6yex - Revision history

OCA at 14:59, 3 March 2021

OCA — Wed, 03 Mar 2021 14:59:07 GMT

←Older revision		Revision as of 14:59, 3 March 2021
Line 1:		Line 1:

	==VcaM4I restriction endonuclease in the absence of DNA==		==VcaM4I restriction endonuclease in the absence of DNA==
-	<StructureSection load='6yex' size='340' side='right'caption='[[6yex]]~~, [[Resolution\|resolution]] 1.50Å~~' scene=''>	+	<StructureSection load='6yex' size='340' side='right'caption='[[6yex]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[6yex]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25920 Atcc 25920].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YEX FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YEX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</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=6yex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yex OCA], [https://pdbe.org/6yex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yex RCSB], [https://www.ebi.ac.uk/pdbsum/6yex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yex ProSAT]</span></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5j3e\|5j3e]], [[6yjb\|6yjb]], [[6ykf\|6ykf]], [[6ymg\|6ymg]]</div></td></tr>	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSB67_20905 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=680 ATCC 25920])</td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6yex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yex OCA], [~~http~~://pdbe.org/6yex PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6yex RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6yex PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6yex ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Modification dependent restriction endonucleases (MDREs) often have separate catalytic and modification dependent domains. We systematically looked for previously uncharacterized fusion proteins featuring a PUA or DUF3427 domain and HNH or PD-(D/E)XK catalytic domain. The enzymes were clustered by similarity of their putative modification sensing domains into several groups. The TspA15I (VcaM4I, CmeDI), ScoA3IV (MsiJI, VcaCI) and YenY4I groups, all featuring a PUA superfamily domain, preferentially cleaved DNA containing 5-methylcytosine or 5-hydroxymethylcytosine. ScoA3V, also featuring a PUA superfamily domain, but of a different clade, exhibited 6-methyladenine stimulated nicking activity. With few exceptions, ORFs for PUA-superfamily domain containing endonucleases were not close to DNA methyltransferase ORFs, strongly supporting modification dependent activity of the endonucleases. DUF3427 domain containing fusion proteins had very little or no endonuclease activity, despite the presence of a putative PD-(D/E)XK catalytic domain. However, their expression potently restricted phage T4gt in Escherichia coli cells. In contrast to the ORFs for PUA domain containing endonucleases, the ORFs for DUF3427 fusion proteins were frequently found in defense islands, often also featuring DNA methyltransferases.
-
-	A protein architecture guided screen for modification dependent restriction endonucleases.,Lutz T, Flodman K, Copelas A, Czapinska H, Mabuchi M, Fomenkov A, He X, Bochtler M, Xu SY Nucleic Acids Res. 2019 Oct 10;47(18):9761-9776. doi: 10.1093/nar/gkz755. PMID:31504772<ref>PMID:31504772</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6yex" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 25920]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bochtler, M]]	+	[[Category: Bochtler M]]
-	[[Category: Czapinska, H]]	+	[[Category: Czapinska H]]
-	[[Category: Helbrecht, I]]	+	[[Category: Helbrecht I]]
-	[[Category: Lutz, T]]	+	[[Category: Lutz T]]
-	[[Category: Pastor, M]]	+	[[Category: Pastor M]]
-	[[Category: Xu, S]]	+	[[Category: Xu S]]
-	~~[[Category: Dna endonuclease]]~~	+
-	~~[[Category: Eve domain]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mdre]]~~	+
-	~~[[Category: Modification-dependent restriction endonuclease]]~~	+
-	~~[[Category: Pua superfamily]]~~	+
-	~~[[Category: Single stranded dna~~]]	+

OCA at 10:58, 24 December 2020

OCA — Thu, 24 Dec 2020 10:58:50 GMT

←Older revision		Revision as of 10:58, 24 December 2020
Line 1:		Line 1:

	==VcaM4I restriction endonuclease in the absence of DNA==		==VcaM4I restriction endonuclease in the absence of DNA==
-	<StructureSection load='6yex' size='340' side='right'caption='[[6yex]]' scene=''>	+	<StructureSection load='6yex' size='340' side='right'caption='[[6yex]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YEX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yex]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25920 Atcc 25920]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YEX FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6yex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yex OCA], [http://pdbe.org/6yex PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yex RCSB], [http://www.ebi.ac.uk/pdbsum/6yex PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yex ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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"><div style='overflow: auto; max-height: 3em;'>[[5j3e\|5j3e]], [[6yjb\|6yjb]], [[6ykf\|6ykf]], [[6ymg\|6ymg]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSB67_20905 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=680 ATCC 25920])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6yex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yex OCA], [http://pdbe.org/6yex PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yex RCSB], [http://www.ebi.ac.uk/pdbsum/6yex PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yex ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Modification dependent restriction endonucleases (MDREs) often have separate catalytic and modification dependent domains. We systematically looked for previously uncharacterized fusion proteins featuring a PUA or DUF3427 domain and HNH or PD-(D/E)XK catalytic domain. The enzymes were clustered by similarity of their putative modification sensing domains into several groups. The TspA15I (VcaM4I, CmeDI), ScoA3IV (MsiJI, VcaCI) and YenY4I groups, all featuring a PUA superfamily domain, preferentially cleaved DNA containing 5-methylcytosine or 5-hydroxymethylcytosine. ScoA3V, also featuring a PUA superfamily domain, but of a different clade, exhibited 6-methyladenine stimulated nicking activity. With few exceptions, ORFs for PUA-superfamily domain containing endonucleases were not close to DNA methyltransferase ORFs, strongly supporting modification dependent activity of the endonucleases. DUF3427 domain containing fusion proteins had very little or no endonuclease activity, despite the presence of a putative PD-(D/E)XK catalytic domain. However, their expression potently restricted phage T4gt in Escherichia coli cells. In contrast to the ORFs for PUA domain containing endonucleases, the ORFs for DUF3427 fusion proteins were frequently found in defense islands, often also featuring DNA methyltransferases.
		+
		+	A protein architecture guided screen for modification dependent restriction endonucleases.,Lutz T, Flodman K, Copelas A, Czapinska H, Mabuchi M, Fomenkov A, He X, Bochtler M, Xu SY Nucleic Acids Res. 2019 Oct 10;47(18):9761-9776. doi: 10.1093/nar/gkz755. PMID:31504772<ref>PMID:31504772</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yex" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 25920]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bochtler M]]	+	[[Category: Bochtler, M]]
-	[[Category: Czapinska H]]	+	[[Category: Czapinska, H]]
-	[[Category: Helbrecht I]]	+	[[Category: Helbrecht, I]]
-	[[Category: Lutz T]]	+	[[Category: Lutz, T]]
-	[[Category: Pastor M]]	+	[[Category: Pastor, M]]
-	[[Category: Xu S]]	+	[[Category: Xu, S]]
		+	[[Category: Dna endonuclease]]
		+	[[Category: Eve domain]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mdre]]
		+	[[Category: Modification-dependent restriction endonuclease]]
		+	[[Category: Pua superfamily]]
		+	[[Category: Single stranded dna]]

OCA at 12:33, 16 December 2020

OCA — Wed, 16 Dec 2020 12:33:00 GMT

←Older revision		Revision as of 12:33, 16 December 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6yex is ~~ON HOLD until Paper Publication~~	+	==VcaM4I restriction endonuclease in the absence of DNA==
-		+	<StructureSection load='6yex' size='340' side='right'caption='[[6yex]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YEX FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6yex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yex OCA], [http://pdbe.org/6yex PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yex RCSB], [http://www.ebi.ac.uk/pdbsum/6yex PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yex ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bochtler M]]
		+	[[Category: Czapinska H]]
		+	[[Category: Helbrecht I]]
		+	[[Category: Lutz T]]
		+	[[Category: Pastor M]]
		+	[[Category: Xu S]]

OCA at 05:22, 29 April 2020

OCA — Wed, 29 Apr 2020 05:22:00 GMT

←Older revision		Revision as of 05:22, 29 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 01 Apr 2020 07:46:33 GMT

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

←Older revision

Revision as of 07:46, 1 April 2020

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

OCA — Wed, 01 Apr 2020 07:46:32 GMT

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

New page

'''Unreleased structure'''

The entry 6yex is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]