1m0i - Revision history

OCA at 07:38, 14 February 2024

OCA — Wed, 14 Feb 2024 07:38:03 GMT

←Older revision		Revision as of 07:38, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1m0i' size='340' side='right'caption='[[1m0i]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='1m0i' size='340' side='right'caption='[[1m0i]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m0i]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpt7 Bpt7~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1M0I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m0i]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M0I 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></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]] 2.55Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[1fzr\|1fzr]]~~, [[~~1m0d~~\|~~1m0d~~]]~~</div>~~</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></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~10760 BPT7])</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=1m0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0i OCA], [https://pdbe.org/1m0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m0i RCSB], [https://www.ebi.ac.uk/pdbsum/1m0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m0i ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </~~span~~></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1m0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0i OCA], [~~http~~://pdbe.org/1m0i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1m0i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1m0i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1m0i ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ENDO_BPT7 ENDO_BPT7]] Junction-resolving enzyme that selectively binds and cleaves four-way (Holliday) DNA junctions present after viral genomic replication. These intermediates are created during DNA repair, processing of stalled replication forks and homologous genetic recombination. Introduces two nicks on the two non-crossing strands, at 5' sides of the junction. Participates also together with gp6 in the degradation of host chromosome to provide nucleotides for phage DNA synthesis.<ref>PMID:12628932</ref> <ref>PMID:23207296</ref> <ref>PMID:3972821</ref> <ref>PMID:9236119</ref>	+	[https://www.uniprot.org/uniprot/ENDO_BPT7 ENDO_BPT7] Junction-resolving enzyme that selectively binds and cleaves four-way (Holliday) DNA junctions present after viral genomic replication. These intermediates are created during DNA repair, processing of stalled replication forks and homologous genetic recombination. Introduces two nicks on the two non-crossing strands, at 5' sides of the junction. Participates also together with gp6 in the degradation of host chromosome to provide nucleotides for phage DNA synthesis.<ref>PMID:12628932</ref> <ref>PMID:23207296</ref> <ref>PMID:3972821</ref> <ref>PMID:9236119</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m0i ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m0i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	T7 endonuclease I is a nuclease that is selective for the structure of the four-way DNA junction. The active site is similar to those of a number of restriction enzymes. We have solved the crystal structure of endonuclease I with a wild-type active site. Diffusion of manganese ions into the crystal revealed two peaks of electron density per active site, defining two metal ion-binding sites. Site 1 is fully occupied, and the manganese ion is coordinated by the carboxylate groups of Asp55 and Glu65, and the main chain carbonyl of Thr66. Site 2 is partially occupied, and the metal ion has a single protein ligand, the remaining carboxylate oxygen atom of Asp55. Isothermal titration calorimetry showed the sequential exothermic binding of two manganese ions in solution, with dissociation constants of 0.58 +/- 0.019 and 14 +/- 1.5 mM. These results are consistent with a two metal ion mechanism for the cleavage reaction, in which the hydrolytic water molecule is contained in the first coordination sphere of the site 1-bound metal ion.
-
-	Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I.,Hadden JM, Declais AC, Phillips SE, Lilley DM EMBO J. 2002 Jul 1;21(13):3505-15. PMID:12093751<ref>PMID:12093751</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1m0i" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt7~~]]	+	[[Category: Escherichia phage T7]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Declais~~, A C~~]]	+	[[Category: Declais AC]]
-	[[Category: Hadden~~, J M~~]]	+	[[Category: Hadden JM]]
-	[[Category: Lilley~~, D M~~]]	+	[[Category: Lilley DM]]
-	[[Category: Phillips~~, S E]]~~	+	[[Category: Phillips SE]]
-	~~[[Category: Composite active site]]~~	+
-	~~[[Category: Domain swapped]]~~	+
-	~~[[Category: Holliday junction resolvase]]~~	+
-	~~[[Category: Homodimer]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 08:31, 2 December 2020

OCA — Wed, 02 Dec 2020 08:31:51 GMT

←Older revision		Revision as of 08:31, 2 December 2020
Line 1:		Line 1:

	==Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site==		==Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site==
-	<StructureSection load='1m0i' size='340' side='right' caption='[[1m0i]], [[Resolution\|resolution]] 2.55Å' scene=''>	+	<StructureSection load='1m0i' size='340' side='right'caption='[[1m0i]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m0i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt7 Bpt7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0I OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1M0I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m0i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt7 Bpt7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1M0I 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></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></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fzr\|1fzr]], [[1m0d\|1m0d]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fzr\|1fzr]], [[1m0d\|1m0d]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 BPT7])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 BPT7])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </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=1m0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0i OCA], [http://pdbe.org/1m0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m0i RCSB], [http://www.ebi.ac.uk/pdbsum/1m0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m0i ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1m0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0i OCA], [http://pdbe.org/1m0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m0i RCSB], [http://www.ebi.ac.uk/pdbsum/1m0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m0i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1m0i" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1m0i" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bpt7]]		[[Category: Bpt7]]
		+	[[Category: Large Structures]]
	[[Category: Declais, A C]]		[[Category: Declais, A C]]
	[[Category: Hadden, J M]]		[[Category: Hadden, J M]]

