2o6m - Revision history

OCA at 13:09, 26 July 2023

2023-07-26T13:09:50Z

←Older revision		Revision as of 13:09, 26 July 2023
Line 3:		Line 3:
	<StructureSection load='2o6m' size='340' side='right'caption='[[2o6m]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2o6m' size='340' side='right'caption='[[2o6m]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2o6m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Phypo Phypo~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O6M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2o6m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Physarum_polycephalum Physarum polycephalum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O6M 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=ZN:ZINC+ION'>ZN</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]] 2.3Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~I-PpoI ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=5791 PHYPO])~~</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=ZN:ZINC+ION'>ZN</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=2o6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6m OCA], [https://pdbe.org/2o6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o6m RCSB], [https://www.ebi.ac.uk/pdbsum/2o6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o6m 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=2o6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6m OCA], [https://pdbe.org/2o6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o6m RCSB], [https://www.ebi.ac.uk/pdbsum/2o6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o6m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PPO1_PHYPO PPO1_PHYPO]] Mediates the homing of a group I intron in the ribosomal DNA. Makes a four-base staggered cut in its ribosomal DNA target sequence.	+	[https://www.uniprot.org/uniprot/PPO1_PHYPO PPO1_PHYPO] Mediates the homing of a group I intron in the ribosomal DNA. Makes a four-base staggered cut in its ribosomal DNA target sequence.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Phypo~~]]	+	[[Category: Physarum polycephalum]]
-	[[Category: Eastberg~~, J H~~]]	+	[[Category: Eastberg JH]]
-	[[Category: Stoddard~~, B L]]~~	+	[[Category: Stoddard BL]]
-	~~[[Category: Hnh]]~~	+
-	~~[[Category: Homing endonuclease]]~~	+
-	~~[[Category: Homodimer]]~~	+
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Protein-dna complex~~]]	+

OCA at 16:01, 8 June 2021

2021-06-08T16:01:35Z

←Older revision		Revision as of 16:01, 8 June 2021
Line 1:		Line 1:

	==H98Q mutant of the homing endonuclease I-PPOI complexed with DNA==		==H98Q mutant of the homing endonuclease I-PPOI complexed with DNA==
-	<StructureSection load='2o6m' size='340' side='right' caption='[[2o6m]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='2o6m' size='340' side='right'caption='[[2o6m]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2o6m]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Phypo Phypo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2O6M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2o6m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Phypo Phypo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O6M 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=ZN:ZINC+ION'>ZN</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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">I-PpoI ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5791 PHYPO])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">I-PpoI ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5791 PHYPO])</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=2o6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6m OCA], [~~http~~://pdbe.org/2o6m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2o6m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2o6m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2o6m 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=2o6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6m OCA], [https://pdbe.org/2o6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o6m RCSB], [https://www.ebi.ac.uk/pdbsum/2o6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o6m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PPO1_PHYPO PPO1_PHYPO]] Mediates the homing of a group I intron in the ribosomal DNA. Makes a four-base staggered cut in its ribosomal DNA target sequence.	+	[[https://www.uniprot.org/uniprot/PPO1_PHYPO PPO1_PHYPO]] Mediates the homing of a group I intron in the ribosomal DNA. Makes a four-base staggered cut in its ribosomal DNA target sequence.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Endonuclease\|Endonuclease]]	+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Phypo]]		[[Category: Phypo]]
	[[Category: Eastberg, J H]]		[[Category: Eastberg, J H]]

OCA at 07:35, 22 August 2018

2018-08-22T07:35:14Z

←Older revision		Revision as of 07:35, 22 August 2018
Line 1:		Line 1:
		+
	==H98Q mutant of the homing endonuclease I-PPOI complexed with DNA==		==H98Q mutant of the homing endonuclease I-PPOI complexed with DNA==
	<StructureSection load='2o6m' size='340' side='right' caption='[[2o6m]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2o6m' size='340' side='right' caption='[[2o6m]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 5:		Line 6:
	</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=ZN:ZINC+ION'>ZN</scene></td></tr>		</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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">I-PpoI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5791 PHYPO])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">I-PpoI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5791 PHYPO])</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=2o6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6m OCA], [http://pdbe.org/2o6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o6m RCSB], [http://www.ebi.ac.uk/pdbsum/2o6m 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=2o6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6m OCA], [http://pdbe.org/2o6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o6m RCSB], [http://www.ebi.ac.uk/pdbsum/2o6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2o6m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 12:18, 10 September 2015

