2dch - Revision history

OCA at 13:47, 13 March 2024

2024-03-13T13:47:13Z

← Older revision		Revision as of 13:47, 13 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dch]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DCH FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dch]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DCH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.06Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2dch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dch OCA], [https://pdbe.org/2dch PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dch RCSB], [https://www.ebi.ac.uk/pdbsum/2dch PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dch 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=2dch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dch OCA], [https://pdbe.org/2dch PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dch RCSB], [https://www.ebi.ac.uk/pdbsum/2dch PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dch ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q8J309_9CREN Q8J309_9CREN]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dch ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dch ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	A novel LAGLIDADG-type homing endonuclease (HEase), I-Tsp061I, from the hyperthermophilic archaeon Thermoproteus sp. IC-061 16 S rRNA gene (rDNA) intron was characterized with respect to its structure, catalytic properties and thermostability. It was found that I-Tsp061I is a HEase isoschizomer of the previously described I-PogI and exhibits the highest thermostability among the known LAGLIDADG-type HEases. Determination of the crystal structure of I-Tsp061I at 2.1 A resolution using the multiple isomorphous replacement and anomalous scattering method revealed that the overall fold is similar to that of other known LAGLIDADG-type HEases, despite little sequence similarity between I-Tsp061I and those HEases. However, I-Tsp061I contains important cross-domain polar networks, unlike its mesophilic counterparts. Notably, the polar network Tyr6-Asp104-His180-107O-HOH12-104O-Asn177 exists across the two packed alpha-helices containing both the LAGLIDADG catalytic motif and the GxxxG hydrophobic helix bundle motif. Another important structural feature is the salt-bridge network Asp29-Arg31-Glu182 across N and C-terminal domain interface, which appears to contribute to the stability of the domain/domain packing. On the basis of these structural analyses and extensive mutational studies, we conclude that such cross-domain polar networks play key roles in stabilizing the catalytic center and domain packing, and underlie the hyperthermostability of I-Tsp061I.

	Structure of a hyperthermophilic archaeal homing endonuclease, I-Tsp061I: contribution of cross-domain polar networks to thermostability.,Nakayama H, Shimamura T, Imagawa T, Shirai N, Itoh T, Sako Y, Miyano M, Sakuraba H, Ohshima T, Nomura N, Tsuge H J Mol Biol. 2007 Jan 12;365(2):362-78. Epub 2006 Sep 29. PMID:17069851<ref>PMID:17069851</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2dch" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]		*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Thermoproteus]]		[[Category: Thermoproteus]]
	[[Category: Miyano, M]]		[[Category: Miyano M]]
	[[Category: Nakayama, H]]		[[Category: Nakayama H]]
	[[Category: Nomura, N]]		[[Category: Nomura N]]
	[[Category: Sako, Y]]		[[Category: Sako Y]]
	[[Category: Shimamura, T]]		[[Category: Shimamura T]]
	[[Category: Tsuge, H]]		[[Category: Tsuge H]]
	~~[[Category: Alpha/beta fold]]~~
	~~[[Category: Hydrolase~~]]

OCA at 10:29, 8 December 2021

2021-12-08T10:29:40Z

← Older revision		Revision as of 10:29, 8 December 2021
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	<StructureSection load='2dch' size='340' side='right'caption='[[2dch]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2dch' size='340' side='right'caption='[[2dch]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dch]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DCH FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dch]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DCH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2dch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dch OCA], [~~http~~://pdbe.org/2dch PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dch RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dch PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dch 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=2dch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dch OCA], [https://pdbe.org/2dch PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dch RCSB], [https://www.ebi.ac.uk/pdbsum/2dch PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dch ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:54, 4 March 2020

2020-03-04T07:54:33Z

← Older revision		Revision as of 07:54, 4 March 2020
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	==Crystal structure of archaeal intron-encoded homing endonuclease I-Tsp061I==		==Crystal structure of archaeal intron-encoded homing endonuclease I-Tsp061I==
	<StructureSection load='2dch' size='340' side='right' caption='[[2dch]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2dch' size='340' side='right'caption='[[2dch]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dch]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DCH FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dch]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DCH FirstGlance]. <br>
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	==See Also==		==See Also==
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Thermoproteus]]		[[Category: Thermoproteus]]
	[[Category: Miyano, M]]		[[Category: Miyano, M]]

OCA at 06:46, 30 May 2018

2018-05-30T06:46:50Z

← Older revision		Revision as of 06:46, 30 May 2018
Line 1:		Line 1:

	==Crystal structure of archaeal intron-encoded homing endonuclease I-Tsp061I==		==Crystal structure of archaeal intron-encoded homing endonuclease I-Tsp061I==
	<StructureSection load='2dch' size='340' side='right' caption='[[2dch]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2dch' size='340' side='right' caption='[[2dch]], [[Resolution\|resolution]] 2.06Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2dch]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DCH FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dch]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DCH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2dch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dch OCA], [http://pdbe.org/2dch PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dch RCSB], [http://www.ebi.ac.uk/pdbsum/2dch 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=2dch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dch OCA], [http://pdbe.org/2dch PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dch RCSB], [http://www.ebi.ac.uk/pdbsum/2dch PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dch ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dc/2dch_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dc/2dch_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 13:56, 9 February 2016

2016-02-09T13:56:53Z

← Older revision		Revision as of 13:56, 9 February 2016
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dch ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:53, 10 September 2015

