4oq2 - Revision history

OCA at 07:39, 25 January 2023

OCA — Wed, 25 Jan 2023 07:39:22 GMT

←Older revision		Revision as of 07:39, 25 January 2023
Line 1:		Line 1:

	==5hmC specific restriction endonuclease PvuRTs1I==		==5hmC specific restriction endonuclease PvuRTs1I==
-	<StructureSection load='4oq2' size='340' side='right' caption='[[4oq2]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='4oq2' size='340' side='right'caption='[[4oq2]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4oq2]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_29905 Atcc 29905~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQ2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4OQ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4oq2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OQ2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4oq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oq2 OCA], [https://pdbe.org/4oq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oq2 RCSB], [https://www.ebi.ac.uk/pdbsum/4oq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oq2 ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">1239102, pvuRts1I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585 ATCC 29905])~~</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=4oq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oq2 OCA], [~~http~~://pdbe.org/4oq2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4oq2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4oq2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4oq2 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q52612_PROVU Q52612_PROVU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 29905~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Bochtler, M~~]]	+	[[Category: Proteus vulgaris]]
-	[[Category: ~~Czapinska, H]]~~	+	[[Category: Bochtler M]]
-	~~[[Category: Kazrani, A A]]~~	+	[[Category: Czapinska H]]
-	~~[[Category: Kowalska,~~ M]]	+	[[Category: Kazrani AA]]
-	[[Category: ~~5-hydroxymethylcytosine~~]]	+	[[Category: Kowalska M]]
-	[[Category: ~~Cytosine hydroxymethylation~~]]	+
-	[[Category: ~~Dna]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Restriction endonuclease]]~~	+
-	~~[[Category: Sra dna binding domain~~]]	+

OCA at 14:18, 11 August 2016

OCA — Thu, 11 Aug 2016 14:18:48 GMT

←Older revision		Revision as of 14:18, 11 August 2016
Line 1:		Line 1:
		+
	==5hmC specific restriction endonuclease PvuRTs1I==		==5hmC specific restriction endonuclease PvuRTs1I==
	<StructureSection load='4oq2' size='340' side='right' caption='[[4oq2]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='4oq2' size='340' side='right' caption='[[4oq2]], [[Resolution\|resolution]] 2.35Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">1239102, pvuRts1I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585 ATCC 29905])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">1239102, pvuRts1I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585 ATCC 29905])</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=4oq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oq2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oq2 RCSB], [http://www.ebi.ac.uk/pdbsum/4oq2 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=4oq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oq2 OCA], [http://pdbe.org/4oq2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oq2 RCSB], [http://www.ebi.ac.uk/pdbsum/4oq2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oq2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		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 4oq2" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:35, 5 January 2015

OCA — Mon, 05 Jan 2015 08:35:15 GMT

←Older revision		Revision as of 08:35, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4oq2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29905 Atcc 29905]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQ2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4oq2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29905 Atcc 29905]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQ2 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">1239102, pvuRts1I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585 ATCC 29905])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">1239102, pvuRts1I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585 ATCC 29905])</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=4oq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oq2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oq2 RCSB], [http://www.ebi.ac.uk/pdbsum/4oq2 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=4oq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oq2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oq2 RCSB], [http://www.ebi.ac.uk/pdbsum/4oq2 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 14:		Line 14:
	Crystal structure of the 5hmC specific endonuclease PvuRts1I.,Kazrani AA, Kowalska M, Czapinska H, Bochtler M Nucleic Acids Res. 2014 Mar 25. PMID:24634440<ref>PMID:24634440</ref>		Crystal structure of the 5hmC specific endonuclease PvuRts1I.,Kazrani AA, Kowalska M, Czapinska H, Bochtler M Nucleic Acids Res. 2014 Mar 25. PMID:24634440<ref>PMID:24634440</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 29905]]		[[Category: Atcc 29905]]
-	[[Category: Bochtler, M.]]	+	[[Category: Bochtler, M]]
-	[[Category: Czapinska, H.]]	+	[[Category: Czapinska, H]]
-	[[Category: Kazrani, A A.]]	+	[[Category: Kazrani, A A]]
-	[[Category: Kowalska, M.]]	+	[[Category: Kowalska, M]]
	[[Category: 5-hydroxymethylcytosine]]		[[Category: 5-hydroxymethylcytosine]]
	[[Category: Cytosine hydroxymethylation]]		[[Category: Cytosine hydroxymethylation]]

