5w7y - Revision history

OCA at 14:08, 4 October 2023

OCA — Wed, 04 Oct 2023 14:08:39 GMT

←Older revision		Revision as of 14:08, 4 October 2023
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	<StructureSection load='5w7y' size='340' side='right'caption='[[5w7y]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5w7y' size='340' side='right'caption='[[5w7y]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w7y]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W7Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5W7Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w7y]] is a 4 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=5W7Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W7Y FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=TPO:PHOSPHOTHREONINE'>TPO</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]] 2.1Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</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=5w7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w7y OCA], [~~http~~://pdbe.org/5w7y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5w7y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5w7y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5w7y 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=5w7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w7y OCA], [https://pdbe.org/5w7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w7y RCSB], [https://www.ebi.ac.uk/pdbsum/5w7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w7y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/APLF_HUMAN APLF_HUMAN]] Nuclease involved in single-strand and double-strand DNA break repair. Recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. Displays apurinic-apyrimidinic (AP) endonuclease and 3'-5' exonuclease activities in vitro. Also able to introduce nicks at hydroxyuracil and other types of pyrimidine base damage.<ref>PMID:17396150</ref> <ref>PMID:17353262</ref> ~~[[http://www.uniprot.org/uniprot/XRCC1_HUMAN XRCC1_HUMAN]] Corrects defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents.~~	+	[https://www.uniprot.org/uniprot/APLF_HUMAN APLF_HUMAN] Nuclease involved in single-strand and double-strand DNA break repair. Recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. Displays apurinic-apyrimidinic (AP) endonuclease and 3'-5' exonuclease activities in vitro. Also able to introduce nicks at hydroxyuracil and other types of pyrimidine base damage.<ref>PMID:17396150</ref> <ref>PMID:17353262</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim, K]]	+	[[Category: Kim K]]
-	[[Category: London~~, R E~~]]	+	[[Category: London RE]]
-	[[Category: Pedersen~~, L C]]~~	+	[[Category: Pedersen LC]]
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Nhej]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Scaffold protein~~]]	+

OCA at 08:48, 30 September 2020

OCA — Wed, 30 Sep 2020 08:48:54 GMT

←Older revision		Revision as of 08:48, 30 September 2020
Line 1:		Line 1:

	==Crystal Structure of FHA domain of human APLF in complex with XRCC1 monophosphorylated mutated peptide==		==Crystal Structure of FHA domain of human APLF in complex with XRCC1 monophosphorylated mutated peptide==
-	<StructureSection load='5w7y' size='340' side='right' caption='[[5w7y]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5w7y' size='340' side='right'caption='[[5w7y]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w7y]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W7Y OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5W7Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w7y]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W7Y OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5W7Y FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</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='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=5w7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w7y OCA], [http://pdbe.org/5w7y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w7y RCSB], [http://www.ebi.ac.uk/pdbsum/5w7y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w7y 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=5w7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w7y OCA], [http://pdbe.org/5w7y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w7y RCSB], [http://www.ebi.ac.uk/pdbsum/5w7y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w7y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5w7y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5w7y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Apurinic/apyrimidinic endonuclease 3D structures\|Apurinic/apyrimidinic endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Kim, K]]		[[Category: Kim, K]]
	[[Category: London, R E]]		[[Category: London, R E]]

OCA at 07:59, 2 May 2018

OCA — Wed, 02 May 2018 07:59:26 GMT

←Older revision		Revision as of 07:59, 2 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5w7y is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal Structure of FHA domain of human APLF in complex with XRCC1 monophosphorylated mutated peptide==
		+	<StructureSection load='5w7y' size='340' side='right' caption='[[5w7y]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5w7y]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W7Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W7Y FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</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=5w7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w7y OCA], [http://pdbe.org/5w7y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w7y RCSB], [http://www.ebi.ac.uk/pdbsum/5w7y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w7y ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/APLF_HUMAN APLF_HUMAN]] Nuclease involved in single-strand and double-strand DNA break repair. Recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. Displays apurinic-apyrimidinic (AP) endonuclease and 3'-5' exonuclease activities in vitro. Also able to introduce nicks at hydroxyuracil and other types of pyrimidine base damage.<ref>PMID:17396150</ref> <ref>PMID:17353262</ref> [[http://www.uniprot.org/uniprot/XRCC1_HUMAN XRCC1_HUMAN]] Corrects defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aprataxin and PNKP-like factor (APLF) is a DNA repair factor containing a forkhead-associated (FHA) domain that supports binding to the phosphorylated FHA domain binding motifs (FBMs) in XRCC1 and XRCC4. We have characterized the interaction of the APLF FHA domain with phosphorylated XRCC1 peptides using crystallographic, NMR, and fluorescence polarization studies. The FHA-FBM interactions exhibit significant pH dependence in the physiological range as a consequence of the atypically high pK values of the phosphoserine and phosphothreonine residues and the preference for a dianionic charge state of FHA-bound pThr. These high pK values are characteristic of the polyanionic peptides typically produced by CK2 phosphorylation. Binding affinity is greatly enhanced by residues flanking the crystallographically-defined recognition motif, apparently as a consequence of non-specific electrostatic interactions, supporting the role of XRCC1 in nuclear cotransport of APLF. The FHA domain-dependent interaction of XRCC1 with APLF joins repair scaffolds that support single-strand break repair and non-homologous end joining (NHEJ). It is suggested that for double-strand DNA breaks that have initially formed a complex with PARP1 and its binding partner XRCC1, this interaction acts as a backup attempt to intercept the more error-prone alternative NHEJ repair pathway by recruiting Ku and associated NHEJ factors.

-	~~Authors: Pedersen, L.C~~., Kim, K., ~~London~~, R.E.	+	Characterization of the APLF FHA-XRCC1 phosphopeptide interaction and its structural and functional implications.,Kim K, Pedersen LC, Kirby TW, DeRose EF, London RE Nucleic Acids Res. 2017 Dec 1;45(21):12374-12387. doi: 10.1093/nar/gkx941. PMID:29059378<ref>PMID:29059378</ref>

-	~~Description: Crystal Structure~~ of ~~FHA domain~~ of ~~human APLF in complex with XRCC1 monophosphorylated mutated peptide~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5w7y" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Kim, K]]		[[Category: Kim, K]]
-	[[Category: London, R.E]]	+	[[Category: London, R E]]
-	[[Category: Pedersen, L.C]]	+	[[Category: Pedersen, L C]]
		+	[[Category: Dna repair]]
		+	[[Category: Nhej]]
		+	[[Category: Protein binding]]
		+	[[Category: Scaffold protein]]

OCA: Protected "5w7y" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 14:33:35 GMT

Protected "5w7y" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:33, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5w7y is ON HOLD until Paper Publication Authors: Pedersen, L.C., Kim, K., London, R.E. Description: Crystal Structure of FHA domain of human APLF i...

OCA — Wed, 27 Sep 2017 14:33:34 GMT

New page: '''Unreleased structure''' The entry 5w7y is ON HOLD until Paper Publication Authors: Pedersen, L.C., Kim, K., London, R.E. Description: Crystal Structure of FHA domain of human APLF i...

New page

'''Unreleased structure'''

The entry 5w7y is ON HOLD until Paper Publication

Authors: Pedersen, L.C., Kim, K., London, R.E.

Description: Crystal Structure of FHA domain of human APLF in complex with XRCC1 monophosphorylated mutated peptide
[[Category: Unreleased Structures]]
[[Category: Kim, K]]
[[Category: London, R.E]]
[[Category: Pedersen, L.C]]