4un9 - Revision history

OCA at 10:30, 10 January 2024

OCA — Wed, 10 Jan 2024 10:30:55 GMT

←Older revision		Revision as of 10:30, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4un9]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfurococcus_mucosus Desulfurococcus mucosus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UN9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4un9]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfurococcus_mucosus Desulfurococcus mucosus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UN9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.734Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=4un9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4un9 OCA], [https://pdbe.org/4un9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4un9 RCSB], [https://www.ebi.ac.uk/pdbsum/4un9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4un9 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=4un9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4un9 OCA], [https://pdbe.org/4un9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4un9 RCSB], [https://www.ebi.ac.uk/pdbsum/4un9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4un9 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:25, 29 March 2023

OCA — Wed, 29 Mar 2023 07:25:30 GMT

←Older revision		Revision as of 07:25, 29 March 2023
Line 3:		Line 3:
	<StructureSection load='4un9' size='340' side='right'caption='[[4un9]], [[Resolution\|resolution]] 2.73Å' scene=''>		<StructureSection load='4un9' size='340' side='right'caption='[[4un9]], [[Resolution\|resolution]] 2.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4un9]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UN9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4UN9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4un9]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfurococcus_mucosus Desulfurococcus mucosus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UN9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4un6\|4un6]], [[4un7\|4un7]], [[4un8\|4un8]], [[4una\|4una]], [[4unb\|4unb]], [[4unc\|4unc]]~~</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=4un9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4un9 OCA], [https://pdbe.org/4un9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4un9 RCSB], [https://www.ebi.ac.uk/pdbsum/4un9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4un9 ProSAT]</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=4un9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4un9 OCA], [~~http~~://pdbe.org/4un9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4un9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4un9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4un9 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DMO1_DESMO DMO1_DESMO]] Endonuclease involved in intron homing. Recognizes a recognizes up to 20 bp of DNA in the 23S rRNA gene intron. It has a slow turnover rate and cuts the coding strand with a slight preference over the non-coding strand.	+	[https://www.uniprot.org/uniprot/DMO1_DESMO DMO1_DESMO] Endonuclease involved in intron homing. Recognizes a recognizes up to 20 bp of DNA in the 23S rRNA gene intron. It has a slow turnover rate and cuts the coding strand with a slight preference over the non-coding strand.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 20:

	==See Also==		==See Also==
-	*[[Endonuclease\|Endonuclease]]	+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Desulfurococcus mucosus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gomez, H]]	+	[[Category: Synthetic construct]]
-	[[Category: Marcaida~~, M J~~]]	+	[[Category: Gomez H]]
-	[[Category: Molina, R]]	+	[[Category: Marcaida MJ]]
-	[[Category: Montoya, G]]	+	[[Category: Molina R]]
-	[[Category: Orozco, M]]	+	[[Category: Montoya G]]
-	[[Category: Prieto, J]]	+	[[Category: Orozco M]]
-	[[Category: Redondo, P]]	+	[[Category: Prieto J]]
-	[[Category: Stella, S]]	+	[[Category: Redondo P]]
-	~~[[Category: Catalysis]]~~	+	[[Category: Stella S]]
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Protein-dna interaction~~]]	+

OCA at 09:00, 21 May 2019

OCA — Tue, 21 May 2019 09:00:38 GMT

←Older revision		Revision as of 09:00, 21 May 2019
Line 1:		Line 1:

	==THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8H INCUBATION IN 5MM MN (STATE 3)==		==THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8H INCUBATION IN 5MM MN (STATE 3)==
-	<StructureSection load='4un9' size='340' side='right' caption='[[4un9]], [[Resolution\|resolution]] 2.73Å' scene=''>	+	<StructureSection load='4un9' size='340' side='right'caption='[[4un9]], [[Resolution\|resolution]] 2.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4un9]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UN9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UN9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4un9]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UN9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UN9 FirstGlance]. <br>
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Gomez, H]]		[[Category: Gomez, H]]
	[[Category: Marcaida, M J]]		[[Category: Marcaida, M J]]

OCA at 14:22, 27 April 2017

OCA — Thu, 27 Apr 2017 14:22:52 GMT

←Older revision		Revision as of 14:22, 27 April 2017
Line 1:		Line 1:
		+
	==THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8H INCUBATION IN 5MM MN (STATE 3)==		==THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8H INCUBATION IN 5MM MN (STATE 3)==
	<StructureSection load='4un9' size='340' side='right' caption='[[4un9]], [[Resolution\|resolution]] 2.73Å' scene=''>		<StructureSection load='4un9' size='340' side='right' caption='[[4un9]], [[Resolution\|resolution]] 2.73Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4un6\|4un6]], [[4un7\|4un7]], [[4un8\|4un8]], [[4una\|4una]], [[4unb\|4unb]], [[4unc\|4unc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4un6\|4un6]], [[4un7\|4un7]], [[4un8\|4un8]], [[4una\|4una]], [[4unb\|4unb]], [[4unc\|4unc]]</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=4un9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4un9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4un9 RCSB], [http://www.ebi.ac.uk/pdbsum/4un9 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=4un9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4un9 OCA], [http://pdbe.org/4un9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4un9 RCSB], [http://www.ebi.ac.uk/pdbsum/4un9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4un9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 4un9" style="background-color:#fffaf0;"></div>