2015-09-10T22:53:57Z

← Older revision		Revision as of 22:53, 10 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[2dch]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DCH FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dch]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DCH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2dch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dch OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dch RCSB], [http://www.ebi.ac.uk/pdbsum/2dch 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=2dch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dch OCA], [http://pdbe.org/2dch PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dch RCSB], [http://www.ebi.ac.uk/pdbsum/2dch PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2dch" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 17:04, 15 January 2015

2015-01-15T17:04:43Z

← Older revision		Revision as of 17:04, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dch]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DCH FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dch]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DCH FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dch OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dch RCSB], [http://www.ebi.ac.uk/pdbsum/2dch 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=2dch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dch OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dch RCSB], [http://www.ebi.ac.uk/pdbsum/2dch PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Thermoproteus]]		[[Category: Thermoproteus]]
	[[Category: Miyano, M.]]		[[Category: Miyano, M]]
	[[Category: Nakayama, H.]]		[[Category: Nakayama, H]]
	[[Category: Nomura, N.]]		[[Category: Nomura, N]]
	[[Category: Sako, Y.]]		[[Category: Sako, Y]]
	[[Category: Shimamura, T.]]		[[Category: Shimamura, T]]
	[[Category: Tsuge, H.]]		[[Category: Tsuge, H]]
	[[Category: Alpha/beta fold]]		[[Category: Alpha/beta fold]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 02:36, 29 September 2014

2014-09-29T02:36:26Z

← Older revision		Revision as of 02:36, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2dch~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of archaeal intron-encoded homing endonuclease I-Tsp061I==
			<StructureSection load='2dch' size='340' side='right' caption='[[2dch]], [[Resolution\|resolution]] 2.06Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dch]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DCH FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dch OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dch RCSB], [http://www.ebi.ac.uk/pdbsum/2dch PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dc/2dch_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			A novel LAGLIDADG-type homing endonuclease (HEase), I-Tsp061I, from the hyperthermophilic archaeon Thermoproteus sp. IC-061 16 S rRNA gene (rDNA) intron was characterized with respect to its structure, catalytic properties and thermostability. It was found that I-Tsp061I is a HEase isoschizomer of the previously described I-PogI and exhibits the highest thermostability among the known LAGLIDADG-type HEases. Determination of the crystal structure of I-Tsp061I at 2.1 A resolution using the multiple isomorphous replacement and anomalous scattering method revealed that the overall fold is similar to that of other known LAGLIDADG-type HEases, despite little sequence similarity between I-Tsp061I and those HEases. However, I-Tsp061I contains important cross-domain polar networks, unlike its mesophilic counterparts. Notably, the polar network Tyr6-Asp104-His180-107O-HOH12-104O-Asn177 exists across the two packed alpha-helices containing both the LAGLIDADG catalytic motif and the GxxxG hydrophobic helix bundle motif. Another important structural feature is the salt-bridge network Asp29-Arg31-Glu182 across N and C-terminal domain interface, which appears to contribute to the stability of the domain/domain packing. On the basis of these structural analyses and extensive mutational studies, we conclude that such cross-domain polar networks play key roles in stabilizing the catalytic center and domain packing, and underlie the hyperthermostability of I-Tsp061I.

	~~{{STRUCTURE_2dch\| PDB=2dch \| SCENE= }}~~		Structure of a hyperthermophilic archaeal homing endonuclease, I-Tsp061I: contribution of cross-domain polar networks to thermostability.,Nakayama H, Shimamura T, Imagawa T, Shirai N, Itoh T, Sako Y, Miyano M, Sakuraba H, Ohshima T, Nomura N, Tsuge H J Mol Biol. 2007 Jan 12;365(2):362-78. Epub 2006 Sep 29. PMID:17069851<ref>PMID:17069851</ref>

	~~===Crystal structure~~ of ~~archaeal intron-encoded homing endonuclease I-Tsp061I===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17069851}}~~

	~~==About this Structure==~~
	~~[[2dch]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermoproteus Thermoproteus]~~. ~~Full crystallographic information is available from [http://oca.weizmann.ac.il~~/~~oca-bin/ocashort?id=2DCH OCA].~~

	==See Also==		==See Also==
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:017069851<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Thermoproteus]]		[[Category: Thermoproteus]]
	[[Category: Miyano, M.]]		[[Category: Miyano, M.]]

OCA at 14:03, 20 October 2012

2012-10-20T14:03:50Z

← Older revision		Revision as of 14:03, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2dch]] is a 1 chain structure ~~of [[Endonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA].		[[2dch]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA].

	==See Also==		==See Also==

OCA at 13:56, 26 July 2012

2012-07-26T13:56:00Z

← Older revision		Revision as of 13:56, 26 July 2012
Line 1:		Line 1:
	[[Image:2dch.png\|left\|200px]]		[[Image:2dch.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2dch", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2dch\| PDB=2dch \| SCENE= }}		{{STRUCTURE_2dch\| PDB=2dch \| SCENE= }}

	===Crystal structure of archaeal intron-encoded homing endonuclease I-Tsp061I===		===Crystal structure of archaeal intron-encoded homing endonuclease I-Tsp061I===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17069851}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17069851 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17069851}}		{{ABSTRACT_PUBMED_17069851}}

	==About this Structure==		==About this Structure==
	[[2dch]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA].		[[2dch]] is a 1 chain structure of [[Endonuclease]] with sequence from [http://en.wikipedia.org/wiki/Thermoproteus Thermoproteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCH OCA].

			==See Also==
			*[[Endonuclease\|Endonuclease]]

	==Reference==		==Reference==