2gzj - Revision history

OCA at 09:49, 30 August 2023

OCA — Wed, 30 Aug 2023 09:49:21 GMT

←Older revision		Revision as of 09:49, 30 August 2023
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	<StructureSection load='2gzj' size='340' side='right'caption='[[2gzj]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2gzj' size='340' side='right'caption='[[2gzj]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gzj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GZJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GZJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gzj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GZJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GZJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1emv\|1emv]], [[1bxi\|1bxi]], [[2gyk\|2gyk]], [[2gze\|2gze]], [[2gzf\|2gzf]], [[2gzg\|2gzg]], [[2gzi\|2gzi]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>imm, ceiE9 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~83333 ECOLI]), col, cei ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Deoxyribonuclease_I Deoxyribonuclease I], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1]~~ </~~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=2gzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gzj OCA], [https://pdbe.org/2gzj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gzj RCSB], [https://www.ebi.ac.uk/pdbsum/2gzj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gzj 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=2gzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gzj OCA], [https://pdbe.org/2gzj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gzj RCSB], [https://www.ebi.ac.uk/pdbsum/2gzj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gzj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/IMM9_ECOLX IMM9_ECOLX]] This protein is able to protect a cell, which harbors the plasmid ColE9 encoding colicin E9, against colicin E9, it binds specifically to the DNase-type colicin and inhibits its bactericidal activity. [[https://www.uniprot.org/uniprot/CEA9_ECOLX CEA9_ECOLX]] This plasmid-coded bactericidal protein is an endonuclease active on both single- and double-stranded DNA but with undefined specificity. Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria.	+	[https://www.uniprot.org/uniprot/IMM9_ECOLX IMM9_ECOLX] This protein is able to protect a cell, which harbors the plasmid ColE9 encoding colicin E9, against colicin E9, it binds specifically to the DNase-type colicin and inhibits its bactericidal activity.
	== 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=2gzj 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=2gzj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of the cytotoxic endonuclease domain from the bacterial toxin colicin E9 in complex with its cognate immunity protein Im9 reveals that the inhibitor does not bind at the active site, the core of which comprises the HNH motif found in intron-encoded homing endonucleases, but rather at an adjacent position leaving the active site exposed yet unable to bind DNA because of steric and electrostatic clashes with incoming substrate. Although its mode of action is unorthodox, Im9 is a remarkably effective inhibitor since it folds within milliseconds and then associates with its target endonuclease at the rate of diffusion to form an inactive complex with sub-femtomolar binding affinity. This hyperefficient mechanism of inhibition could be well suited to other toxic enzyme systems, particularly where the substrate is a polymer extending beyond the boundaries of the active site.
-
-	Structural and mechanistic basis of immunity toward endonuclease colicins.,Kleanthous C, Kuhlmann UC, Pommer AJ, Ferguson N, Radford SE, Moore GR, James R, Hemmings AM Nat Struct Biol. 1999 Mar;6(3):243-52. PMID:10074943<ref>PMID:10074943</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2gzj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Colicin 3D structures\|Colicin 3D structures]]		*[[Colicin 3D structures\|Colicin 3D structures]]
	*[[Colicin immunity protein 3D structures\|Colicin immunity protein 3D structures]]		*[[Colicin immunity protein 3D structures\|Colicin immunity protein 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Deoxyribonuclease I]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hemmings~~, A M~~]]	+	[[Category: Hemmings AM]]
-	[[Category: Kleanthous, C]]	+	[[Category: Kleanthous C]]
-	[[Category: Kolade~~, O O~~]]	+	[[Category: Kolade OO]]
-	[[Category: Kuhlmann~~, U C~~]]	+	[[Category: Kuhlmann UC]]
-	[[Category: Santi~~, P S]]~~	+	[[Category: Santi PS]]
-	~~[[Category: 4-helix bundle]]~~	+
-	~~[[Category: Antibiotic-antibiotic inhibitor complex]]~~	+
-	~~[[Category: Dnase domain]]~~	+
-	~~[[Category: Hnh-motif]]~~	+
-	~~[[Category: Protein-protein complex~~]]	+