2015-09-10T12:18:07Z

←Older revision		Revision as of 12:18, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2o6m' size='340' side='right' caption='[[2o6m]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2o6m' size='340' side='right' caption='[[2o6m]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2o6m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Physarum_polycephalum Physarum polycephalum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O6M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2o6m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Phypo Phypo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O6M 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=ZN:ZINC+ION'>ZN</scene></td></tr>		</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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">I-PpoI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5791 ~~Physarum polycephalum~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">I-PpoI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5791 PHYPO])</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=2o6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o6m RCSB], [http://www.ebi.ac.uk/pdbsum/2o6m 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=2o6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6m OCA], [http://pdbe.org/2o6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o6m RCSB], [http://www.ebi.ac.uk/pdbsum/2o6m PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	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 2o6m" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Physarum polycephalum~~]]	+	[[Category: Phypo]]
	[[Category: Eastberg, J H]]		[[Category: Eastberg, J H]]
	[[Category: Stoddard, B L]]		[[Category: Stoddard, B L]]

OCA at 23:53, 24 December 2014

2014-12-24T23:53:22Z

←Older revision		Revision as of 23:53, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2o6m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Physarum_polycephalum Physarum polycephalum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O6M FirstGlance]. <br>		<table><tr><td colspan='2'>[[2o6m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Physarum_polycephalum Physarum polycephalum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O6M FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">I-PpoI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5791 Physarum polycephalum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">I-PpoI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5791 Physarum polycephalum])</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=2o6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o6m RCSB], [http://www.ebi.ac.uk/pdbsum/2o6m 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=2o6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o6m RCSB], [http://www.ebi.ac.uk/pdbsum/2o6m PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PPO1_PHYPO PPO1_PHYPO]] Mediates the homing of a group I intron in the ribosomal DNA. Makes a four-base staggered cut in its ribosomal DNA target sequence.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Physarum polycephalum]]		[[Category: Physarum polycephalum]]
-	[[Category: Eastberg, J H.]]	+	[[Category: Eastberg, J H]]
-	[[Category: Stoddard, B L.]]	+	[[Category: Stoddard, B L]]
	[[Category: Hnh]]		[[Category: Hnh]]
	[[Category: Homing endonuclease]]		[[Category: Homing endonuclease]]

OCA at 03:49, 29 September 2014

2014-09-29T03:49:09Z

←Older revision		Revision as of 03:49, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2o6m.~~png~~\|~~left~~\|~~200px~~]]	+	==H98Q mutant of the homing endonuclease I-PPOI complexed with DNA==
		+	<StructureSection load='2o6m' size='340' side='right' caption='[[2o6m]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2o6m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Physarum_polycephalum Physarum polycephalum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O6M FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">I-PpoI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5791 Physarum polycephalum])</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=2o6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o6m RCSB], [http://www.ebi.ac.uk/pdbsum/2o6m PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Several unique protein folds that catalyze the hydrolysis of phosphodiester bonds have arisen independently in nature, including the PD(D/E)XK superfamily (typified by type II restriction endonucleases and many recombination and repair enzymes) and the HNH superfamily (found in an equally wide array of enzymes, including bacterial colicins and homing endonucleases). Whereas the identity and position of catalytic residues within the PD(D/E)XK superfamily are highly variable, the active sites of HNH nucleases are much more strongly conserved. In this study, the ability of an HNH nuclease to tolerate a mutation of its most conserved catalytic residue (its histidine general base), and the mechanism of the most active enzyme variant, were characterized. Conversion of this residue into several altered chemistries, glutamine, lysine, or glutamate, resulted in measurable activity. The histidine to glutamine mutant displays the highest residual activity and a pH profile similar to that of the wild-type enzyme. This activity is dependent on the presence of a neighboring imidazole ring, which has taken over as a less efficient general base for the reaction. This result implies that mutational pathways to alternative HNH-derived catalytic sites do exist but are not as extensively or successfully diverged or reoptimized in nature as variants of the PD(D/E)XK nuclease superfamily. This is possibly due to multiple steric constraints placed on the compact HNH motif, which is simultaneously involved in protein folding, DNA binding, and catalysis, as well as the use of a planar, aromatic imidazole group as a general base.

-	~~{{STRUCTURE_2o6m\| PDB=2o6m \| SCENE= }}~~	+	Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism.,Eastberg JH, Eklund J, Monnat R Jr, Stoddard BL Biochemistry. 2007 Jun 19;46(24):7215-25. Epub 2007 May 22. PMID:17516660<ref>PMID:17516660</ref>

-	~~===H98Q mutant~~ of the ~~homing endonuclease I-PPOI complexed with DNA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17516660}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2o6m]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Physarum_polycephalum Physarum polycephalum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2O6M OCA].~~	+

	==See Also==		==See Also==
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017516660<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Physarum polycephalum]]		[[Category: Physarum polycephalum]]
	[[Category: Eastberg, J H.]]		[[Category: Eastberg, J H.]]

OCA at 10:24, 20 October 2012

2012-10-20T10:24:15Z

←Older revision		Revision as of 10:24, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2o6m]] is a 4 chain structure ~~of [[Endonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Physarum_polycephalum Physarum polycephalum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6M OCA].	+	[[2o6m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Physarum_polycephalum Physarum polycephalum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6M OCA].

