6nhx - Revision history

OCA at 14:47, 13 March 2024

OCA — Wed, 13 Mar 2024 14:47:41 GMT

←Older revision		Revision as of 14:47, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6nhx' size='340' side='right'caption='[[6nhx]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='6nhx' size='340' side='right'caption='[[6nhx]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nhx]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NHX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NHX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nhx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NHX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NHX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=ATP:ADENOSINE~~-~~5-TRIPHOSPHATE'>ATP</scene>~~, ~~<scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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]] 1.4Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ERS027656_00724 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1773~~ "~~Bacillus tuberculosis~~" ~~(Zopf 1883) Klein 1884])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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=6nhx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nhx OCA], [https://pdbe.org/6nhx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nhx RCSB], [https://www.ebi.ac.uk/pdbsum/6nhx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nhx 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=6nhx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nhx OCA], [~~http~~://pdbe.org/6nhx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6nhx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6nhx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6nhx ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	DNA ligases are the sine qua non of genome integrity and essential for DNA replication and repair in all organisms. DNA ligases join 3'-OH and 5'-PO4 ends via a series of three nucleotidyl transfer steps. In step 1, ligase reacts with ATP or NAD(+) to form a covalent ligase-(lysyl-Nzeta)-AMP intermediate and release pyrophosphate (PPi) or nicotinamide mononucleotide (NMN). In step 2, AMP is transferred from ligase-adenylate to the 5'-PO4 DNA end to form a DNA-adenylate intermediate (AppDNA). In step 3, ligase catalyzes attack by a DNA 3'-OH on the DNA-adenylate to seal the two ends via a phosphodiester bond and release AMP. Eukaryal, archaeal, and many bacterial and viral DNA ligases are ATP-dependent. The catalytic core of ATP-dependent DNA ligases consists of an N-terminal nucleotidyltransferase (NTase) domain fused to a C-terminal OB domain. Here we report crystal structures at 1.4-1.6 A resolution of Mycobacterium tuberculosis LigD, an ATP-dependent DNA ligase dedicated to non-homologous end joining, in complexes with ATP that highlight large movements of the OB domain (~50 A), from a closed conformation in the ATP complex to an open conformation in the covalent ligase-AMP intermediate. The LigD*ATP structures revealed a network of amino acid contacts to the ATP phosphates that stabilize the transition state and orient the PPi leaving group. A complex with ATP and magnesium suggested a two-metal mechanism of lysine adenylylation driven by a catalytic Mg(2+) that engages the ATP alpha phosphate and a second metal that bridges the ATP beta and gamma phosphates.
-
-	Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates.,Unciuleac MC, Goldgur Y, Shuman S J Biol Chem. 2019 Feb 4. pii: RA119.007445. doi: 10.1074/jbc.RA119.007445. PMID:30718283<ref>PMID:30718283</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6nhx" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[DNA ligase 3D structures\|DNA ligase 3D structures]]		*[[DNA ligase 3D structures\|DNA ligase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Goldgur, Y~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Shuman, S~~]]	+	[[Category: Goldgur Y]]
-	[[Category: ~~Unciuleac, M~~]]	+	[[Category: Shuman S]]
-	[[Category: ~~Dna ligase]]~~	+	[[Category: Unciuleac M]]
-	~~[[Category: Ligase~~]]	+

OCA at 10:34, 4 December 2019

OCA — Wed, 04 Dec 2019 10:34:47 GMT

←Older revision		Revision as of 10:34, 4 December 2019
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 6nhx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6nhx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA ligase 3D structures\|DNA ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:58, 10 April 2019

OCA — Wed, 10 Apr 2019 07:58:17 GMT

←Older revision		Revision as of 07:58, 10 April 2019
Line 1:		Line 1:

	==mycobacterial DNA ligase D complexed with ATP and MES==		==mycobacterial DNA ligase D complexed with ATP and MES==
-	<StructureSection load='6nhx' size='340' side='right' caption='[[6nhx]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='6nhx' size='340' side='right'caption='[[6nhx]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6nhx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NHX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NHX FirstGlance]. <br>		<table><tr><td colspan='2'>[[6nhx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NHX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NHX FirstGlance]. <br>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Goldgur, Y]]		[[Category: Goldgur, Y]]
	[[Category: Shuman, S]]		[[Category: Shuman, S]]

