6obj - Revision history

OCA at 09:23, 20 March 2024

2024-03-20T09:23:40Z

← Older revision		Revision as of 09:23, 20 March 2024
Line 3:		Line 3:
	<SX load='6obj' size='340' side='right' viewer='molstar' caption='[[6obj]], [[Resolution\|resolution]] 3.50Å' scene=''>		<SX load='6obj' size='340' side='right' viewer='molstar' caption='[[6obj]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6obj]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"actinomyces_griseus"_krainsky_1914 "actinomyces~~ griseus~~" krainsky 1914~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OBJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6OBJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[6obj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_griseus Streptomyces griseus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OBJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OBJ FirstGlance]. <br>
	</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>~~</td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.5Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>sgraIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1911~~ "~~Actinomyces griseus~~" ~~Krainsky 1914])~~</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></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=6obj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6obj OCA], [~~http~~://pdbe.org/6obj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6obj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6obj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6obj ProSAT]</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=6obj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6obj OCA], [https://pdbe.org/6obj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6obj RCSB], [https://www.ebi.ac.uk/pdbsum/6obj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6obj ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~		== Function ==
	== ~~Publication Abstract from PubMed~~ ==		[https://www.uniprot.org/uniprot/Q9F6L0_STRGR Q9F6L0_STRGR]
	Filament formation by enzymes is increasingly recognized as an important phenomenon with potentially unique regulatory properties and biological roles. SgrAI is an allosterically regulated type II restriction endonuclease that forms filaments with enhanced DNA cleavage activity and altered sequence specificity. Here, we present the cryoelectron microscopy (cryo-EM) structure of the filament of SgrAI in its activated configuration. The structural data illuminate the mechanistic origin of hyperaccelerated DNA cleavage activity and suggests how indirect DNA sequence readout within filamentous SgrAI may enable recognition of substantially more nucleotide sequences than its low-activity form, thereby altering and partially relaxing its DNA sequence specificity. Together, substrate DNA binding, indirect readout, and filamentation simultaneously enhance SgrAI's catalytic activity and modulate substrate preference. This unusual enzyme mechanism may have evolved to perform the specialized functions of bacterial innate immunity in rapid defense against invading phage DNA without causing damage to the host DNA.

	~~Mechanism of Filamentation-Induced Allosteric Activation of the SgrAI Endonuclease.,Polley S, Lyumkis D, Horton NC Structure. 2019 Oct 1;27(10):1497-1507.e3. doi~~: ~~10.1016~~/~~j.str.2019.08.001. Epub, 2019 Aug 22. PMID:31447289<ref>PMID:31447289</ref>~~

	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 6obj" style="background-color:#fffaf0;"><~~/~~div>~~
	~~== References ==~~
	~~<references~~/>
	__TOC__		__TOC__
	</SX>		</SX>
	~~[[Category: Actinomyces griseus krainsky 1914]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Horton, N C~~]]		[[Category: Streptomyces griseus]]
	[[Category: ~~Lyumkis, D~~]]		[[Category: Horton NC]]
	[[Category: ~~Polley, S~~]]		[[Category: Lyumkis D]]
	[[Category: ~~Allostery]]~~		[[Category: Polley S]]
	~~[[Category: Bacterial innate immunity]]~~
	~~[[Category: Dnase]]~~
	~~[[Category: Filament]]~~
	~~[[Category: Hydrolase-dna complex]]~~
	~~[[Category: Hyper-activation]]~~
	~~[[Category: Restriction endonuclease]]~~
	~~[[Category: Substrate specificity~~]]

OCA at 09:51, 9 September 2020

2020-09-09T09:51:07Z

← Older revision		Revision as of 09:51, 9 September 2020
Line 3:		Line 3:
	<SX load='6obj' size='340' side='right' viewer='molstar' caption='[[6obj]], [[Resolution\|resolution]] 3.50Å' scene=''>		<SX load='6obj' size='340' side='right' viewer='molstar' caption='[[6obj]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6obj]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OBJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OBJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[6obj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_griseus"_krainsky_1914 "actinomyces griseus" krainsky 1914]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OBJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OBJ FirstGlance]. <br>
	</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></td></tr>		</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></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sgraIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1911 "Actinomyces griseus" Krainsky 1914])</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=6obj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6obj OCA], [http://pdbe.org/6obj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6obj RCSB], [http://www.ebi.ac.uk/pdbsum/6obj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6obj ProSAT]</span></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=6obj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6obj OCA], [http://pdbe.org/6obj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6obj RCSB], [http://www.ebi.ac.uk/pdbsum/6obj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6obj ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Filament formation by enzymes is increasingly recognized as an important phenomenon with potentially unique regulatory properties and biological roles. SgrAI is an allosterically regulated type II restriction endonuclease that forms filaments with enhanced DNA cleavage activity and altered sequence specificity. Here, we present the cryoelectron microscopy (cryo-EM) structure of the filament of SgrAI in its activated configuration. The structural data illuminate the mechanistic origin of hyperaccelerated DNA cleavage activity and suggests how indirect DNA sequence readout within filamentous SgrAI may enable recognition of substantially more nucleotide sequences than its low-activity form, thereby altering and partially relaxing its DNA sequence specificity. Together, substrate DNA binding, indirect readout, and filamentation simultaneously enhance SgrAI's catalytic activity and modulate substrate preference. This unusual enzyme mechanism may have evolved to perform the specialized functions of bacterial innate immunity in rapid defense against invading phage DNA without causing damage to the host DNA.

