6bkf - Revision history

OCA at 14:44, 4 October 2023

2023-10-04T14:44:23Z

←Older revision		Revision as of 14:44, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='6bkf' size='340' side='right'caption='[[6bkf]], [[Resolution\|resolution]] 3.25Å' scene=''>		<StructureSection load='6bkf' size='340' side='right'caption='[[6bkf]], [[Resolution\|resolution]] 3.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bkf]] is a 4 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=6BKF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BKF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bkf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=6BKF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BKF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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]] 3.25Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">LIG4 ([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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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_ligase_(ATP) DNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.1 6.5.1.1]~~ </~~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=6bkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bkf OCA], [https://pdbe.org/6bkf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bkf RCSB], [https://www.ebi.ac.uk/pdbsum/6bkf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bkf 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=6bkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bkf OCA], [~~http~~://pdbe.org/6bkf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bkf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bkf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bkf ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/DNLI4_HUMAN DNLI4_HUMAN]] Defects in LIG4 are the cause of LIG4 syndrome (LIG4S) [MIM:[~~http~~://omim.org/entry/606593 606593]]. This disease is characterized by immunodeficiency and developmental and growth delay. Patients display unusual facial features, microcephaly, growth and/or developmental delay, pancytopenia, and various skin abnormalities.<ref>PMID:11779494</ref> Defects in LIG4 are a cause of severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-negative/NK-cell-positive with sensitivity to ionizing radiation (RSSCID) [MIM:[~~http~~://omim.org/entry/602450 602450]]. SCID refers to a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients with SCID present in infancy with recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. Individuals affected by RS-SCID show defects in the DNA repair machinery necessary for coding joint formation and the completion of V(D)J recombination. A subset of cells from such patients show increased radiosensitivity.	+	[https://www.uniprot.org/uniprot/DNLI4_HUMAN DNLI4_HUMAN] Defects in LIG4 are the cause of LIG4 syndrome (LIG4S) [MIM:[https://omim.org/entry/606593 606593]. This disease is characterized by immunodeficiency and developmental and growth delay. Patients display unusual facial features, microcephaly, growth and/or developmental delay, pancytopenia, and various skin abnormalities.<ref>PMID:11779494</ref> Defects in LIG4 are a cause of severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-negative/NK-cell-positive with sensitivity to ionizing radiation (RSSCID) [MIM:[https://omim.org/entry/602450 602450]. SCID refers to a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients with SCID present in infancy with recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. Individuals affected by RS-SCID show defects in the DNA repair machinery necessary for coding joint formation and the completion of V(D)J recombination. A subset of cells from such patients show increased radiosensitivity.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DNLI4_HUMAN DNLI4_HUMAN]] Efficiently joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends.<ref>PMID:9809069</ref> <ref>PMID:10854421</ref>	+	[https://www.uniprot.org/uniprot/DNLI4_HUMAN DNLI4_HUMAN] Efficiently joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends.<ref>PMID:9809069</ref> <ref>PMID:10854421</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bebenek, B]]	+	[[Category: Synthetic construct]]
-	[[Category: Kunkel~~, T A~~]]	+	[[Category: Bebenek B]]
-	[[Category: Moon~~, A F~~]]	+	[[Category: Kunkel TA]]
-	[[Category: Pedersen~~, L C~~]]	+	[[Category: Moon AF]]
-	[[Category: Schellenberg~~, M J~~]]	+	[[Category: Pedersen LC]]
-	[[Category: Tumbale~~, P P~~]]	+	[[Category: Schellenberg MJ]]
-	[[Category: Williams~~, J G~~]]	+	[[Category: Tumbale PP]]
-	[[Category: Williams~~, R S]]~~	+	[[Category: Williams JG]]
-	~~[[Category: Dna double-strand break repair]]~~	+	[[Category: Williams RS]]
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Ligase-dna complex]]~~	+
-	~~[[Category: Nonhomologous end-joining~~]]	+

OCA at 09:20, 18 December 2019

2019-12-18T09:20:51Z

←Older revision		Revision as of 09:20, 18 December 2019
Line 1:		Line 1:

	==Lysyl-adenylate form of human LigIV catalytic domain with bound DNA substrate in open conformation==		==Lysyl-adenylate form of human LigIV catalytic domain with bound DNA substrate in open conformation==
-	<StructureSection load='6bkf' size='340' side='right' caption='[[6bkf]], [[Resolution\|resolution]] 3.25Å' scene=''>	+	<StructureSection load='6bkf' size='340' side='right'caption='[[6bkf]], [[Resolution\|resolution]] 3.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bkf]] is a 4 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=6BKF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BKF FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bkf]] is a 4 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=6BKF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BKF FirstGlance]. <br>
Line 22:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 6bkf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6bkf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA ligase 3D structures\|DNA ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Bebenek, B]]		[[Category: Bebenek, B]]
	[[Category: Kunkel, T A]]		[[Category: Kunkel, T A]]

