6bcn - Revision history

OCA at 14:21, 13 March 2024

2024-03-13T14:21:36Z

←Older revision		Revision as of 14:21, 13 March 2024
Line 1:		Line 1:

	==I-LtrI E184D bound to cognate substrate (pre-cleavage complex)==		==I-LtrI E184D bound to cognate substrate (pre-cleavage complex)==
-	<StructureSection load='6bcn' size='340' side='right' caption='[[6bcn]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='6bcn' size='340' side='right'caption='[[6bcn]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bcn]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_58100 Atcc 58100~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BCN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BCN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bcn]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Leptographium_truncatum Leptographium truncatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BCN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BCN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CA:CALCIUM+ION'>CA</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]] 2.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~HEG fusion, rps3 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=330483 ATCC 58100])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=6bcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bcn OCA], [~~http~~://pdbe.org/6bcn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bcn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bcn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bcn 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=6bcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bcn OCA], [https://pdbe.org/6bcn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bcn RCSB], [https://www.ebi.ac.uk/pdbsum/6bcn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bcn ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/C7SWF3_9PEZI C7SWF3_9PEZI]
-	LAGLIDADG homing endonucleases (meganucleases) are site-specific mobile endonucleases that can be adapted for genome-editing applications. However, one problem when reprogramming meganucleases on non-native substrates is indirect readout of DNA shape and flexibility at the central 4 bases where cleavage occurs. To understand how the meganuclease active site regulates DNA cleavage, we used functional selections and deep sequencing to profile the fitness landscape of 1600 I-LtrI and I-OnuI active site variants individually challenged with 67 substrates with central 4 base substitutions. The wild-type active site was not optimal for cleavage on many substrates, including the native I-LtrI and I-OnuI targets. Novel combinations of active site residues not observed in known meganucleases supported activity on substrates poorly cleaved by the wild-type enzymes. Strikingly, combinations of E or D substitutions in the two metal-binding residues greatly influenced cleavage activity, and E184D variants had a broadened cleavage profile. Analyses of I-LtrI E184D and the wild-type proteins co-crystallized with the non-cognate AACC central 4 sequence revealed structural differences that correlated with kinetic constants for cleavage of individual DNA strands. Optimizing meganuclease active sites to enhance cleavage of non-native central 4 target sites is a straightforward addition to engineering workflows that will expand genome-editing applications.	+
-		+
-	Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases.,McMurrough TA, Brown CM, Zhang K, Hausner G, Junop MS, Gloor GB, Edgell DR Nucleic Acids Res. 2018 Oct 24. pii: ~~5144155. doi: 10.1093~~/~~nar~~/~~gky976~~. ~~PMID:30357419<ref>PMID:30357419</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.~~S. National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6bcn" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 58100~~]]	+	[[Category: Large Structures]]
-	[[Category: Brown, C]]	+	[[Category: Leptographium truncatum]]
-	[[Category: Edgell~~, D R~~]]	+	[[Category: Brown C]]
-	[[Category: Gloor~~, G B~~]]	+	[[Category: Edgell DR]]
-	[[Category: Junop, M]]	+	[[Category: Gloor GB]]
-	[[Category: McMurrough~~, T A~~]]	+	[[Category: Junop M]]
-	[[Category: Zhang, K]]	+	[[Category: McMurrough TA]]
-	~~[[Category: Hydrolase]]~~	+	[[Category: Zhang K]]
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Nucleic acid~~]]	+

OCA at 12:39, 7 November 2018

2018-11-07T12:39:19Z

←Older revision		Revision as of 12:39, 7 November 2018
Line 8:		Line 8:
	<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=6bcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bcn OCA], [http://pdbe.org/6bcn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bcn RCSB], [http://www.ebi.ac.uk/pdbsum/6bcn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bcn 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=6bcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bcn OCA], [http://pdbe.org/6bcn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bcn RCSB], [http://www.ebi.ac.uk/pdbsum/6bcn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bcn ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	LAGLIDADG homing endonucleases (meganucleases) are site-specific mobile endonucleases that can be adapted for genome-editing applications. However, one problem when reprogramming meganucleases on non-native substrates is indirect readout of DNA shape and flexibility at the central 4 bases where cleavage occurs. To understand how the meganuclease active site regulates DNA cleavage, we used functional selections and deep sequencing to profile the fitness landscape of 1600 I-LtrI and I-OnuI active site variants individually challenged with 67 substrates with central 4 base substitutions. The wild-type active site was not optimal for cleavage on many substrates, including the native I-LtrI and I-OnuI targets. Novel combinations of active site residues not observed in known meganucleases supported activity on substrates poorly cleaved by the wild-type enzymes. Strikingly, combinations of E or D substitutions in the two metal-binding residues greatly influenced cleavage activity, and E184D variants had a broadened cleavage profile. Analyses of I-LtrI E184D and the wild-type proteins co-crystallized with the non-cognate AACC central 4 sequence revealed structural differences that correlated with kinetic constants for cleavage of individual DNA strands. Optimizing meganuclease active sites to enhance cleavage of non-native central 4 target sites is a straightforward addition to engineering workflows that will expand genome-editing applications.
		+
		+	Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases.,McMurrough TA, Brown CM, Zhang K, Hausner G, Junop MS, Gloor GB, Edgell DR Nucleic Acids Res. 2018 Oct 24. pii: 5144155. doi: 10.1093/nar/gky976. PMID:30357419<ref>PMID:30357419</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6bcn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:11, 31 October 2018