OCA at 07:58, 31 January 2018

OCA — Wed, 31 Jan 2018 07:58:32 GMT

←Older revision		Revision as of 07:58, 31 January 2018
Line 1:		Line 1:
		+
	==Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site==		==Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site==
	<StructureSection load='1m0i' size='340' side='right' caption='[[1m0i]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='1m0i' size='340' side='right' caption='[[1m0i]], [[Resolution\|resolution]] 2.55Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 BPT7])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 BPT7])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </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=1m0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0i OCA], [http://pdbe.org/1m0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m0i RCSB], [http://www.ebi.ac.uk/pdbsum/1m0i 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=1m0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0i OCA], [http://pdbe.org/1m0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m0i RCSB], [http://www.ebi.ac.uk/pdbsum/1m0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m0i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m0/1m0i_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m0/1m0i_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1m0i" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1m0i" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Endonuclease\|Endonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:13, 10 February 2016

OCA — Wed, 10 Feb 2016 03:13:20 GMT

←Older revision		Revision as of 03:13, 10 February 2016
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m0i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:49, 11 September 2015

OCA — Fri, 11 Sep 2015 04:49:02 GMT

←Older revision		Revision as of 04:49, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1m0i' size='340' side='right' caption='[[1m0i]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='1m0i' size='340' side='right' caption='[[1m0i]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m0i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_t7 Enterobacteria phage t7~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M0I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m0i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt7 Bpt7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M0I 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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fzr\|1fzr]], [[1m0d\|1m0d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fzr\|1fzr]], [[1m0d\|1m0d]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 ~~Enterobacteria phage T7~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 BPT7])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </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=1m0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m0i RCSB], [http://www.ebi.ac.uk/pdbsum/1m0i 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=1m0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0i OCA], [http://pdbe.org/1m0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m0i RCSB], [http://www.ebi.ac.uk/pdbsum/1m0i PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~ENRN_BPT7 ENRN_BPT7~~]] Junction-resolving enzyme that selectively binds and cleaves four-way (Holliday) DNA junctions present after viral genomic replication. These intermediates are created during DNA repair, processing of stalled replication forks and homologous genetic recombination. Introduces two nicks on the two non-crossing strands, at 5' sides of the junction. Participates also together with gp6 in the degradation of host chromosome to provide nucleotides for phage DNA synthesis.<ref>PMID:~~3972821~~</ref> <ref>PMID:~~9236119~~</ref> <ref>PMID:~~12628932~~</ref> <ref>PMID:~~23207296~~</ref>	+	[[http://www.uniprot.org/uniprot/ENDO_BPT7 ENDO_BPT7]] Junction-resolving enzyme that selectively binds and cleaves four-way (Holliday) DNA junctions present after viral genomic replication. These intermediates are created during DNA repair, processing of stalled replication forks and homologous genetic recombination. Introduces two nicks on the two non-crossing strands, at 5' sides of the junction. Participates also together with gp6 in the degradation of host chromosome to provide nucleotides for phage DNA synthesis.<ref>PMID:12628932</ref> <ref>PMID:23207296</ref> <ref>PMID:3972821</ref> <ref>PMID:9236119</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	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 1m0i" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage t7~~]]	+	[[Category: Bpt7]]
	[[Category: Declais, A C]]		[[Category: Declais, A C]]
	[[Category: Hadden, J M]]		[[Category: Hadden, J M]]

