6f1s - Revision history

OCA at 06:23, 8 March 2018

OCA — Thu, 08 Mar 2018 06:23:28 GMT

←Older revision		Revision as of 06:23, 8 March 2018
Line 9:		Line 9:
	<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=6f1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f1s OCA], [http://pdbe.org/6f1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f1s RCSB], [http://www.ebi.ac.uk/pdbsum/6f1s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f1s 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=6f1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f1s OCA], [http://pdbe.org/6f1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f1s RCSB], [http://www.ebi.ac.uk/pdbsum/6f1s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f1s ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	CglI is a restriction endonuclease from Corynebacterium glutamicum that forms a complex between: two R-subunits that have site specific-recognition and nuclease domains; and two H-subunits, with Superfamily 2 helicase-like DEAD domains, and uncharacterized Z1 and C-terminal domains. ATP hydrolysis by the H-subunits catalyses dsDNA translocation that is necessary for long-range movement along DNA that activates nuclease activity. Here, we provide biochemical and molecular modelling evidence that shows that Z1 has a fold distantly-related to RecA, and that the DEAD-Z1 domains together form an ATP binding interface and are the prototype of a previously undescribed monomeric helicase-like motor. The DEAD-Z1 motor has unusual Walker A and Motif VI sequences those nonetheless have their expected functions. Additionally, it contains DEAD-Z1-specific features: an H/H motif and a loop (aa 163-aa 172), that both play a role in the coupling of ATP hydrolysis to DNA cleavage. We also solved the crystal structure of the C-terminal domain which has a unique fold, and demonstrate that the Z1-C domains are the principal DNA binding interface of the H-subunit. Finally, we use small angle X-ray scattering to provide a model for how the H-subunit domains are arranged in a dimeric complex.
		+
		+	The H-subunit of the restriction endonuclease CglI contains a prototype DEAD-Z1 helicase-like motor.,Toliusis P, Tamulaitiene G, Grigaitis R, Tuminauskaite D, Silanskas A, Manakova E, Venclovas C, Szczelkun MD, Siksnys V, Zaremba M Nucleic Acids Res. 2018 Feb 20. pii: 4877023. doi: 10.1093/nar/gky107. PMID:29471489<ref>PMID:29471489</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6f1s" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:30, 22 February 2018

OCA — Thu, 22 Feb 2018 08:30:04 GMT

←Older revision		Revision as of 08:30, 22 February 2018
Line 3:		Line 3:
	<StructureSection load='6f1s' size='340' side='right' caption='[[6f1s]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6f1s' size='340' side='right' caption='[[6f1s]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6f1s]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F1S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6f1s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_glutamicus"_kinoshita_et_al._1958 "micrococcus glutamicus" kinoshita et al. 1958]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F1S FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cglIIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1718 "Micrococcus glutamicus" Kinoshita et al. 1958])</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=6f1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f1s OCA], [http://pdbe.org/6f1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f1s RCSB], [http://www.ebi.ac.uk/pdbsum/6f1s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f1s 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=6f1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f1s OCA], [http://pdbe.org/6f1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f1s RCSB], [http://www.ebi.ac.uk/pdbsum/6f1s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f1s ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Micrococcus glutamicus kinoshita et al. 1958]]
	[[Category: Grigaitis, R]]		[[Category: Grigaitis, R]]
	[[Category: Silanskas, A]]		[[Category: Silanskas, A]]

OCA at 06:36, 15 February 2018

OCA — Thu, 15 Feb 2018 06:36:37 GMT

←Older revision		Revision as of 06:36, 15 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6f1s ~~is ON HOLD~~	+	==C-terminal domain of CglI restriction endonuclease H subunit==
-		+	<StructureSection load='6f1s' size='340' side='right' caption='[[6f1s]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~Authors~~: ~~Tamulaitiene, G~~., ~~Grigaitis~~, R., ~~Zaremba~~, M., ~~Silanskas~~, A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6f1s]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F1S FirstGlance]. <br>
-	~~Description~~: C-~~terminal domain of CglI restriction endonuclease H subunit~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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=MSE:SELENOMETHIONINE'>MSE</scene></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=6f1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f1s OCA], [http://pdbe.org/6f1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f1s RCSB], [http://www.ebi.ac.uk/pdbsum/6f1s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f1s ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Grigaitis, R]]
	[[Category: Silanskas, A]]		[[Category: Silanskas, A]]
-	[[Category: Grigaitis, R]]
	[[Category: Tamulaitiene, G]]		[[Category: Tamulaitiene, G]]
	[[Category: Zaremba, M]]		[[Category: Zaremba, M]]
		+	[[Category: Hydrolase]]
		+	[[Category: Ntpase]]
		+	[[Category: Restriction endonuclease]]

OCA: Protected "6f1s" [edit=sysop:move=sysop]

OCA — Wed, 29 Nov 2017 05:16:37 GMT

Protected "6f1s" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:16, 29 November 2017

OCA: New page: '''Unreleased structure''' The entry 6f1s is ON HOLD Authors: Tamulaitiene, G., Grigaitis, R., Zaremba, M., Silanskas, A. Description: C-terminal domain of CglI restriction endonucleas...

OCA — Wed, 29 Nov 2017 05:16:35 GMT

New page: '''Unreleased structure''' The entry 6f1s is ON HOLD Authors: Tamulaitiene, G., Grigaitis, R., Zaremba, M., Silanskas, A. Description: C-terminal domain of CglI restriction endonucleas...

New page

'''Unreleased structure'''

The entry 6f1s is ON HOLD

Authors: Tamulaitiene, G., Grigaitis, R., Zaremba, M., Silanskas, A.

Description: C-terminal domain of CglI restriction endonuclease H subunit
[[Category: Unreleased Structures]]
[[Category: Silanskas, A]]
[[Category: Grigaitis, R]]
[[Category: Tamulaitiene, G]]
[[Category: Zaremba, M]]