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

OCA: Protected "2o6m" [edit=sysop:move=sysop]

2012-07-26T01:59:29Z

Protected "2o6m" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:59, 26 July 2012

OCA at 01:59, 26 July 2012

2012-07-26T01:59:27Z

←Older revision		Revision as of 01:59, 26 July 2012
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-	{{Seed}}
	[[Image:2o6m.png\|left\|200px]]		[[Image:2o6m.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2o6m", 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.
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	{{STRUCTURE_2o6m\| PDB=2o6m \| SCENE= }}		{{STRUCTURE_2o6m\| PDB=2o6m \| SCENE= }}

	===H98Q mutant of the homing endonuclease I-PPOI complexed with DNA===		===H98Q mutant of the homing endonuclease I-PPOI complexed with DNA===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17516660}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17516660 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17516660}}		{{ABSTRACT_PUBMED_17516660}}

	==About this Structure==		==About this Structure==
-	~~2O6M is a~~ [[~~Protein complex~~]] structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Physarum_polycephalum Physarum polycephalum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6M OCA].	+	[[2o6m]] is a 4 chain structure of [[Endonuclease]] with sequence from [http://en.wikipedia.org/wiki/Physarum_polycephalum Physarum polycephalum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6M OCA].
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]

	==Reference==		==Reference==
-	Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism., Eastberg JH, Eklund J, Monnat R Jr, Stoddard BL, Biochemistry. 2007 Jun 19;46(24):7215-25. Epub 2007 May 22. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~17516660 17516660]~~	+	<ref group="xtra">PMID:017516660</ref><references group="xtra"/>
	[[Category: Physarum polycephalum]]		[[Category: Physarum polycephalum]]
-	[[Category: Protein complex]]
	[[Category: Eastberg, J H.]]		[[Category: Eastberg, J H.]]
	[[Category: Stoddard, B L.]]		[[Category: Stoddard, B L.]]
Line 31:		Line 21:
	[[Category: Homing endonuclease]]		[[Category: Homing endonuclease]]
	[[Category: Homodimer]]		[[Category: Homodimer]]
-	[[Category: Hydrolase/dna complex]]	+	[[Category: Hydrolase-dna complex]]
-	[[Category: Protein/dna complex]]	+	[[Category: Protein-dna complex]]
-		+
-	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 03:46:22 2008''~~	+

OCA at 00:46, 28 July 2008

2008-07-28T00:46:25Z

←Older revision		Revision as of 00:46, 28 July 2008
Line 1:		Line 1:
-	[[Image:2o6m.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2o6m.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2o6m\| PDB=2o6m \| SCENE= }}		{{STRUCTURE_2o6m\| PDB=2o6m \| SCENE= }}

-	~~'''~~H98Q mutant of the homing endonuclease I-PPOI complexed with DNA~~'''~~	+	===H98Q mutant of the homing endonuclease I-PPOI complexed with DNA===


-	~~==Overview==~~	+	<!--
-	~~Several unique protein folds that catalyze the hydrolysis of phosphodiester bonds have arisen independently in nature~~, ~~including the PD(D/E)XK superfamily (typified by type II restriction endonucleases and many recombination and repair enzymes) and the HNH superfamily (found in an equally wide array of enzymes~~, ~~including bacterial colicins and homing endonucleases). Whereas~~ the ~~identity and position of catalytic residues within~~ the PD(D/~~E)XK superfamily are highly variable, the active sites of HNH nucleases are much more strongly conserved~~. ~~In this study, the ability of an HNH nuclease to tolerate a mutation of its most conserved catalytic residue (its histidine general base~~), and the mechanism of the most active enzyme variant, were characterized. Conversion of this residue into several altered chemistries, glutamine, lysine, or glutamate, resulted in measurable activity. The histidine to glutamine mutant displays the highest residual activity and a pH profile similar to that of the wild-type enzyme. This activity is ~~dependent on~~ the ~~presence of a neighboring imidazole ring, which has taken over as a less efficient general base for the reaction~~. ~~This result implies that mutational pathways to alternative HNH~~-derived catalytic sites do exist but are not as extensively or successfully diverged or reoptimized in nature as variants of the PD(D/E)XK nuclease superfamily. This is possibly due to multiple steric constraints placed on the compact HNH motif, which is simultaneously involved in protein folding, DNA binding, and catalysis, as well as the use of a planar, aromatic imidazole group as a general base.	+	The line below this paragraph, {{ABSTRACT_PUBMED_17516660}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17516660 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17516660}}

	==About this Structure==		==About this Structure==
Line 29:		Line 33:
	[[Category: Hydrolase/dna complex]]		[[Category: Hydrolase/dna complex]]
	[[Category: Protein/dna complex]]		[[Category: Protein/dna complex]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 10~~:23:25 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 03:46:22 2008''