1evx - Revision history

OCA at 07:07, 7 February 2024

2024-02-07T07:07:39Z

←Older revision		Revision as of 07:07, 7 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EVX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EVX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [https://pdbe.org/1evx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [https://www.ebi.ac.uk/pdbsum/1evx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1evx 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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [https://pdbe.org/1evx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [https://www.ebi.ac.uk/pdbsum/1evx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1evx 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;">
-	== Publication Abstract from PubMed ==
-	The homing endonuclease I-PpoI severely bends its DNA target, resulting in significant deformations of the minor and major groove near the scissile phosphate groups. To study the role of conformational changes within the protein catalyst and the DNA substrate, we have determined the structure of the enzyme in the absence of bound DNA, performed gel retardation analyses of DNA binding and bending, and have mutagenized a leucine residue that contacts an adenine nucleotide at the site of cleavage. The structure of the L116A/DNA complex has been determined and the effects of the mutation on affinity and catalysis have been measured. The wild-type protein displays a rigid-body rotation of its individual subunits upon DNA binding. Homing site DNA is not detectably bent in the absence of protein, but is sharply bent in both the wild-type and L116A complexes. These results indicate that binding involves a large distortion of the DNA and a smaller change in protein conformation. Leucine 116 is critical for binding and catalysis: it appears to be important for forming a well-ordered protein-DNA complex at the cleavage site, for maximal deformation of the DNA, and for desolvation of the nucleotide bases that are partially unstacked in the enzyme complex.
-
-	Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site.,Galburt EA, Chadsey MS, Jurica MS, Chevalier BS, Erho D, Tang W, Monnat RJ Jr, Stoddard BL J Mol Biol. 2000 Jul 21;300(4):877-87. PMID:10891275<ref>PMID:10891275</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1evx" 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>

OCA at 07:21, 18 May 2023

2023-05-18T07:21:34Z

←Older revision		Revision as of 07:21, 18 May 2023
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	<StructureSection load='1evx' size='340' side='right'caption='[[1evx]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1evx' size='340' side='right'caption='[[1evx]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EVX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EVX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1a73\|1a73]], [[1cz0\|1cz0]], [[1cyq\|1cyq]], [[1evw\|1evw]]</div></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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [https://pdbe.org/1evx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [https://www.ebi.ac.uk/pdbsum/1evx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1evx 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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [https://pdbe.org/1evx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [https://www.ebi.ac.uk/pdbsum/1evx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1evx 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 26:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Phypo~~]]	+	[[Category: Physarum polycephalum]]
-	[[Category: Chevalier~~, B S~~]]	+	[[Category: Chevalier BS]]
-	[[Category: Erho, D]]	+	[[Category: Erho D]]
-	[[Category: Galburt~~, E A~~]]	+	[[Category: Galburt EA]]
-	[[Category: Jurica~~, M S~~]]	+	[[Category: Jurica MS]]
-	[[Category: Stoddard~~, B L]]~~	+	[[Category: Stoddard BL]]
-	~~[[Category: C-terminal exchanged dimer interface]]~~	+
-	~~[[Category: Dna binding b-sheet]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 06:32, 11 August 2021

2021-08-11T06:32:58Z

←Older revision		Revision as of 06:32, 11 August 2021
Line 3:		Line 3:
	<StructureSection load='1evx' size='340' side='right'caption='[[1evx]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1evx' size='340' side='right'caption='[[1evx]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1EVX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EVX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a73\|1a73]], [[1cz0\|1cz0]], [[1cyq\|1cyq]], [[1evw\|1evw]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1a73\|1a73]], [[1cz0\|1cz0]], [[1cyq\|1cyq]], [[1evw\|1evw]]</div></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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [~~http~~://pdbe.org/1evx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1evx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1evx 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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [https://pdbe.org/1evx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [https://www.ebi.ac.uk/pdbsum/1evx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1evx 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 ==

OCA at 09:27, 6 November 2019

2019-11-06T09:27:44Z

←Older revision		Revision as of 09:27, 6 November 2019
Line 1:		Line 1:

	==APO CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE, I-PPOI==		==APO CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE, I-PPOI==
-	<StructureSection load='1evx' size='340' side='right' caption='[[1evx]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1evx' size='340' side='right'caption='[[1evx]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EVX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EVX FirstGlance]. <br>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 1evx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1evx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Phypo]]		[[Category: Phypo]]
	[[Category: Chevalier, B S]]		[[Category: Chevalier, B S]]

OCA at 06:15, 31 January 2018

2018-01-31T06:15:18Z

←Older revision		Revision as of 06:15, 31 January 2018
Line 3:		Line 3:
	<StructureSection load='1evx' size='340' side='right' caption='[[1evx]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1evx' size='340' side='right' caption='[[1evx]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1evx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EVX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EVX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a73\|1a73]], [[1cz0\|1cz0]], [[1cyq\|1cyq]], [[1evw\|1evw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a73\|1a73]], [[1cz0\|1cz0]], [[1cyq\|1cyq]], [[1evw\|1evw]]</td></tr>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 1evx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1evx" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Endonuclease\|Endonuclease]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Phypo]]
	[[Category: Chevalier, B S]]		[[Category: Chevalier, B S]]
	[[Category: Erho, D]]		[[Category: Erho, D]]