OCA at 04:39, 4 June 2014

OCA — Wed, 04 Jun 2014 04:39:00 GMT

←Older revision		Revision as of 04:39, 4 June 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4oq2~~\| ~~PDB~~=4oq2 \| ~~SCENE~~= }}	+	==5hmC specific restriction endonuclease PvuRTs1I==
-	===~~5hmC specific restriction endonuclease PvuRTs1I~~===	+	<StructureSection load='4oq2' size='340' side='right' caption='[[4oq2]], [[Resolution\|resolution]] 2.35Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24634440}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4oq2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29905 Atcc 29905]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQ2 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">1239102, pvuRts1I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585 ATCC 29905])</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=4oq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oq2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oq2 RCSB], [http://www.ebi.ac.uk/pdbsum/4oq2 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	PvuRts1I is a prototype for a larger family of restriction endonucleases that cleave DNA containing 5-hydroxymethylcytosine (5hmC) or 5-glucosylhydroxymethylcytosine (5ghmC), but not 5-methylcytosine (5mC) or cytosine. Here, we report a crystal structure of the enzyme at 2.35 A resolution. Although the protein has been crystallized in the absence of DNA, the structure is very informative. It shows that PvuRts1I consists of an N-terminal, atypical PD-(D/E)XK catalytic domain and a C-terminal SRA domain that might accommodate a flipped 5hmC or 5ghmC base. Changes to predicted catalytic residues of the PD-(D/E)XK domain or to the putative pocket for a flipped base abolish catalytic activity. Surprisingly, fluorescence changes indicative of base flipping are not observed when PvuRts1I is added to DNA substrates containing pyrrolocytosine in place of 5hmC (5ghmC). Despite this caveat, the structure suggests a model for PvuRts1I activity and presents opportunities for protein engineering to alter the enzyme properties for biotechnological applications.

-	~~==About this Structure==~~	+	Crystal structure of the 5hmC specific endonuclease PvuRts1I.,Kazrani AA, Kowalska M, Czapinska H, Bochtler M Nucleic Acids Res. 2014 Mar 25. PMID:24634440<ref>PMID:24634440</ref>
-	~~[[4oq2]] is a 1 chain~~ structure. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4OQ2 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024634440</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Atcc 29905]]
	[[Category: Bochtler, M.]]		[[Category: Bochtler, M.]]
	[[Category: Czapinska, H.]]		[[Category: Czapinska, H.]]

OCA at 07:41, 2 April 2014

OCA — Wed, 02 Apr 2014 07:41:35 GMT

←Older revision		Revision as of 07:41, 2 April 2014
Line 1:		Line 1:
	{{STRUCTURE_4oq2\| PDB=4oq2 \| SCENE= }}		{{STRUCTURE_4oq2\| PDB=4oq2 \| SCENE= }}
	===5hmC specific restriction endonuclease PvuRTs1I===		===5hmC specific restriction endonuclease PvuRTs1I===
		+	{{ABSTRACT_PUBMED_24634440}}

	==About this Structure==		==About this Structure==
	[[4oq2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQ2 OCA].		[[4oq2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQ2 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024634440</ref><references group="xtra"/><references/>
	[[Category: Bochtler, M.]]		[[Category: Bochtler, M.]]
	[[Category: Czapinska, H.]]		[[Category: Czapinska, H.]]

OCA at 14:04, 12 March 2014

OCA — Wed, 12 Mar 2014 14:04:15 GMT

←Older revision		Revision as of 14:04, 12 March 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4oq2\| PDB=4oq2 \| SCENE= }}
		+	===5hmC specific restriction endonuclease PvuRTs1I===

-	~~The entry~~ 4oq2 is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4oq2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQ2 OCA].
-	~~Authors~~: ~~Kazrani, A~~.A.~~, Kowalska~~, M., Czapinska, H., ~~Bochtler~~, M.	+	[[Category: Bochtler, M.]]
-		+	[[Category: Czapinska, H.]]
-	~~Description~~: ~~5hmC specific restriction~~ endonuclease ~~PvuRTs1I~~	+	[[Category: Kazrani, A A.]]
		+	[[Category: Kowalska, M.]]
		+	[[Category: 5-hydroxymethylcytosine]]
		+	[[Category: Cytosine hydroxymethylation]]
		+	[[Category: Dna]]
		+	[[Category: Hydrolase]]
		+	[[Category: Restriction endonuclease]]
		+	[[Category: Sra dna binding domain]]

OCA: Protected "4oq2" [edit=sysop:move=sysop]

OCA — Wed, 19 Feb 2014 16:18:47 GMT

Protected "4oq2" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:18, 19 February 2014

OCA: New page: '''Unreleased structure''' The entry 4oq2 is ON HOLD Authors: Kazrani, A.A., Kowalska, M., Czapinska, H., Bochtler, M. Description: 5hmC specific restriction endonuclease PvuRTs1I

OCA — Wed, 19 Feb 2014 16:18:46 GMT

New page: '''Unreleased structure''' The entry 4oq2 is ON HOLD Authors: Kazrani, A.A., Kowalska, M., Czapinska, H., Bochtler, M. Description: 5hmC specific restriction endonuclease PvuRTs1I

New page

'''Unreleased structure'''

The entry 4oq2 is ON HOLD

Authors: Kazrani, A.A., Kowalska, M., Czapinska, H., Bochtler, M.

Description: 5hmC specific restriction endonuclease PvuRTs1I