5e5p - Revision history

OCA at 14:08, 13 March 2024

2024-03-13T14:08:19Z

←Older revision		Revision as of 14:08, 13 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/F7WD42_SORMK F7WD42_SORMK]		[https://www.uniprot.org/uniprot/F7WD42_SORMK F7WD42_SORMK]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	LAGLIDADG homing endonucleases ("meganucleases") are highly specific DNA cleaving enzymes that are used for genome engineering. Like other enzymes that act on DNA targets, meganucleases often display binding affinities and cleavage activities that are dominated by one protein domain. To decipher the underlying mechanism of asymmetric DNA recognition and catalysis, we identified and characterized a new monomeric meganuclease (I-SmaMI), which belongs to a superfamily of homologous enzymes that recognize divergent DNA sequences. We solved a series of crystal structures of the enzyme-DNA complex representing a progression of sequential reaction states, and we compared the structural rearrangements and surface potential distributions within each protein domain against their relative contribution to binding affinity. We then determined the effects of equivalent point mutations in each of the two enzyme active sites to determine whether asymmetry in DNA recognition is translated into corresponding asymmetry in DNA cleavage activity. These experiments demonstrate the structural basis for "dominance" by one protein domain over the other and provide insights into this enzyme's conformational switch from a nonspecific search mode to a more specific recognition mode.
-
-	The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease.,Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser BK J Mol Biol. 2015 Dec 15. pii: S0022-2836(15)00696-8. doi:, 10.1016/j.jmb.2015.12.005. PMID:26705195<ref>PMID:26705195</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5e5p" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:13, 5 July 2023

2023-07-05T06:13:53Z

←Older revision		Revision as of 06:13, 5 July 2023
Line 3:		Line 3:
	<StructureSection load='5e5p' size='340' side='right'caption='[[5e5p]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='5e5p' size='340' side='right'caption='[[5e5p]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e5p]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sormk Sormk~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E5P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5E5P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e5p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sordaria_macrospora_k-hell Sordaria macrospora k-hell]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E5P 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=PG0:~~2~~-(2-METHOXYETHOXY)ETHANOL'>PG0</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]] 2.65Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5e5o\|5e5o]]~~, ~~[[5e5s\|5e5s]], [[5e63\|5e63]], [[5e67\|5e67]], [[4lox\|4lox]]</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">SMAC_12671 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=771870 SORMK])~~</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=5e5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e5p OCA], [https://pdbe.org/5e5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e5p RCSB], [https://www.ebi.ac.uk/pdbsum/5e5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e5p 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=5e5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e5p OCA], [~~http~~://pdbe.org/5e5p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5e5p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5e5p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5e5p ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F7WD42_SORMK F7WD42_SORMK]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sormk~~]]	+	[[Category: Sordaria macrospora k-hell]]
-	[[Category: Shen~~, B W]]~~	+	[[Category: Shen BW]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: I-smami]]~~	+
-	~~[[Category: Laglidadg~~]]	+

OCA at 11:30, 25 December 2019

2019-12-25T11:30:28Z

←Older revision		Revision as of 11:30, 25 December 2019
Line 1:		Line 1:

	==Wild type I-SmaMI in the space group of C121==		==Wild type I-SmaMI in the space group of C121==
-	<StructureSection load='5e5p' size='340' side='right' caption='[[5e5p]], [[Resolution\|resolution]] 2.65Å' scene=''>	+	<StructureSection load='5e5p' size='340' side='right'caption='[[5e5p]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e5p]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E5P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e5p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sormk Sormk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E5P 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=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</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=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5e5o\|5e5o]], [[5e5s\|5e5s]], [[5e63\|5e63]], [[5e67\|5e67]], [[4lox\|4lox]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5e5o\|5e5o]], [[5e5s\|5e5s]], [[5e63\|5e63]], [[5e67\|5e67]], [[4lox\|4lox]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SMAC_12671 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=771870 SORMK])</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=5e5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e5p OCA], [http://pdbe.org/5e5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e5p RCSB], [http://www.ebi.ac.uk/pdbsum/5e5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e5p 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=5e5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e5p OCA], [http://pdbe.org/5e5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e5p RCSB], [http://www.ebi.ac.uk/pdbsum/5e5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e5p ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Sormk]]
	[[Category: Shen, B W]]		[[Category: Shen, B W]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: I-smami]]		[[Category: I-smami]]
	[[Category: Laglidadg]]		[[Category: Laglidadg]]