			Mechanism of Filamentation-Induced Allosteric Activation of the SgrAI Endonuclease.,Polley S, Lyumkis D, Horton NC Structure. 2019 Oct 1;27(10):1497-1507.e3. doi: 10.1016/j.str.2019.08.001. Epub, 2019 Aug 22. PMID:31447289<ref>PMID:31447289</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6obj" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</SX>		</SX>
			[[Category: Actinomyces griseus krainsky 1914]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Horton, N C]]		[[Category: Horton, N C]]

OCA at 03:51, 11 April 2020

2020-04-11T03:51:16Z

← Older revision		Revision as of 03:51, 11 April 2020
Line 3:		Line 3:
	<SX load='6obj' size='340' side='right' viewer='molstar' caption='[[6obj]], [[Resolution\|resolution]] 3.50Å' scene=''>		<SX load='6obj' size='340' side='right' viewer='molstar' caption='[[6obj]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6obj]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OBJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OBJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[6obj]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OBJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OBJ 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></td></tr>		</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></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=6obj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6obj OCA], [http://pdbe.org/6obj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6obj RCSB], [http://www.ebi.ac.uk/pdbsum/6obj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6obj ProSAT]</span></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=6obj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6obj OCA], [http://pdbe.org/6obj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6obj RCSB], [http://www.ebi.ac.uk/pdbsum/6obj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6obj ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 23:09, 6 March 2020

2020-03-06T23:09:28Z

← Older revision		Revision as of 23:09, 6 March 2020
Line 1:		Line 1:

	==Structure of a DNA-bound dimer extracted from filamentous SgrAI endonuclease in its activated form==		==Structure of a DNA-bound dimer extracted from filamentous SgrAI endonuclease in its activated form==
	<~~StructureSection~~ load='6obj' size='340' side='right'caption='[[6obj]], [[Resolution\|resolution]] 3.50Å' scene=''>		<SX load='6obj' size='340' side='right' viewer='molstar' caption='[[6obj]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6obj]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OBJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OBJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[6obj]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OBJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OBJ FirstGlance]. <br>
Line 8:		Line 8:
	</table>		</table>
	__TOC__		__TOC__
	</~~StructureSection~~>		</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Horton, N C]]		[[Category: Horton, N C]]

OCA at 09:17, 26 February 2020

2020-02-26T09:17:58Z

← Older revision		Revision as of 09:17, 26 February 2020
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 6obj is ~~ON HOLD until Paper Publication~~		==Structure of a DNA-bound dimer extracted from filamentous SgrAI endonuclease in its activated form==
			<StructureSection load='6obj' size='340' side='right'caption='[[6obj]], [[Resolution\|resolution]] 3.50Å' scene=''>
	~~Authors~~: ~~Polley~~, S., ~~Lyumkis~~, D., ~~Horton~~, N.C.		== Structural highlights ==
			<table><tr><td colspan='2'>[[6obj]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OBJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OBJ FirstGlance]. <br>
	~~Description: Structure of a DNA-bound dimer extracted from filamentous SgrAI endonuclease in its activated form~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		<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=6obj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6obj OCA], [http://pdbe.org/6obj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6obj RCSB], [http://www.ebi.ac.uk/pdbsum/6obj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6obj ProSAT]</span></td></tr>
	[[Category: Horton, N.C]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Horton, N C]]
	[[Category: Lyumkis, D]]		[[Category: Lyumkis, D]]
	[[Category: Polley, S]]		[[Category: Polley, S]]
			[[Category: Allostery]]
			[[Category: Bacterial innate immunity]]
			[[Category: Dnase]]
			[[Category: Filament]]
			[[Category: Hydrolase-dna complex]]
			[[Category: Hyper-activation]]
			[[Category: Restriction endonuclease]]
			[[Category: Substrate specificity]]

OCA at 04:38, 3 April 2019

2019-04-03T04:38:02Z

← Older revision		Revision as of 04:38, 3 April 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6obj is ON HOLD		The entry 6obj is ON HOLD until Paper Publication

	Authors: Polley, S., Lyumkis, D., Horton, N.C.		Authors: Polley, S., Lyumkis, D., Horton, N.C.
Line 7:		Line 7:
	Description: Structure of a DNA-bound dimer extracted from filamentous SgrAI endonuclease in its activated form		Description: Structure of a DNA-bound dimer extracted from filamentous SgrAI endonuclease in its activated form
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
			[[Category: Horton, N.C]]
	[[Category: Lyumkis, D]]		[[Category: Lyumkis, D]]
	~~[[Category: Horton, N.C]]~~
	[[Category: Polley, S]]		[[Category: Polley, S]]

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

2019-03-27T05:06:24Z

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

← Older revision	Revision as of 05:06, 27 March 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6obj is ON HOLD Authors: Polley, S., Lyumkis, D., Horton, N.C. Description: Structure of a DNA-bound dimer extracted from filamentous SgrAI endonuc...

2019-03-27T05:06:23Z

New page: '''Unreleased structure''' The entry 6obj is ON HOLD Authors: Polley, S., Lyumkis, D., Horton, N.C. Description: Structure of a DNA-bound dimer extracted from filamentous SgrAI endonuc...

New page

'''Unreleased structure'''

The entry 6obj is ON HOLD

Authors: Polley, S., Lyumkis, D., Horton, N.C.

Description: Structure of a DNA-bound dimer extracted from filamentous SgrAI endonuclease in its activated form
[[Category: Unreleased Structures]]
[[Category: Lyumkis, D]]
[[Category: Horton, N.C]]
[[Category: Polley, S]]