OCA at 11:24, 25 December 2014

OCA — Thu, 25 Dec 2014 11:24:16 GMT

←Older revision		Revision as of 11:24, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m0i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M0I FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m0i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M0I FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fzr\|1fzr]], [[1m0d\|1m0d]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fzr\|1fzr]], [[1m0d\|1m0d]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 Enterobacteria phage T7])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 Enterobacteria phage T7])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </span></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=1m0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m0i RCSB], [http://www.ebi.ac.uk/pdbsum/1m0i 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=1m0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m0i RCSB], [http://www.ebi.ac.uk/pdbsum/1m0i PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ENRN_BPT7 ENRN_BPT7]] Junction-resolving enzyme that selectively binds and cleaves four-way (Holliday) DNA junctions present after viral genomic replication. These intermediates are created during DNA repair, processing of stalled replication forks and homologous genetic recombination. Introduces two nicks on the two non-crossing strands, at 5' sides of the junction. Participates also together with gp6 in the degradation of host chromosome to provide nucleotides for phage DNA synthesis.<ref>PMID:3972821</ref> <ref>PMID:9236119</ref> <ref>PMID:12628932</ref> <ref>PMID:23207296</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Enterobacteria phage t7]]		[[Category: Enterobacteria phage t7]]
-	[[Category: Declais, A C.]]	+	[[Category: Declais, A C]]
-	[[Category: Hadden, J M.]]	+	[[Category: Hadden, J M]]
-	[[Category: Lilley, D M.]]	+	[[Category: Lilley, D M]]
-	[[Category: Phillips, S E.]]	+	[[Category: Phillips, S E]]
	[[Category: Composite active site]]		[[Category: Composite active site]]
	[[Category: Domain swapped]]		[[Category: Domain swapped]]

OCA at 13:21, 28 September 2014

OCA — Sun, 28 Sep 2014 13:21:16 GMT

←Older revision		Revision as of 13:21, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1m0i.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site==
		+	<StructureSection load='1m0i' size='340' side='right' caption='[[1m0i]], [[Resolution\|resolution]] 2.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1m0i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M0I FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fzr\|1fzr]], [[1m0d\|1m0d]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 Enterobacteria phage T7])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </span></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=1m0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m0i RCSB], [http://www.ebi.ac.uk/pdbsum/1m0i PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m0/1m0i_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	T7 endonuclease I is a nuclease that is selective for the structure of the four-way DNA junction. The active site is similar to those of a number of restriction enzymes. We have solved the crystal structure of endonuclease I with a wild-type active site. Diffusion of manganese ions into the crystal revealed two peaks of electron density per active site, defining two metal ion-binding sites. Site 1 is fully occupied, and the manganese ion is coordinated by the carboxylate groups of Asp55 and Glu65, and the main chain carbonyl of Thr66. Site 2 is partially occupied, and the metal ion has a single protein ligand, the remaining carboxylate oxygen atom of Asp55. Isothermal titration calorimetry showed the sequential exothermic binding of two manganese ions in solution, with dissociation constants of 0.58 +/- 0.019 and 14 +/- 1.5 mM. These results are consistent with a two metal ion mechanism for the cleavage reaction, in which the hydrolytic water molecule is contained in the first coordination sphere of the site 1-bound metal ion.

-	~~{{STRUCTURE_1m0i\| PDB=1m0i \| SCENE= }}~~	+	Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I.,Hadden JM, Declais AC, Phillips SE, Lilley DM EMBO J. 2002 Jul 1;21(13):3505-15. PMID:12093751<ref>PMID:12093751</ref>

-	~~===Crystal Structure~~ of ~~Bacteriophage T7 Endonuclease I with a Wild-Type Active Site===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12093751}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1m0i]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1M0I OCA].~~	+

	==See Also==		==See Also==
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012093751<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t7]]		[[Category: Enterobacteria phage t7]]
	[[Category: Declais, A C.]]		[[Category: Declais, A C.]]

OCA at 16:08, 20 October 2012

OCA — Sat, 20 Oct 2012 16:08:04 GMT

←Older revision		Revision as of 16:08, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1m0i]] is a 4 chain structure ~~of [[Endonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0I OCA].	+	[[1m0i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0I OCA].

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

OCA: Protected "1m0i" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 20:42:23 GMT

Protected "1m0i" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:42, 26 July 2012

OCA at 20:42, 26 July 2012

OCA — Thu, 26 Jul 2012 20:42:22 GMT

←Older revision		Revision as of 20:42, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1m0i.png\|left\|200px]]		[[Image:1m0i.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1m0i", 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.
-	-->
	{{STRUCTURE_1m0i\| PDB=1m0i \| SCENE= }}		{{STRUCTURE_1m0i\| PDB=1m0i \| SCENE= }}

	===Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site===		===Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12093751}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12093751 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12093751}}		{{ABSTRACT_PUBMED_12093751}}

	==About this Structure==		==About this Structure==
-	~~1M0I~~ is a 4 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0I OCA].	+	[[1m0i]] is a 4 chain structure of [[Endonuclease]] with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0I OCA].
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12093751~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012093751</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t7]]		[[Category: Enterobacteria phage t7]]
	[[Category: Declais, A C.]]		[[Category: Declais, A C.]]
Line 33:		Line 24:
	[[Category: Holliday junction resolvase]]		[[Category: Holliday junction resolvase]]
	[[Category: Homodimer]]		[[Category: Homodimer]]
-		+	[[Category: Hydrolase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 14:58:23 2009''~~	+