6k1d - Revision history

OCA at 10:25, 22 November 2023

OCA — Wed, 22 Nov 2023 10:25:27 GMT

←Older revision		Revision as of 10:25, 22 November 2023
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	<StructureSection load='6k1d' size='340' side='right'caption='[[6k1d]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='6k1d' size='340' side='right'caption='[[6k1d]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k1d]] is a 2 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=6K1D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6K1D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k1d]] is a 2 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=6K1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K1D FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 3Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>EXD2, C14orf114, EXDL2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_I Exodeoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.1 3.1.11.1]~~ </~~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=6k1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k1d OCA], [https://pdbe.org/6k1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k1d RCSB], [https://www.ebi.ac.uk/pdbsum/6k1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k1d 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=6k1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k1d OCA], [~~http~~://pdbe.org/6k1d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k1d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k1d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k1d ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/EXD2_HUMAN EXD2_HUMAN]] Exonuclease required for double-strand breaks resection and efficient homologous recombination. Plays a key role in controlling the initial steps of chromosomal break repair, it is recruited to chromatin in a damage-dependent manner and functionally interacts with the MRN complex to accelerate resection through its 3'-5' exonuclease activity, which efficiently processes double-stranded DNA substrates containing nicks.<ref>PMID:20603073</ref> <ref>PMID:26807646</ref>	+	[https://www.uniprot.org/uniprot/EXD2_HUMAN EXD2_HUMAN] Exonuclease required for double-strand breaks resection and efficient homologous recombination. Plays a key role in controlling the initial steps of chromosomal break repair, it is recruited to chromatin in a damage-dependent manner and functionally interacts with the MRN complex to accelerate resection through its 3'-5' exonuclease activity, which efficiently processes double-stranded DNA substrates containing nicks.<ref>PMID:20603073</ref> <ref>PMID:26807646</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: ~~Exodeoxyribonuclease I]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lee, C]]	+	[[Category: Lee C]]
-	[[Category: Park, J]]	+	[[Category: Park J]]
-	~~[[Category: 3'-5' exonuclease]]~~	+
-	~~[[Category: Dnaq family]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 10:19, 4 December 2019

OCA — Wed, 04 Dec 2019 10:19:55 GMT

←Older revision		Revision as of 10:19, 4 December 2019
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	<StructureSection load='6k1d' size='340' side='right'caption='[[6k1d]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='6k1d' size='340' side='right'caption='[[6k1d]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k1d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K1D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k1d]] is a 2 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=6K1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K1D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EXD2, C14orf114, EXDL2 ([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/Exodeoxyribonuclease_I Exodeoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.1 3.1.11.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_I Exodeoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.1 3.1.11.1] </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=6k1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k1d OCA], [http://pdbe.org/6k1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k1d RCSB], [http://www.ebi.ac.uk/pdbsum/6k1d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k1d 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=6k1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k1d OCA], [http://pdbe.org/6k1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k1d RCSB], [http://www.ebi.ac.uk/pdbsum/6k1d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k1d ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/EXD2_HUMAN EXD2_HUMAN]] Exonuclease required for double-strand breaks resection and efficient homologous recombination. Plays a key role in controlling the initial steps of chromosomal break repair, it is recruited to chromatin in a damage-dependent manner and functionally interacts with the MRN complex to accelerate resection through its 3'-5' exonuclease activity, which efficiently processes double-stranded DNA substrates containing nicks.<ref>PMID:20603073</ref> <ref>PMID:26807646</ref>		[[http://www.uniprot.org/uniprot/EXD2_HUMAN EXD2_HUMAN]] Exonuclease required for double-strand breaks resection and efficient homologous recombination. Plays a key role in controlling the initial steps of chromosomal break repair, it is recruited to chromatin in a damage-dependent manner and functionally interacts with the MRN complex to accelerate resection through its 3'-5' exonuclease activity, which efficiently processes double-stranded DNA substrates containing nicks.<ref>PMID:20603073</ref> <ref>PMID:26807646</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	EXD2 (3'-5' exonuclease domain-containing protein 2) is an essential protein with a conserved DEDDy superfamily 3'-5' exonuclease domain. Recent research suggests that EXD2 has two potential functions: as a component of the DNA double-strand break repair machinery and as a ribonuclease for the regulation of mitochondrial translation. Herein, electron microscope imaging analysis and proximity labeling revealed that EXD2 is anchored to the mitochondrial outer membrane through a conserved N-terminal transmembrane domain, while the C-terminal region is cytosolic. Crystal structures of the exonuclease domain in complex with Mn2+/Mg2+ revealed a domain-swapped dimer in which the central alpha5-alpha7 helices are mutually crossed over, resulting in chimeric active sites. Additionally, the C-terminal segments absent in other DnaQ family exonucleases enclose the central chimeric active sites. Combined structural and biochemical analyses demonstrated that the unusual dimeric organization stabilizes the active site, facilitates discrimination between DNA and RNA substrates based on divalent cation coordination and generates a positively charged groove that binds substrates.
		+
		+	The structure of human EXD2 reveals a chimeric 3' to 5' exonuclease domain that discriminates substrates via metal coordination.,Park J, Lee SY, Jeong H, Kang MG, Van Haute L, Minczuk M, Seo JK, Jun Y, Myung K, Rhee HW, Lee C Nucleic Acids Res. 2019 Jul 26;47(13):7078-7093. doi: 10.1093/nar/gkz454. PMID:31127291<ref>PMID:31127291</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6k1d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Exodeoxyribonuclease I]]		[[Category: Exodeoxyribonuclease I]]
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Lee, C]]		[[Category: Lee, C]]

