6rar - Revision history

OCA at 12:18, 24 January 2024

2024-01-24T12:18:15Z

←Older revision		Revision as of 12:18, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6rar' size='340' side='right'caption='[[6rar]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='6rar' size='340' side='right'caption='[[6rar]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rar]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Prochlorococcus_marinus_str.~~_mit_9302~~ Prochlorococcus marinus str. ~~mit~~ 9302]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RAR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6RAR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rar]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Prochlorococcus_marinus_str._MIT_9302 Prochlorococcus marinus str. MIT 9302] 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=6RAR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RAR 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~~>, ~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.785Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~OMC~~:~~O2-METHYLYCYTIDINE-5-~~MONOPHOSPHATE'>~~OMC~~</scene><~~/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>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[6rau\|6rau]]~~, ~~[[6rce\|6rce]], [[6ras\|6ras]]~~<~~/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=6rar FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rar OCA], [https://pdbe.org/6rar PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rar RCSB], [https://www.ebi.ac.uk/pdbsum/6rar PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rar ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">EU96_0746 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=74545 Prochlorococcus marinus str. MIT 9302])~~</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=6rar FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rar OCA], [~~http~~://pdbe.org/6rar PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6rar RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6rar PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6rar ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0A2ACP7_PROMR A0A0A2ACP7_PROMR]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6rar" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6rar" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA ligase 3D structures\|DNA ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Prochlorococcus marinus str. ~~mit~~ 9302]]	+	[[Category: Prochlorococcus marinus str. MIT 9302]]
-	[[Category: ~~Leiros, H K.S~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Williamson, A~~]]	+	[[Category: Leiros HKS]]
-	[[Category: ~~Atp-dependent]]~~	+	[[Category: Williamson A]]
-	~~[[Category: Determinants in dna binding]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna ligase]]~~	+
-	~~[[Category: Ligase-dna co-crystal structure~~]]	+

OCA at 16:18, 29 January 2020

2020-01-29T16:18:18Z

←Older revision		Revision as of 16:18, 29 January 2020
Line 3:		Line 3:
	<StructureSection load='6rar' size='340' side='right'caption='[[6rar]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='6rar' size='340' side='right'caption='[[6rar]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rar]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RAR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RAR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rar]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Prochlorococcus_marinus_str._mit_9302 Prochlorococcus marinus str. mit 9302]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RAR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RAR 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>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6rau\|6rau]], [[6rce\|6rce]], [[6ras\|6ras]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6rau\|6rau]], [[6rce\|6rce]], [[6ras\|6ras]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EU96_0746 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=74545 Prochlorococcus marinus str. MIT 9302])</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=6rar FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rar OCA], [http://pdbe.org/6rar PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rar RCSB], [http://www.ebi.ac.uk/pdbsum/6rar PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rar 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=6rar FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rar OCA], [http://pdbe.org/6rar PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rar RCSB], [http://www.ebi.ac.uk/pdbsum/6rar PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rar ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA ligases join adjacent 5' phosphate (5'P) and 3' hydroxyl (3'OH) termini of double-stranded DNA via a three-step mechanism requiring a nucleotide cofactor and divalent metal ion. Although considerable structural detail is available for the first two steps, less is known about step 3 where the DNA-backbone is joined or about the cation role at this step. We have captured high-resolution structures of an adenosine triphosphate (ATP)-dependent DNA ligase from Prochlorococcus marinus including a Mn-bound pre-ternary ligase-DNA complex poised for phosphodiester bond formation, and a post-ternary intermediate retaining product DNA and partially occupied AMP in the active site. The pre-ternary structure unambiguously identifies the binding site of the catalytic metal ion and confirms both its role in activating the 3'OH terminus for nucleophilic attack on the 5'P group and stabilizing the pentavalent transition state. The post-ternary structure indicates that DNA distortion and most enzyme-AMP contacts remain after phosphodiester bond formation, implying loss of covalent linkage to the DNA drives release of AMP, rather than active site rearrangement. Additionally, comparisons of this cyanobacterial DNA ligase with homologs from bacteria and bacteriophage pose interesting questions about the structural origin of double-strand break joining activity and the evolution of these ATP-dependent DNA ligase enzymes.
		+
		+	Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation.,Williamson A, Leiros HS Nucleic Acids Res. 2019 Aug 22;47(14):7147-7162. doi: 10.1093/nar/gkz596. PMID:31312841<ref>PMID:31312841</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6rar" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Prochlorococcus marinus str. mit 9302]]
	[[Category: Leiros, H K.S]]		[[Category: Leiros, H K.S]]
	[[Category: Williamson, A]]		[[Category: Williamson, A]]

OCA at 05:58, 10 July 2019

2019-07-10T05:58:35Z

←Older revision		Revision as of 05:58, 10 July 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6rar ~~is ON HOLD until Paper Publication~~	+	==Pmar-Lig_PreS3-Mn==
-		+	<StructureSection load='6rar' size='340' side='right'caption='[[6rar]], [[Resolution\|resolution]] 1.79Å' scene=''>
-	~~Authors~~: ~~Leiros, H~~.K.S., ~~Williamson~~, A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6rar]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RAR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RAR FirstGlance]. <br>
-	~~Description~~: ~~Pmar~~-~~Lig_PreS3~~-Mn	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene></td></tr>
-	[[Category: Leiros, H.K.S]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6rau\|6rau]], [[6rce\|6rce]], [[6ras\|6ras]]</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=6rar FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rar OCA], [http://pdbe.org/6rar PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rar RCSB], [http://www.ebi.ac.uk/pdbsum/6rar PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rar ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Leiros, H K.S]]
	[[Category: Williamson, A]]		[[Category: Williamson, A]]
		+	[[Category: Atp-dependent]]
		+	[[Category: Determinants in dna binding]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna ligase]]
		+	[[Category: Ligase-dna co-crystal structure]]

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

2019-04-17T04:22:41Z

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

←Older revision

Revision as of 04:22, 17 April 2019

OCA: New page: '''Unreleased structure''' The entry 6rar is ON HOLD until Paper Publication Authors: Leiros, H.K.S., Williamson, A. Description: Pmar-Lig_PreS3-Mn Category: Unreleased Structures ...

2019-04-17T04:22:39Z

New page: '''Unreleased structure''' The entry 6rar is ON HOLD until Paper Publication Authors: Leiros, H.K.S., Williamson, A. Description: Pmar-Lig_PreS3-Mn Category: Unreleased Structures ...

New page

'''Unreleased structure'''

The entry 6rar is ON HOLD until Paper Publication

Authors: Leiros, H.K.S., Williamson, A.

Description: Pmar-Lig_PreS3-Mn
[[Category: Unreleased Structures]]
[[Category: Leiros, H.K.S]]
[[Category: Williamson, A]]