OCA at 07:52, 21 February 2019

2019-02-21T07:52:36Z

←Older revision		Revision as of 07:52, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='6bkf' size='340' side='right' caption='[[6bkf]], [[Resolution\|resolution]] 3.25Å' scene=''>		<StructureSection load='6bkf' size='340' side='right' caption='[[6bkf]], [[Resolution\|resolution]] 3.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bkf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BKF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BKF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bkf]] is a 4 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=6BKF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BKF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LIG4 ([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_ligase_(ATP) DNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.1 6.5.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_ligase_(ATP) DNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.1 6.5.1.1] </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=6bkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bkf OCA], [http://pdbe.org/6bkf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bkf RCSB], [http://www.ebi.ac.uk/pdbsum/6bkf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bkf 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=6bkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bkf OCA], [http://pdbe.org/6bkf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bkf RCSB], [http://www.ebi.ac.uk/pdbsum/6bkf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bkf ProSAT]</span></td></tr>
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Bebenek, B]]		[[Category: Bebenek, B]]
	[[Category: Kunkel, T A]]		[[Category: Kunkel, T A]]

OCA at 07:34, 18 July 2018

2018-07-18T07:34:35Z

←Older revision		Revision as of 07:34, 18 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6bkf is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Lysyl-adenylate form of human LigIV catalytic domain with bound DNA substrate in open conformation==
		+	<StructureSection load='6bkf' size='340' side='right' caption='[[6bkf]], [[Resolution\|resolution]] 3.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6bkf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BKF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BKF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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_ligase_(ATP) DNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.1 6.5.1.1] </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=6bkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bkf OCA], [http://pdbe.org/6bkf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bkf RCSB], [http://www.ebi.ac.uk/pdbsum/6bkf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bkf ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/DNLI4_HUMAN DNLI4_HUMAN]] Defects in LIG4 are the cause of LIG4 syndrome (LIG4S) [MIM:[http://omim.org/entry/606593 606593]]. This disease is characterized by immunodeficiency and developmental and growth delay. Patients display unusual facial features, microcephaly, growth and/or developmental delay, pancytopenia, and various skin abnormalities.<ref>PMID:11779494</ref> Defects in LIG4 are a cause of severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-negative/NK-cell-positive with sensitivity to ionizing radiation (RSSCID) [MIM:[http://omim.org/entry/602450 602450]]. SCID refers to a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients with SCID present in infancy with recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. Individuals affected by RS-SCID show defects in the DNA repair machinery necessary for coding joint formation and the completion of V(D)J recombination. A subset of cells from such patients show increased radiosensitivity.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DNLI4_HUMAN DNLI4_HUMAN]] Efficiently joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends.<ref>PMID:9809069</ref> <ref>PMID:10854421</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA ligase IV (LigIV) performs the final DNA nick-sealing step of classical nonhomologous end-joining, which is critical for immunoglobulin gene maturation and efficient repair of genotoxic DNA double-strand breaks. Hypomorphic LigIV mutations cause extreme radiation sensitivity and immunodeficiency in humans. To better understand the unique features of LigIV function, here we report the crystal structure of the catalytic core of human LigIV in complex with a nicked nucleic acid substrate in two distinct states-an open lysyl-AMP intermediate, and a closed DNA-adenylate form. Results from structural and mutagenesis experiments unveil a dynamic LigIV DNA encirclement mechanism characterized by extensive interdomain interactions and active site phosphoanhydride coordination, all of which are required for efficient DNA nick sealing. These studies provide a scaffold for defining impacts of LigIV catalytic core mutations and deficiencies in human LIG4 syndrome.

-	~~Authors~~:	+	Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis.,Kaminski AM, Tumbale PP, Schellenberg MJ, Williams RS, Williams JG, Kunkel TA, Pedersen LC, Bebenek K Nat Commun. 2018 Jul 6;9(1):2642. doi: 10.1038/s41467-018-05024-8. PMID:29980672<ref>PMID:29980672</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6bkf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bebenek, B]]
		+	[[Category: Kunkel, T A]]
		+	[[Category: Moon, A F]]
		+	[[Category: Pedersen, L C]]
		+	[[Category: Schellenberg, M J]]
		+	[[Category: Tumbale, P P]]
		+	[[Category: Williams, J G]]
		+	[[Category: Williams, R S]]
		+	[[Category: Dna double-strand break repair]]
		+	[[Category: Ligase]]
		+	[[Category: Ligase-dna complex]]
		+	[[Category: Nonhomologous end-joining]]

OCA at 06:34, 22 November 2017

2017-11-22T06:34:03Z

←Older revision		Revision as of 06:34, 22 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6bkf is ON HOLD	+	The entry 6bkf is ON HOLD until Paper Publication

	Authors:		Authors:

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

2017-11-15T06:24:57Z

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

←Older revision

Revision as of 06:24, 15 November 2017

OCA: New page: '''Unreleased structure''' The entry 6bkf is ON HOLD Authors: Description: Category: Unreleased Structures

2017-11-15T06:24:56Z

New page: '''Unreleased structure''' The entry 6bkf is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6bkf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]