2018-10-31T07:11:01Z

←Older revision		Revision as of 07:11, 31 October 2018
Line 3:		Line 3:
	<StructureSection load='6bcn' size='340' side='right' caption='[[6bcn]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6bcn' size='340' side='right' caption='[[6bcn]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bcn]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BCN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BCN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bcn]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_58100 Atcc 58100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BCN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BCN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HEG fusion, rps3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=330483 ATCC 58100])</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=6bcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bcn OCA], [http://pdbe.org/6bcn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bcn RCSB], [http://www.ebi.ac.uk/pdbsum/6bcn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bcn 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=6bcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bcn OCA], [http://pdbe.org/6bcn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bcn RCSB], [http://www.ebi.ac.uk/pdbsum/6bcn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bcn ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 58100]]
	[[Category: Brown, C]]		[[Category: Brown, C]]
	[[Category: Edgell, D R]]		[[Category: Edgell, D R]]

OCA at 05:50, 24 October 2018

2018-10-24T05:50:36Z

←Older revision		Revision as of 05:50, 24 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6bcn is ~~ON HOLD until Paper Publication~~	+	==I-LtrI E184D bound to cognate substrate (pre-cleavage complex)==
-		+	<StructureSection load='6bcn' size='340' side='right' caption='[[6bcn]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~Authors~~: ~~Brown, C~~.~~, Zhang, K~~., ~~McMurrough, T~~.A., ~~Gloor~~, G.B., ~~Edgell, D~~.R., ~~Junop, M~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6bcn]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BCN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BCN FirstGlance]. <br>
-	~~Description~~: ~~I-LtrI E184D bound to cognate substrate (pre-cleavage complex)~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=6bcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bcn OCA], [http://pdbe.org/6bcn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bcn RCSB], [http://www.ebi.ac.uk/pdbsum/6bcn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bcn ProSAT]</span></td></tr>
-	[[Category: Gloor, G.B]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Brown, C]]
		+	[[Category: Edgell, D R]]
		+	[[Category: Gloor, G B]]
	[[Category: Junop, M]]		[[Category: Junop, M]]
-	[[Category: ~~Mcmurrough~~, T.A]]	+	[[Category: McMurrough, T A]]
	[[Category: Zhang, K]]		[[Category: Zhang, K]]
-	[[Category: ~~Edgell, D.R~~]]	+	[[Category: Hydrolase]]
-	[[Category: ~~Brown, C~~]]	+	[[Category: Hydrolase-dna complex]]
		+	[[Category: Nucleic acid]]

OCA at 05:55, 23 May 2018

2018-05-23T05:55:23Z

←Older revision		Revision as of 05:55, 23 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Brown, C., Zhang, K., McMurrough, T.A., Gloor, G.B., Edgell, D.R., Junop, M.		Authors: Brown, C., Zhang, K., McMurrough, T.A., Gloor, G.B., Edgell, D.R., Junop, M.
Line 9:		Line 9:
	[[Category: Gloor, G.B]]		[[Category: Gloor, G.B]]
	[[Category: Junop, M]]		[[Category: Junop, M]]
-	[[Category: Brown, C]]
	[[Category: Mcmurrough, T.A]]		[[Category: Mcmurrough, T.A]]
	[[Category: Zhang, K]]		[[Category: Zhang, K]]
	[[Category: Edgell, D.R]]		[[Category: Edgell, D.R]]
		+	[[Category: Brown, C]]

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

2017-11-01T04:55:17Z

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

←Older revision

Revision as of 04:55, 1 November 2017

OCA: New page: '''Unreleased structure''' The entry 6bcn is ON HOLD Authors: Brown, C., Zhang, K., McMurrough, T.A., Gloor, G.B., Edgell, D.R., Junop, M. Description: I-LtrI E184D bound to cognate su...

2017-11-01T04:55:16Z

New page: '''Unreleased structure''' The entry 6bcn is ON HOLD Authors: Brown, C., Zhang, K., McMurrough, T.A., Gloor, G.B., Edgell, D.R., Junop, M. Description: I-LtrI E184D bound to cognate su...

New page

'''Unreleased structure'''

The entry 6bcn is ON HOLD

Authors: Brown, C., Zhang, K., McMurrough, T.A., Gloor, G.B., Edgell, D.R., Junop, M.

Description: I-LtrI E184D bound to cognate substrate (pre-cleavage complex)
[[Category: Unreleased Structures]]
[[Category: Gloor, G.B]]
[[Category: Junop, M]]
[[Category: Brown, C]]
[[Category: Mcmurrough, T.A]]
[[Category: Zhang, K]]
[[Category: Edgell, D.R]]