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

OCA at 08:29, 22 July 2015

OCA — Wed, 22 Jul 2015 08:29:41 GMT

←Older revision		Revision as of 08:29, 22 July 2015
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/DMO1_DESMO DMO1_DESMO]] Endonuclease involved in intron homing. Recognizes a recognizes up to 20 bp of DNA in the 23S rRNA gene intron. It has a slow turnover rate and cuts the coding strand with a slight preference over the non-coding strand.		[[http://www.uniprot.org/uniprot/DMO1_DESMO DMO1_DESMO]] Endonuclease involved in intron homing. Recognizes a recognizes up to 20 bp of DNA in the 23S rRNA gene intron. It has a slow turnover rate and cuts the coding strand with a slight preference over the non-coding strand.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The enzymatic hydrolysis of DNA phosphodiester bonds has been widely studied, but the chemical reaction has not yet been observed. Here we follow the generation of a DNA double-strand break (DSB) by the Desulfurococcus mobilis homing endonuclease I-DmoI, trapping sequential stages of a two-metal-ion cleavage mechanism. We captured intermediates of the different catalytic steps, and this allowed us to watch the reaction by 'freezing' multiple states. We observed the successive entry of two metals involved in the reaction and the arrival of a third cation in a central position of the active site. This third metal ion has a crucial role, triggering the consecutive hydrolysis of the targeted phosphodiester bonds in the DNA strands and leaving its position once the DSB is generated. The multiple structures show the orchestrated conformational changes in the protein residues, nucleotides and metals during catalysis.
		+
		+	Visualizing phosphodiester-bond hydrolysis by an endonuclease.,Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G Nat Struct Mol Biol. 2014 Dec 8. doi: 10.1038/nsmb.2932. PMID:25486305<ref>PMID:25486305</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:46, 14 January 2015

OCA — Wed, 14 Jan 2015 13:46:20 GMT

←Older revision		Revision as of 13:46, 14 January 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8H INCUBATION IN 5MM MN (STATE 3)==
-		+	<StructureSection load='4un9' size='340' side='right' caption='[[4un9]], [[Resolution\|resolution]] 2.73Å' scene=''>
-	~~The entry~~ 4un9 is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4un9]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UN9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UN9 FirstGlance]. <br>
-	~~Authors~~: ~~Molina~~, R., ~~Stella~~, S., ~~Redondo~~, P.~~, Gomez, H~~.~~, Marcaida, M~~.J., ~~Orozco, M~~., ~~Prieto, J~~., ~~Montoya, G~~.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4un6\|4un6]], [[4un7\|4un7]], [[4un8\|4un8]], [[4una\|4una]], [[4unb\|4unb]], [[4unc\|4unc]]</td></tr>
-	~~Description~~: ~~THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET~~ DNA ~~AT 8H INCUBATION IN 5MM MN (STATE 3)~~	+	<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=4un9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4un9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4un9 RCSB], [http://www.ebi.ac.uk/pdbsum/4un9 PDBsum]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: ~~Stella~~, S]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DMO1_DESMO DMO1_DESMO]] Endonuclease involved in intron homing. Recognizes a recognizes up to 20 bp of DNA in the 23S rRNA gene intron. It has a slow turnover rate and cuts the coding strand with a slight preference over the non-coding strand.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gomez, H]]
		+	[[Category: Marcaida, M J]]
	[[Category: Molina, R]]		[[Category: Molina, R]]
		+	[[Category: Montoya, G]]
	[[Category: Orozco, M]]		[[Category: Orozco, M]]
-	[[Category: Marcaida, M.J]]
-	[[Category: Gomez, H]]
	[[Category: Prieto, J]]		[[Category: Prieto, J]]
	[[Category: Redondo, P]]		[[Category: Redondo, P]]
-	[[Category: ~~Montoya~~, G]]	+	[[Category: Stella, S]]
		+	[[Category: Catalysis]]
		+	[[Category: Hydrolase-dna complex]]
		+	[[Category: Protein-dna interaction]]

OCA at 18:32, 24 December 2014

OCA — Wed, 24 Dec 2014 18:32:15 GMT

←Older revision		Revision as of 18:32, 24 December 2014
Line 6:		Line 6:

	Description: THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8H INCUBATION IN 5MM MN (STATE 3)		Description: THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8H INCUBATION IN 5MM MN (STATE 3)
		+	[[Category: Unreleased Structures]]
		+	[[Category: Stella, S]]
		+	[[Category: Molina, R]]
		+	[[Category: Orozco, M]]
		+	[[Category: Marcaida, M.J]]
		+	[[Category: Gomez, H]]
		+	[[Category: Prieto, J]]
		+	[[Category: Redondo, P]]
		+	[[Category: Montoya, G]]

OCA: Protected "4un9" [edit=sysop:move=sysop]

OCA — Wed, 04 Jun 2014 05:00:39 GMT

Protected "4un9" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:00, 4 June 2014

OCA: New page: '''Unreleased structure''' The entry 4un9 is ON HOLD until Paper Publication Authors: Molina, R., Stella, S., Redondo, P., Gomez, H., Marcaida, M.J., Orozco, M., Prieto, J., Montoya, G....

OCA — Wed, 04 Jun 2014 05:00:38 GMT

New page: '''Unreleased structure''' The entry 4un9 is ON HOLD until Paper Publication Authors: Molina, R., Stella, S., Redondo, P., Gomez, H., Marcaida, M.J., Orozco, M., Prieto, J., Montoya, G....

New page

'''Unreleased structure'''

The entry 4un9 is ON HOLD until Paper Publication

Authors: Molina, R., Stella, S., Redondo, P., Gomez, H., Marcaida, M.J., Orozco, M., Prieto, J., Montoya, G.

Description: THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8H INCUBATION IN 5MM MN (STATE 3)