OCA at 06:44, 6 October 2017

2017-10-06T06:44:14Z

←Older revision		Revision as of 06:44, 6 October 2017
Line 1:		Line 1:
		+
	==Wild type I-SmaMI in the space group of C121==		==Wild type I-SmaMI in the space group of C121==
	<StructureSection load='5e5p' size='340' side='right' caption='[[5e5p]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='5e5p' size='340' side='right' caption='[[5e5p]], [[Resolution\|resolution]] 2.65Å' scene=''>
Line 5:		Line 6:
	</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=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</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=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5e5o\|5e5o]], [[5e5s\|5e5s]], [[5e63\|5e63]], [[5e67\|5e67]], [[4lox\|4lox]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5e5o\|5e5o]], [[5e5s\|5e5s]], [[5e63\|5e63]], [[5e67\|5e67]], [[4lox\|4lox]]</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=5e5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e5p OCA], [http://pdbe.org/5e5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e5p RCSB], [http://www.ebi.ac.uk/pdbsum/5e5p PDBsum]</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=5e5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e5p OCA], [http://pdbe.org/5e5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e5p RCSB], [http://www.ebi.ac.uk/pdbsum/5e5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e5p ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:07, 13 January 2016

2016-01-13T20:07:10Z

←Older revision		Revision as of 20:07, 13 January 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Wild type I-SmaMI in the space group of C121==
		+	<StructureSection load='5e5p' size='340' side='right' caption='[[5e5p]], [[Resolution\|resolution]] 2.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5e5p]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E5P 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=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5e5o\|5e5o]], [[5e5s\|5e5s]], [[5e63\|5e63]], [[5e67\|5e67]], [[4lox\|4lox]]</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=5e5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e5p OCA], [http://pdbe.org/5e5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e5p RCSB], [http://www.ebi.ac.uk/pdbsum/5e5p PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	LAGLIDADG homing endonucleases ("meganucleases") are highly specific DNA cleaving enzymes that are used for genome engineering. Like other enzymes that act on DNA targets, meganucleases often display binding affinities and cleavage activities that are dominated by one protein domain. To decipher the underlying mechanism of asymmetric DNA recognition and catalysis, we identified and characterized a new monomeric meganuclease (I-SmaMI), which belongs to a superfamily of homologous enzymes that recognize divergent DNA sequences. We solved a series of crystal structures of the enzyme-DNA complex representing a progression of sequential reaction states, and we compared the structural rearrangements and surface potential distributions within each protein domain against their relative contribution to binding affinity. We then determined the effects of equivalent point mutations in each of the two enzyme active sites to determine whether asymmetry in DNA recognition is translated into corresponding asymmetry in DNA cleavage activity. These experiments demonstrate the structural basis for "dominance" by one protein domain over the other and provide insights into this enzyme's conformational switch from a nonspecific search mode to a more specific recognition mode.

-	The ~~entry 5e5p is ON HOLD until Paper Publication~~	+	The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease.,Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser BK J Mol Biol. 2015 Dec 15. pii: S0022-2836(15)00696-8. doi:, 10.1016/j.jmb.2015.12.005. PMID:26705195<ref>PMID:26705195</ref>

-	~~Authors~~: Shen, B.W.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Wild type I-SmaMI in the space group of C121~~	+	<div class="pdbe-citations 5e5p" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: ~~Shen, B.W~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Shen, B W]]
		+	[[Category: Hydrolase]]
		+	[[Category: I-smami]]
		+	[[Category: Laglidadg]]

OCA at 04:22, 22 October 2015

2015-10-22T04:22:56Z

←Older revision		Revision as of 04:22, 22 October 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5e5p is ON HOLD	+	The entry 5e5p is ON HOLD until Paper Publication

	Authors: Shen, B.W.		Authors: Shen, B.W.

-	Description: I-SmaMI ~~bound to uncleaved DNA target~~ in the ~~presence~~ of ~~Calcium ions~~	+	Description: Wild type I-SmaMI in the space group of C121
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Shen, B.W]]		[[Category: Shen, B.W]]

OCA: Protected "5e5p" [edit=sysop:move=sysop]

2015-10-16T03:02:37Z

Protected "5e5p" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:02, 16 October 2015

OCA: New page: '''Unreleased structure''' The entry 5e5p is ON HOLD Authors: Shen, B.W. Description: I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions [[Category: Unreleased Struc...

2015-10-16T03:02:34Z

New page: '''Unreleased structure''' The entry 5e5p is ON HOLD Authors: Shen, B.W. Description: I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions [[Category: Unreleased Struc...

New page

'''Unreleased structure'''

The entry 5e5p is ON HOLD

Authors: Shen, B.W.

Description: I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions
[[Category: Unreleased Structures]]
[[Category: Shen, B.W]]