OCA at 07:27, 17 March 2021

OCA — Wed, 17 Mar 2021 07:27:20 GMT

←Older revision		Revision as of 07:27, 17 March 2021
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	==Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A)==		==Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A)==
-	<StructureSection load='2gzj' size='340' side='right' caption='[[2gzj]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='2gzj' size='340' side='right'caption='[[2gzj]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gzj]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GZJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2GZJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gzj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GZJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GZJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=PO4:PHOSPHATE+ION'>PO4</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">[[1emv\|1emv]], [[1bxi\|1bxi]], [[2gyk\|2gyk]], [[2gze\|2gze]], [[2gzf\|2gzf]], [[2gzg\|2gzg]], [[2gzi\|2gzi]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1emv\|1emv]], [[1bxi\|1bxi]], [[2gyk\|2gyk]], [[2gze\|2gze]], [[2gzf\|2gzf]], [[2gzg\|2gzg]], [[2gzi\|2gzi]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">imm, ceiE9 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), col, cei ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">imm, ceiE9 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), col, cei ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Deoxyribonuclease_I Deoxyribonuclease I], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribonuclease_I Deoxyribonuclease I], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1] </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=2gzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gzj OCA], [~~http~~://pdbe.org/2gzj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2gzj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2gzj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2gzj 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=2gzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gzj OCA], [https://pdbe.org/2gzj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gzj RCSB], [https://www.ebi.ac.uk/pdbsum/2gzj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gzj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/IMM9_ECOLX IMM9_ECOLX]] This protein is able to protect a cell, which harbors the plasmid ColE9 encoding colicin E9, against colicin E9, it binds specifically to the DNase-type colicin and inhibits its bactericidal activity. [[~~http~~://www.uniprot.org/uniprot/CEA9_ECOLX CEA9_ECOLX]] This plasmid-coded bactericidal protein is an endonuclease active on both single- and double-stranded DNA but with undefined specificity. Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria.	+	[[https://www.uniprot.org/uniprot/IMM9_ECOLX IMM9_ECOLX]] This protein is able to protect a cell, which harbors the plasmid ColE9 encoding colicin E9, against colicin E9, it binds specifically to the DNase-type colicin and inhibits its bactericidal activity. [[https://www.uniprot.org/uniprot/CEA9_ECOLX CEA9_ECOLX]] This plasmid-coded bactericidal protein is an endonuclease active on both single- and double-stranded DNA but with undefined specificity. Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gz/2gzj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gz/2gzj_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 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 2gzj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2gzj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Colicin 3D structures\|Colicin 3D structures]]
		+	*[[Colicin immunity protein 3D structures\|Colicin immunity protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Deoxyribonuclease I]]		[[Category: Deoxyribonuclease I]]
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Hemmings, A M]]		[[Category: Hemmings, A M]]
	[[Category: Kleanthous, C]]		[[Category: Kleanthous, C]]

OCA at 08:03, 18 October 2017

OCA — Wed, 18 Oct 2017 08:03:33 GMT

←Older revision		Revision as of 08:03, 18 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A)==		==Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A)==
	<StructureSection load='2gzj' size='340' side='right' caption='[[2gzj]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2gzj' size='340' side='right' caption='[[2gzj]], [[Resolution\|resolution]] 1.60Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">imm, ceiE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), col, cei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">imm, ceiE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), col, cei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_I Deoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1] </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_I Deoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1] </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=2gzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gzj OCA], [http://pdbe.org/2gzj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gzj RCSB], [http://www.ebi.ac.uk/pdbsum/2gzj 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=2gzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gzj OCA], [http://pdbe.org/2gzj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gzj RCSB], [http://www.ebi.ac.uk/pdbsum/2gzj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gzj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 2gzj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2gzj" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Colicin\|Colicin]]
-	*[[Colicin Immunity Protein\|Colicin Immunity Protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:57, 8 February 2016

OCA — Mon, 08 Feb 2016 12:57:30 GMT

←Older revision		Revision as of 12:57, 8 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=2gzj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:48, 10 September 2015

