[5y7g]], [[Resolution\|resolution]] 3.40Å' scene=''>		<StructureSection load='5y7g' size='340' side='right'caption='[[5y7g]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y7g]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y7G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Y7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y7g]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y7G FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 3.4Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/Phosphodiesterase_I Phosphodiesterase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.1 3.1.4.1]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=5y7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y7g OCA], [~~http~~://pdbe.org/5y7g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y7g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y7g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y7g 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=5y7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y7g OCA], [https://pdbe.org/5y7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y7g RCSB], [https://www.ebi.ac.uk/pdbsum/5y7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y7g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/FAN1_PSEAE FAN1_PSEAE]] Nuclease required for the repair of DNA interstrand cross-links (ICL). Acts as a 5'-3' exonuclease that anchors at a cut end of DNA and cleaves DNA successively at every third nucleotide, allowing to excise an ICL from one strand through flanking incisions. Also has endonuclease activity toward 5'-flaps (PubMed:25319828).[UniProtKB:Q9Y2M0]<ref>PMID:24981866</ref> <ref>PMID:25319828</ref>	+	[https://www.uniprot.org/uniprot/FAN1_PSEAE FAN1_PSEAE] Nuclease required for the repair of DNA interstrand cross-links (ICL). Acts as a 5'-3' exonuclease that anchors at a cut end of DNA and cleaves DNA successively at every third nucleotide, allowing to excise an ICL from one strand through flanking incisions. Also has endonuclease activity toward 5'-flaps (PubMed:25319828).[UniProtKB:Q9Y2M0]<ref>PMID:24981866</ref> <ref>PMID:25319828</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Phosphodiesterase I~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: ~~Cho, Y~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Jin, H~~]]	+	[[Category: Cho Y]]
-	[[Category: ~~Hydrolase-dna complex]]~~	+	[[Category: Jin H]]
-	~~[[Category: Nuclease~~]]	+

OCA at 09:12, 21 October 2020

OCA — Wed, 21 Oct 2020 09:12:41 GMT

←Older revision		Revision as of 09:12, 21 October 2020
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	==Crystal structure of paFAN1 bound to 1nt 5'flap DNA with gap==		==Crystal structure of paFAN1 bound to 1nt 5'flap DNA with gap==
-	<StructureSection load='5y7g' size='340' side='right' caption='[[5y7g]], [[Resolution\|resolution]] 3.40Å' scene=''>	+	<StructureSection load='5y7g' size='340' side='right'caption='[[5y7g]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y7g]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y7G OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y7g]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y7G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Y7G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphodiesterase_I Phosphodiesterase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.1 3.1.4.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphodiesterase_I Phosphodiesterase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.1 3.1.4.1] </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=5y7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y7g OCA], [http://pdbe.org/5y7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y7g RCSB], [http://www.ebi.ac.uk/pdbsum/5y7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y7g 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=5y7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y7g OCA], [http://pdbe.org/5y7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y7g RCSB], [http://www.ebi.ac.uk/pdbsum/5y7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y7g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Phosphodiesterase I]]		[[Category: Phosphodiesterase I]]
	[[Category: Cho, Y]]		[[Category: Cho, Y]]

OCA at 06:29, 9 May 2018

OCA — Wed, 09 May 2018 06:29:06 GMT

←Older revision		Revision as of 06:29, 9 May 2018
Line 1:		Line 1:

-	==Crystal structure of ~~nuclease~~==	+	==Crystal structure of paFAN1 bound to 1nt 5'flap DNA with gap==
	<StructureSection load='5y7g' size='340' side='right' caption='[[5y7g]], [[Resolution\|resolution]] 3.40Å' scene=''>		<StructureSection load='5y7g' size='340' side='right' caption='[[5y7g]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/FAN1_PSEAE FAN1_PSEAE]] Nuclease required for the repair of DNA interstrand cross-links (ICL). Acts as a 5'-3' exonuclease that anchors at a cut end of DNA and cleaves DNA successively at every third nucleotide, allowing to excise an ICL from one strand through flanking incisions. Also has endonuclease activity toward 5'-flaps (PubMed:25319828).[UniProtKB:Q9Y2M0]<ref>PMID:24981866</ref> <ref>PMID:25319828</ref>		[[http://www.uniprot.org/uniprot/FAN1_PSEAE FAN1_PSEAE]] Nuclease required for the repair of DNA interstrand cross-links (ICL). Acts as a 5'-3' exonuclease that anchors at a cut end of DNA and cleaves DNA successively at every third nucleotide, allowing to excise an ICL from one strand through flanking incisions. Also has endonuclease activity toward 5'-flaps (PubMed:25319828).[UniProtKB:Q9Y2M0]<ref>PMID:24981866</ref> <ref>PMID:25319828</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA interstrand cross-links (ICLs) block the progress of the replication and transcription machineries and can weaken chromosomal stability, resulting in various diseases. FANCD2-FANCI-associated nuclease (FAN1) is a conserved structure-specific nuclease that unhooks DNA ICLs independently of the Fanconi anemia pathway. Recent structural studies have proposed two different mechanistic features for ICL unhooking by human FAN1: a specific basic pocket that recognizes the terminal phosphate of a 1-nucleotide (nt) 5' flap or FAN1 dimerization. Herein, we show that despite lacking these features, Pseudomonas aeruginosa FAN1 (PaFAN1) cleaves substrates at approximately 3-nt intervals and resolves ICLs. Crystal structures of PaFAN1 bound to various DNA substrates revealed that its conserved basic Arg/Lys patch comprising Arg-228 and Lys-260 recognizes phosphate groups near the 5' terminus of a DNA substrate with a 1-nt flap or a nick. Substitution of Lys-260 did not affect PaFAN1's initial endonuclease activity but significantly decreased its subsequent exonuclease activity and ICL unhooking. The Arg/Lys patch also interacted with phosphates at a 3-nt gap, and this interaction could drive movement of the scissile phosphates into the PaFAN1-active site. In human FAN1, the ICL-resolving activity was not affected by individual disruption of the Arg/Lys patch or basic pocket. However, simultaneous substitution of both FAN1 regions significantly reduced its ICL-resolving activity, suggesting that these two basic regions play a complementary role in ICL repair. On the basis of these findings, we propose a conserved role for two basic regions in FAN1 to guide ICL unhooking and to maintain genomic stability.
		+
		+	Structural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease.,Jin H, Roy U, Lee G, Scharer OD, Cho Y J Biol Chem. 2018 Apr 27;293(17):6482-6496. doi: 10.1074/jbc.RA118.002171. Epub, 2018 Mar 7. PMID:29514982<ref>PMID:29514982</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5y7g" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:26, 14 March 2018

OCA — Wed, 14 Mar 2018 06:26:59 GMT

←Older revision		Revision as of 06:26, 14 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5y7g is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of nuclease==
-		+	<StructureSection load='5y7g' size='340' side='right' caption='[[5y7g]], [[Resolution\|resolution]] 3.40Å' scene=''>
-	~~Authors~~: ~~Cho~~, Y., ~~Jin~~, H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5y7g]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y7G FirstGlance]. <br>
-	~~Description~~: ~~nuclease~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphodiesterase_I Phosphodiesterase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.1 3.1.4.1] </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=5y7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y7g OCA], [http://pdbe.org/5y7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y7g RCSB], [http://www.ebi.ac.uk/pdbsum/5y7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y7g ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FAN1_PSEAE FAN1_PSEAE]] Nuclease required for the repair of DNA interstrand cross-links (ICL). Acts as a 5'-3' exonuclease that anchors at a cut end of DNA and cleaves DNA successively at every third nucleotide, allowing to excise an ICL from one strand through flanking incisions. Also has endonuclease activity toward 5'-flaps (PubMed:25319828).[UniProtKB:Q9Y2M0]<ref>PMID:24981866</ref> <ref>PMID:25319828</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Phosphodiesterase I]]
		+	[[Category: Cho, Y]]
	[[Category: Jin, H]]		[[Category: Jin, H]]
-	[[Category: ~~Cho, Y~~]]	+	[[Category: Hydrolase-dna complex]]
		+	[[Category: Nuclease]]

OCA: Protected "5y7g" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:13:59 GMT

Protected "5y7g" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:13, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y7g is ON HOLD until Paper Publication Authors: Cho, Y., Jin, H. Description: nuclease Category: Unreleased Structures Category: Jin, H [[...

OCA — Wed, 27 Sep 2017 16:13:58 GMT

New page: '''Unreleased structure''' The entry 5y7g is ON HOLD until Paper Publication Authors: Cho, Y., Jin, H. Description: nuclease Category: Unreleased Structures Category: Jin, H [[...

New page

'''Unreleased structure'''

The entry 5y7g is ON HOLD until Paper Publication

Authors: Cho, Y., Jin, H.

Description: nuclease
[[Category: Unreleased Structures]]
[[Category: Jin, H]]
[[Category: Cho, Y]]