OCA at 06:51, 23 May 2019

OCA — Thu, 23 May 2019 06:51:43 GMT

←Older revision		Revision as of 06:51, 23 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6k1d is ~~ON HOLD~~	+	==Crystal structure of EXD2 exonuclease domain soaked in Mn and GMP==
-		+	<StructureSection load='6k1d' size='340' side='right'caption='[[6k1d]], [[Resolution\|resolution]] 3.00Å' scene=''>
-	~~Authors~~: ~~Park~~, J., ~~Lee~~, C.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6k1d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K1D FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of ~~EXD2 exonuclease domain soaked~~ in Mn and ~~GMP~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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/Exodeoxyribonuclease_I Exodeoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.1 3.1.11.1] </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=6k1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k1d OCA], [http://pdbe.org/6k1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k1d RCSB], [http://www.ebi.ac.uk/pdbsum/6k1d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k1d ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/EXD2_HUMAN EXD2_HUMAN]] Exonuclease required for double-strand breaks resection and efficient homologous recombination. Plays a key role in controlling the initial steps of chromosomal break repair, it is recruited to chromatin in a damage-dependent manner and functionally interacts with the MRN complex to accelerate resection through its 3'-5' exonuclease activity, which efficiently processes double-stranded DNA substrates containing nicks.<ref>PMID:20603073</ref> <ref>PMID:26807646</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Exodeoxyribonuclease I]]
		+	[[Category: Large Structures]]
	[[Category: Lee, C]]		[[Category: Lee, C]]
	[[Category: Park, J]]		[[Category: Park, J]]
		+	[[Category: 3'-5' exonuclease]]
		+	[[Category: Dnaq family]]
		+	[[Category: Hydrolase]]

OCA: Protected "6k1d" [edit=sysop:move=sysop]

OCA — Tue, 21 May 2019 05:41:51 GMT

Protected "6k1d" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:41, 21 May 2019

OCA: New page: '''Unreleased structure''' The entry 6k1d is ON HOLD Authors: Park, J., Lee, C. Description: Crystal structure of EXD2 exonuclease domain soaked in Mn and GMP [[Category: Unreleased St...

OCA — Tue, 21 May 2019 05:41:50 GMT

New page: '''Unreleased structure''' The entry 6k1d is ON HOLD Authors: Park, J., Lee, C. Description: Crystal structure of EXD2 exonuclease domain soaked in Mn and GMP [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 6k1d is ON HOLD

Authors: Park, J., Lee, C.

Description: Crystal structure of EXD2 exonuclease domain soaked in Mn and GMP
[[Category: Unreleased Structures]]
[[Category: Lee, C]]
[[Category: Park, J]]