OCA at 08:51, 21 February 2019

OCA — Thu, 21 Feb 2019 08:51:20 GMT

←Older revision		Revision as of 08:51, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='6nhx' size='340' side='right' caption='[[6nhx]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='6nhx' size='340' side='right' caption='[[6nhx]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nhx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NHX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NHX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nhx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NHX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NHX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERS027656_00724 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=6nhx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nhx OCA], [http://pdbe.org/6nhx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nhx RCSB], [http://www.ebi.ac.uk/pdbsum/6nhx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nhx 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=6nhx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nhx OCA], [http://pdbe.org/6nhx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nhx RCSB], [http://www.ebi.ac.uk/pdbsum/6nhx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nhx ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA ligases are the sine qua non of genome integrity and essential for DNA replication and repair in all organisms. DNA ligases join 3'-OH and 5'-PO4 ends via a series of three nucleotidyl transfer steps. In step 1, ligase reacts with ATP or NAD(+) to form a covalent ligase-(lysyl-Nzeta)-AMP intermediate and release pyrophosphate (PPi) or nicotinamide mononucleotide (NMN). In step 2, AMP is transferred from ligase-adenylate to the 5'-PO4 DNA end to form a DNA-adenylate intermediate (AppDNA). In step 3, ligase catalyzes attack by a DNA 3'-OH on the DNA-adenylate to seal the two ends via a phosphodiester bond and release AMP. Eukaryal, archaeal, and many bacterial and viral DNA ligases are ATP-dependent. The catalytic core of ATP-dependent DNA ligases consists of an N-terminal nucleotidyltransferase (NTase) domain fused to a C-terminal OB domain. Here we report crystal structures at 1.4-1.6 A resolution of Mycobacterium tuberculosis LigD, an ATP-dependent DNA ligase dedicated to non-homologous end joining, in complexes with ATP that highlight large movements of the OB domain (~50 A), from a closed conformation in the ATP complex to an open conformation in the covalent ligase-AMP intermediate. The LigD*ATP structures revealed a network of amino acid contacts to the ATP phosphates that stabilize the transition state and orient the PPi leaving group. A complex with ATP and magnesium suggested a two-metal mechanism of lysine adenylylation driven by a catalytic Mg(2+) that engages the ATP alpha phosphate and a second metal that bridges the ATP beta and gamma phosphates.
		+
		+	Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates.,Unciuleac MC, Goldgur Y, Shuman S J Biol Chem. 2019 Feb 4. pii: RA119.007445. doi: 10.1074/jbc.RA119.007445. PMID:30718283<ref>PMID:30718283</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6nhx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:37, 13 February 2019

OCA — Wed, 13 Feb 2019 09:37:05 GMT

←Older revision		Revision as of 09:37, 13 February 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6nhx is ~~ON HOLD until Paper Publication~~	+	==mycobacterial DNA ligase D complexed with ATP and MES==
-		+	<StructureSection load='6nhx' size='340' side='right' caption='[[6nhx]], [[Resolution\|resolution]] 1.40Å' scene=''>
-	~~Authors~~: ~~Shuman~~, S., ~~Unciuleac~~, M., ~~Goldgur~~, Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6nhx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NHX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NHX FirstGlance]. <br>
-	~~Description~~: ~~mycobacterial DNA ligase D complexed with ATP and MES~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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/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=6nhx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nhx OCA], [http://pdbe.org/6nhx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nhx RCSB], [http://www.ebi.ac.uk/pdbsum/6nhx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nhx ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Goldgur, Y]]
		+	[[Category: Shuman, S]]
	[[Category: Unciuleac, M]]		[[Category: Unciuleac, M]]
-	[[Category: ~~Shuman, S~~]]	+	[[Category: Dna ligase]]
-	[[Category: ~~Goldgur, Y~~]]	+	[[Category: Ligase]]

OCA at 10:38, 16 January 2019

OCA — Wed, 16 Jan 2019 10:38:44 GMT

←Older revision		Revision as of 10:38, 16 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Shuman, S., Unciuleac, M., Goldgur, Y.		Authors: Shuman, S., Unciuleac, M., Goldgur, Y.

-	Description: mycobacterial DNA ligase D	+	Description: mycobacterial DNA ligase D complexed with ATP and MES
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Unciuleac, M]]		[[Category: Unciuleac, M]]
	[[Category: Shuman, S]]		[[Category: Shuman, S]]
	[[Category: Goldgur, Y]]		[[Category: Goldgur, Y]]

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

OCA — Wed, 02 Jan 2019 04:58:50 GMT

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

←Older revision

Revision as of 04:58, 2 January 2019

OCA: New page: '''Unreleased structure''' The entry 6nhx is ON HOLD Authors: Shuman, S., Unciuleac, M., Goldgur, Y. Description: mycobacterial DNA ligase D Category: Unreleased Structures [[Categ...

OCA — Wed, 02 Jan 2019 04:58:48 GMT

New page: '''Unreleased structure''' The entry 6nhx is ON HOLD Authors: Shuman, S., Unciuleac, M., Goldgur, Y. Description: mycobacterial DNA ligase D Category: Unreleased Structures [[Categ...

New page

'''Unreleased structure'''

The entry 6nhx is ON HOLD

Authors: Shuman, S., Unciuleac, M., Goldgur, Y.

Description: mycobacterial DNA ligase D
[[Category: Unreleased Structures]]
[[Category: Unciuleac, M]]
[[Category: Shuman, S]]
[[Category: Goldgur, Y]]