OCA at 03:48, 6 September 2017

2017-09-06T03:48:14Z

←Older revision		Revision as of 03:48, 6 September 2017
Line 1:		Line 1:
		+
	==APO CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE, I-PPOI==		==APO CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE, I-PPOI==
	<StructureSection load='1evx' size='340' side='right' caption='[[1evx]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1evx' size='340' side='right' caption='[[1evx]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EVX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1evx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EVX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a73\|1a73]], [[1cz0\|1cz0]], [[1cyq\|1cyq]], [[1evw\|1evw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a73\|1a73]], [[1cz0\|1cz0]], [[1cyq\|1cyq]], [[1evw\|1evw]]</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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [http://pdbe.org/1evx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [http://www.ebi.ac.uk/pdbsum/1evx 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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [http://pdbe.org/1evx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [http://www.ebi.ac.uk/pdbsum/1evx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1evx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Phypo]]
	[[Category: Chevalier, B S]]		[[Category: Chevalier, B S]]
	[[Category: Erho, D]]		[[Category: Erho, D]]

OCA at 13:37, 10 September 2015

2015-09-10T13:37:34Z

←Older revision		Revision as of 13:37, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1evx' size='340' side='right' caption='[[1evx]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1evx' size='340' side='right' caption='[[1evx]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EVX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EVX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a73\|1a73]], [[1cz0\|1cz0]], [[1cyq\|1cyq]], [[1evw\|1evw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a73\|1a73]], [[1cz0\|1cz0]], [[1cyq\|1cyq]], [[1evw\|1evw]]</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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [http://www.ebi.ac.uk/pdbsum/1evx 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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [http://pdbe.org/1evx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [http://www.ebi.ac.uk/pdbsum/1evx 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 1evx" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Physarum polycephalum~~]]	+	[[Category: Phypo]]
	[[Category: Chevalier, B S]]		[[Category: Chevalier, B S]]
	[[Category: Erho, D]]		[[Category: Erho, D]]

OCA at 00:51, 25 December 2014

2014-12-25T00:51:14Z

←Older revision		Revision as of 00:51, 25 December 2014
Line 7:		Line 7:
	<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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [http://www.ebi.ac.uk/pdbsum/1evx 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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [http://www.ebi.ac.uk/pdbsum/1evx 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 ==

OCA at 22:10, 22 December 2014

2014-12-22T22:10:41Z

←Older revision		Revision as of 22:10, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EVX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EVX FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a73\|1a73]], [[1cz0\|1cz0]], [[1cyq\|1cyq]], [[1evw\|1evw]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a73\|1a73]], [[1cz0\|1cz0]], [[1cyq\|1cyq]], [[1evw\|1evw]]</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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [http://www.ebi.ac.uk/pdbsum/1evx 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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [http://www.ebi.ac.uk/pdbsum/1evx PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Physarum polycephalum]]		[[Category: Physarum polycephalum]]
-	[[Category: Chevalier, B S.]]	+	[[Category: Chevalier, B S]]
-	[[Category: Erho, D.]]	+	[[Category: Erho, D]]
-	[[Category: Galburt, E A.]]	+	[[Category: Galburt, E A]]
-	[[Category: Jurica, M S.]]	+	[[Category: Jurica, M S]]
-	[[Category: Stoddard, B L.]]	+	[[Category: Stoddard, B L]]
	[[Category: C-terminal exchanged dimer interface]]		[[Category: C-terminal exchanged dimer interface]]
	[[Category: Dna binding b-sheet]]		[[Category: Dna binding b-sheet]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 11:16, 24 September 2014

2014-09-24T11:16:13Z

←Older revision		Revision as of 11:16, 24 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1evx.~~png~~\|~~left~~\|~~200px~~]]	+	==APO CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE, I-PPOI==
		+	<StructureSection load='1evx' size='340' side='right' caption='[[1evx]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1evx]] is a 2 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=1EVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EVX FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a73\|1a73]], [[1cz0\|1cz0]], [[1cyq\|1cyq]], [[1evw\|1evw]]</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=1evx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1evx RCSB], [http://www.ebi.ac.uk/pdbsum/1evx PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The homing endonuclease I-PpoI severely bends its DNA target, resulting in significant deformations of the minor and major groove near the scissile phosphate groups. To study the role of conformational changes within the protein catalyst and the DNA substrate, we have determined the structure of the enzyme in the absence of bound DNA, performed gel retardation analyses of DNA binding and bending, and have mutagenized a leucine residue that contacts an adenine nucleotide at the site of cleavage. The structure of the L116A/DNA complex has been determined and the effects of the mutation on affinity and catalysis have been measured. The wild-type protein displays a rigid-body rotation of its individual subunits upon DNA binding. Homing site DNA is not detectably bent in the absence of protein, but is sharply bent in both the wild-type and L116A complexes. These results indicate that binding involves a large distortion of the DNA and a smaller change in protein conformation. Leucine 116 is critical for binding and catalysis: it appears to be important for forming a well-ordered protein-DNA complex at the cleavage site, for maximal deformation of the DNA, and for desolvation of the nucleotide bases that are partially unstacked in the enzyme complex.

-	~~{{STRUCTURE_1evx\| PDB=1evx \| SCENE= }}~~	+	Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site.,Galburt EA, Chadsey MS, Jurica MS, Chevalier BS, Erho D, Tang W, Monnat RJ Jr, Stoddard BL J Mol Biol. 2000 Jul 21;300(4):877-87. PMID:10891275<ref>PMID:10891275</ref>

-	~~===APO CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE~~, ~~I-PPOI===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10891275}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1evx]] is~~ a ~~2 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=1EVX OCA].~~	+

	==See Also==		==See Also==
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010891275<~~/~~ref~~><~~ref group="xtra">PMID:015048824</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Physarum polycephalum]]		[[Category: Physarum polycephalum]]
	[[Category: Chevalier, B S.]]		[[Category: Chevalier, B S.]]