4una - Revision history

OCA at 10:30, 10 January 2024

2024-01-10T10:30:56Z

←Older revision		Revision as of 10:30, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4una]] is a 12 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=4UNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UNA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4una]] is a 12 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=4UNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UNA 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]] 2.3Å</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=4una FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4una OCA], [https://pdbe.org/4una PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4una RCSB], [https://www.ebi.ac.uk/pdbsum/4una PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4una 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=4una FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4una OCA], [https://pdbe.org/4una PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4una RCSB], [https://www.ebi.ac.uk/pdbsum/4una PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4una ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:25, 29 March 2023

2023-03-29T07:25:48Z

←Older revision		Revision as of 07:25, 29 March 2023
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	<StructureSection load='4una' size='340' side='right'caption='[[4una]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4una' size='340' side='right'caption='[[4una]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4una]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UNA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4UNA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4una]] is a 12 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=4UNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UNA 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]], [[4un9\|4un9]], [[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=4una FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4una OCA], [https://pdbe.org/4una PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4una RCSB], [https://www.ebi.ac.uk/pdbsum/4una PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4una 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=4una FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4una OCA], [~~http~~://pdbe.org/4una PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4una RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4una PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4una 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 09:03, 21 May 2019

2019-05-21T09:03:51Z

←Older revision		Revision as of 09:03, 21 May 2019
Line 1:		Line 1:

	==THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 2 DAYS INCUBATION IN 5MM MN (STATE 4)==		==THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 2 DAYS INCUBATION IN 5MM MN (STATE 4)==
-	<StructureSection load='4una' size='340' side='right' caption='[[4una]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='4una' size='340' side='right'caption='[[4una]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4una]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UNA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UNA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4una]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UNA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UNA 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 20:59, 11 August 2016

2016-08-11T20:59:25Z

←Older revision		Revision as of 20:59, 11 August 2016
Line 1:		Line 1:
		+
	==THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 2 DAYS INCUBATION IN 5MM MN (STATE 4)==		==THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 2 DAYS INCUBATION IN 5MM MN (STATE 4)==
	<StructureSection load='4una' size='340' side='right' caption='[[4una]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4una' size='340' side='right' caption='[[4una]], [[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=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]], [[4un9\|4un9]], [[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]], [[4un9\|4un9]], [[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=4una FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4una OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4una RCSB], [http://www.ebi.ac.uk/pdbsum/4una 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=4una FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4una OCA], [http://pdbe.org/4una PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4una RCSB], [http://www.ebi.ac.uk/pdbsum/4una PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4una 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 4una" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:52, 25 December 2014

2014-12-25T14:52:41Z

←Older revision		Revision as of 14:52, 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=4una FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4una OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4una RCSB], [http://www.ebi.ac.uk/pdbsum/4una 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=4una FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4una OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4una RCSB], [http://www.ebi.ac.uk/pdbsum/4una PDBsum]</span></td></tr>
	</table>		</table>
		+	== 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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 12:35, 17 December 2014

2014-12-17T12:35:54Z

←Older revision		Revision as of 12:35, 17 December 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 2 DAYS INCUBATION IN 5MM MN (STATE 4)==
		+	<StructureSection load='4una' size='340' side='right' caption='[[4una]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4una]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UNA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UNA 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>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4un6\|4un6]], [[4un7\|4un7]], [[4un8\|4un8]], [[4un9\|4un9]], [[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=4una FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4una OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4una RCSB], [http://www.ebi.ac.uk/pdbsum/4una PDBsum]</span></td></tr>
		+	</table>
		+	<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.

-	~~The entry 4una is ON HOLD until Paper Publication~~	+	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>

-	~~Authors: Molina~~, R.~~, Stella,~~ S.~~, Redondo, P~~., Gomez, H., Marcaida, M.J., Orozco, M., Prieto, J., ~~Montoya~~, G.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~THE CRYSTAL STRUCTURE OF I~~-~~DMOI IN COMPLEX WITH ITS TARGET DNA AT 2 DAYS INCUBATION IN 5MM MN (STATE 4)~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gomez, H]]
		+	[[Category: Marcaida, M J]]
		+	[[Category: Molina, R]]
		+	[[Category: Montoya, G]]
		+	[[Category: Orozco, M]]
		+	[[Category: Prieto, J]]
		+	[[Category: Redondo, P]]
		+	[[Category: Stella, S]]
		+	[[Category: Catalysis]]
		+	[[Category: Hydrolase-dna complex]]
		+	[[Category: Protein-dna interaction]]

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

2014-06-04T05:00:39Z

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

←Older revision

Revision as of 05:00, 4 June 2014

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

2014-06-04T05:00:39Z

New page: '''Unreleased structure''' The entry 4una 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 4una 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 2 DAYS INCUBATION IN 5MM MN (STATE 4)