5e63 - Revision history

OCA at 06:14, 5 July 2023

2023-07-05T06:14:17Z

←Older revision		Revision as of 06:14, 5 July 2023
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	<StructureSection load='5e63' size='340' side='right'caption='[[5e63]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5e63' size='340' side='right'caption='[[5e63]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e63]] is a 5 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=5E63 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5E63 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e63]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Sordaria_macrospora_k-hell Sordaria macrospora k-hell] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E63 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>, <scene name='pdbligand=MXE:2-METHOXYETHANOL'>MXE</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]] 2.6Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MXE:2-METHOXYETHANOL'>MXE</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</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=5e63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e63 OCA], [~~http~~://pdbe.org/5e63 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5e63 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5e63 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5e63 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=5e63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e63 OCA], [https://pdbe.org/5e63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e63 RCSB], [https://www.ebi.ac.uk/pdbsum/5e63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e63 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 ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sormk~~]]	+	[[Category: Sordaria macrospora k-hell]]
-	[[Category: ~~Shen, B~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Stoddard,~~ B]]	+	[[Category: Shen B]]
-	[[Category: ~~Hydrolase-dna complex]]~~	+	[[Category: Stoddard B]]
-	~~[[Category: I-smami]]~~	+
-	~~[[Category: K262a]]~~	+
-	~~[[Category: Laglidadg]]~~	+
-	~~[[Category: Mutant~~]]	+

OCA at 06:45, 22 April 2020

2020-04-22T06:45:29Z

←Older revision		Revision as of 06:45, 22 April 2020
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	==K262A mutant of I-SmaMI==		==K262A mutant of I-SmaMI==
-	<StructureSection load='5e63' size='340' side='right' caption='[[5e63]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5e63' size='340' side='right'caption='[[5e63]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e63]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E63 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5E63 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e63]] is a 5 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=5E63 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5E63 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>, <scene name='pdbligand=MXE:2-METHOXYETHANOL'>MXE</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" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MXE:2-METHOXYETHANOL'>MXE</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</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=5e63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e63 OCA], [http://pdbe.org/5e63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e63 RCSB], [http://www.ebi.ac.uk/pdbsum/5e63 PDBsum]</span></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://proteopedia.org/fgij/fg.htm?mol=5e63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e63 OCA], [http://pdbe.org/5e63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e63 RCSB], [http://www.ebi.ac.uk/pdbsum/5e63 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e63 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Sormk]]
	[[Category: Shen, B]]		[[Category: Shen, B]]
	[[Category: Stoddard, B]]		[[Category: Stoddard, B]]

OCA at 18:57, 10 May 2016

2016-05-10T18:57:24Z

←Older revision		Revision as of 18:57, 10 May 2016
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		+
	==K262A mutant of I-SmaMI==		==K262A mutant of I-SmaMI==
	<StructureSection load='5e63' size='340' side='right' caption='[[5e63]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5e63' size='340' side='right' caption='[[5e63]], [[Resolution\|resolution]] 2.60Å' scene=''>

OCA at 20:11, 13 January 2016

2016-01-13T20:11:57Z

←Older revision		Revision as of 20:11, 13 January 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==K262A mutant of I-SmaMI==
		+	<StructureSection load='5e63' size='340' side='right' caption='[[5e63]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5e63]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E63 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>, <scene name='pdbligand=MXE:2-METHOXYETHANOL'>MXE</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</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=5e63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e63 OCA], [http://pdbe.org/5e63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e63 RCSB], [http://www.ebi.ac.uk/pdbsum/5e63 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 5e63 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.~~, Stoddard, B~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: K262A mutant of I~~-~~SmaMI~~	+	<div class="pdbe-citations 5e63" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Shen, B]]
	[[Category: Stoddard, B]]		[[Category: Stoddard, B]]
-	[[Category: ~~Shen, B~~]]	+	[[Category: Hydrolase-dna complex]]
		+	[[Category: I-smami]]
		+	[[Category: K262a]]
		+	[[Category: Laglidadg]]
		+	[[Category: Mutant]]

OCA at 02:27, 1 December 2015

2015-12-01T02:27:12Z

←Older revision		Revision as of 02:27, 1 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5e63 is ON HOLD	+	The entry 5e63 is ON HOLD until Paper Publication

	Authors: Shen, B., Stoddard, B.		Authors: Shen, B., Stoddard, B.

OCA at 04:23, 22 October 2015

2015-10-22T04:23:33Z

←Older revision		Revision as of 04:23, 22 October 2015
Line 3:		Line 3:
	The entry 5e63 is ON HOLD		The entry 5e63 is ON HOLD

-	Authors: Shen, B., Stoddard, B	+	Authors: Shen, B., Stoddard, B.

	Description: K262A mutant of I-SmaMI		Description: K262A mutant of I-SmaMI

OCA: Protected "5e63" [edit=sysop:move=sysop]

2015-10-16T03:03:46Z

Protected "5e63" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:03, 16 October 2015

OCA: New page: '''Unreleased structure''' The entry 5e63 is ON HOLD Authors: Shen, B., Stoddard, B Description: K262A mutant of I-SmaMI Category: Unreleased Structures Category: Stoddard, B [...

2015-10-16T03:03:42Z

New page: '''Unreleased structure''' The entry 5e63 is ON HOLD Authors: Shen, B., Stoddard, B Description: K262A mutant of I-SmaMI Category: Unreleased Structures Category: Stoddard, B [...

New page

'''Unreleased structure'''

The entry 5e63 is ON HOLD

Authors: Shen, B., Stoddard, B

Description: K262A mutant of I-SmaMI
[[Category: Unreleased Structures]]
[[Category: Stoddard, B]]
[[Category: Shen, B]]