5gki - Revision history

OCA at 11:34, 2 August 2023

OCA — Wed, 02 Aug 2023 11:34:28 GMT

←Older revision		Revision as of 11:34, 2 August 2023
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	<StructureSection load='5gki' size='340' side='right'caption='[[5gki]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='5gki' size='340' side='right'caption='[[5gki]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gki]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GKI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gki]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1] 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=5GKI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GKI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MG:MAGNESIUM+ION'>MG</scene~~>, ~~<scene name='pdbligand=MPD:(4S)-~~2~~-METHYL-2,4-PENTANEDIOL'>MPD</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]] 2.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5gke\|5gke]], [[5gkf\|5gkf]], [[5gkg\|5gkg]], [[5gkh\|5gkh]], [[5gkj\|5gkj]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class~~=~~"sblockDat">TK1898 ([http~~:~~//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis~~ (~~strain KOD1)]~~)</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=5gki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gki OCA], [https://pdbe.org/5gki PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gki RCSB], [https://www.ebi.ac.uk/pdbsum/5gki PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gki 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=5gki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gki OCA], [~~http~~://pdbe.org/5gki PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gki RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gki PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gki ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NUCS_THEKO NUCS_THEKO]] Cleaves both 3' and 5' ssDNA extremities of branched DNA structures.	+	[https://www.uniprot.org/uniprot/NUCS_THEKO NUCS_THEKO] Cleaves both 3' and 5' ssDNA extremities of branched DNA structures.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hijikata, A]]	+	[[Category: Synthetic construct]]
-	[[Category: Ishino, S]]	+	[[Category: Thermococcus kodakarensis KOD1]]
-	[[Category: Ishino, Y]]	+	[[Category: Hijikata A]]
-	[[Category: Kouyama, K]]	+	[[Category: Ishino S]]
-	[[Category: Mayanagi, K]]	+	[[Category: Ishino Y]]
-	[[Category: Nakae, S]]	+	[[Category: Kouyama K]]
-	[[Category: Shirai, T]]	+	[[Category: Mayanagi K]]
-	[[Category: Tsuji, T]]	+	[[Category: Nakae S]]
-	[[Category: Yonezawa, K]]	+	[[Category: Shirai T]]
-	~~[[Category: Dna complex]]~~	+	[[Category: Tsuji T]]
-	~~[[Category: Endonuclease]]~~	+	[[Category: Yonezawa K]]
-	~~[[Category: Hydrolase-dna complex~~]]	+

OCA at 10:08, 26 February 2020

OCA — Wed, 26 Feb 2020 10:08:15 GMT

←Older revision		Revision as of 10:08, 26 February 2020
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	==Structure of EndoMS-dsDNA3 complex==		==Structure of EndoMS-dsDNA3 complex==
-	<StructureSection load='5gki' size='340' side='right' caption='[[5gki]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='5gki' size='340' side='right'caption='[[5gki]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gki]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GKI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gki]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GKI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gke\|5gke]], [[5gkf\|5gkf]], [[5gkg\|5gkg]], [[5gkh\|5gkh]], [[5gkj\|5gkj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gke\|5gke]], [[5gkf\|5gkf]], [[5gkg\|5gkg]], [[5gkh\|5gkh]], [[5gkj\|5gkj]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK1898 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=5gki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gki OCA], [http://pdbe.org/5gki PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gki RCSB], [http://www.ebi.ac.uk/pdbsum/5gki PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gki 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=5gki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gki OCA], [http://pdbe.org/5gki PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gki RCSB], [http://www.ebi.ac.uk/pdbsum/5gki PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gki ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 5gki" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5gki" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Hijikata, A]]		[[Category: Hijikata, A]]
	[[Category: Ishino, S]]		[[Category: Ishino, S]]

OCA at 18:20, 2 November 2016

OCA — Wed, 02 Nov 2016 18:20:57 GMT

←Older revision		Revision as of 18:20, 2 November 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5gki is ~~ON HOLD~~	+	==Structure of EndoMS-dsDNA3 complex==
		+	<StructureSection load='5gki' size='340' side='right' caption='[[5gki]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5gki]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GKI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gke\|5gke]], [[5gkf\|5gkf]], [[5gkg\|5gkg]], [[5gkh\|5gkh]], [[5gkj\|5gkj]]</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=5gki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gki OCA], [http://pdbe.org/5gki PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gki RCSB], [http://www.ebi.ac.uk/pdbsum/5gki PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gki ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NUCS_THEKO NUCS_THEKO]] Cleaves both 3' and 5' ssDNA extremities of branched DNA structures.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases. In this study, we determined the structure of the EndoMS-DNA complex. The complex structure of the EndoMS dimer with dsDNA unexpectedly revealed that the mismatched bases were flipped out into binding sites, and the overall architecture most resembled that of restriction enzymes. The structure of the apo form was similar to the reported structure of Pyrococcus abyssi NucS, indicating that movement of the C-terminal domain from the resting state was required for activity. In addition, a model of the EndoMS-PCNA-DNA complex was preliminarily verified with electron microscopy. The structures strongly support the idea that EndoMS acts in a mismatch repair pathway.

-	~~Authors~~:	+	Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease.,Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI, Mayanagi K, Ishino S, Ishino Y, Shirai T Structure. 2016 Oct 17. pii: S0969-2126(16)30294-5. doi:, 10.1016/j.str.2016.09.005. PMID:27773688<ref>PMID:27773688</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5gki" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hijikata, A]]
		+	[[Category: Ishino, S]]
		+	[[Category: Ishino, Y]]
		+	[[Category: Kouyama, K]]
		+	[[Category: Mayanagi, K]]
		+	[[Category: Nakae, S]]
		+	[[Category: Shirai, T]]
		+	[[Category: Tsuji, T]]
		+	[[Category: Yonezawa, K]]
		+	[[Category: Dna complex]]
		+	[[Category: Endonuclease]]
		+	[[Category: Hydrolase-dna complex]]

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

OCA — Thu, 14 Jul 2016 06:37:36 GMT

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

←Older revision

Revision as of 06:37, 14 July 2016

OCA: New page: '''Unreleased structure''' The entry 5gki is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 14 Jul 2016 06:37:34 GMT

New page: '''Unreleased structure''' The entry 5gki is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5gki is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]