OCA — Thu, 10 Sep 2015 11:48:36 GMT

←Older revision		Revision as of 11:48, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2gzj' size='340' side='right' caption='[[2gzj]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2gzj' size='340' side='right' caption='[[2gzj]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gzj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k-12 Escherichia coli k-12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GZJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GZJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gzj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GZJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GZJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=PO4:PHOSPHATE+ION'>PO4</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">[[1emv\|1emv]], [[1bxi\|1bxi]], [[2gyk\|2gyk]], [[2gze\|2gze]], [[2gzf\|2gzf]], [[2gzg\|2gzg]], [[2gzi\|2gzi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1emv\|1emv]], [[1bxi\|1bxi]], [[2gyk\|2gyk]], [[2gze\|2gze]], [[2gzf\|2gzf]], [[2gzg\|2gzg]], [[2gzi\|2gzi]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">imm, ceiE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ~~Escherichia coli K-12~~]), col, cei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ~~Escherichia coli K-12~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">imm, ceiE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), col, cei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_I Deoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1] </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_I Deoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1] </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=2gzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gzj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gzj RCSB], [http://www.ebi.ac.uk/pdbsum/2gzj 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=2gzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gzj OCA], [http://pdbe.org/2gzj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gzj RCSB], [http://www.ebi.ac.uk/pdbsum/2gzj PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/IMM9_ECOLX IMM9_ECOLX]] This protein is able to protect a cell, which harbors the plasmid ColE9 encoding colicin E9, against colicin E9, it binds specifically to the DNase-type colicin and inhibits its bactericidal activity. [[http://www.uniprot.org/uniprot/CEA9_ECOLX CEA9_ECOLX]] This plasmid-coded bactericidal protein is an endonuclease active on both single- and double-stranded DNA but with undefined specificity. Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		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 2gzj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Deoxyribonuclease I]]		[[Category: Deoxyribonuclease I]]
-	[[Category: ~~Escherichia coli k-12~~]]	+	[[Category: Ecoli]]
	[[Category: Hemmings, A M]]		[[Category: Hemmings, A M]]
	[[Category: Kleanthous, C]]		[[Category: Kleanthous, C]]

OCA at 08:11, 16 January 2015

OCA — Fri, 16 Jan 2015 08:11:41 GMT

←Older revision		Revision as of 08:11, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2gzj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GZJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GZJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2gzj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GZJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GZJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1emv\|1emv]], [[1bxi\|1bxi]], [[2gyk\|2gyk]], [[2gze\|2gze]], [[2gzf\|2gzf]], [[2gzg\|2gzg]], [[2gzi\|2gzi]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1emv\|1emv]], [[1bxi\|1bxi]], [[2gyk\|2gyk]], [[2gze\|2gze]], [[2gzf\|2gzf]], [[2gzg\|2gzg]], [[2gzi\|2gzi]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">imm, ceiE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12]), col, cei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">imm, ceiE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12]), col, cei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_I Deoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1] </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_I Deoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1] </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=2gzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gzj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gzj RCSB], [http://www.ebi.ac.uk/pdbsum/2gzj 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=2gzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gzj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gzj RCSB], [http://www.ebi.ac.uk/pdbsum/2gzj PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 37:
	[[Category: Deoxyribonuclease I]]		[[Category: Deoxyribonuclease I]]
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
-	[[Category: Hemmings, A M.]]	+	[[Category: Hemmings, A M]]
-	[[Category: Kleanthous, C.]]	+	[[Category: Kleanthous, C]]
-	[[Category: Kolade, O O.]]	+	[[Category: Kolade, O O]]
-	[[Category: Kuhlmann, U C.]]	+	[[Category: Kuhlmann, U C]]
-	[[Category: Santi, P S.]]	+	[[Category: Santi, P S]]
	[[Category: 4-helix bundle]]		[[Category: 4-helix bundle]]
	[[Category: Antibiotic-antibiotic inhibitor complex]]		[[Category: Antibiotic-antibiotic inhibitor complex]]

OCA at 03:27, 29 September 2014

OCA — Mon, 29 Sep 2014 03:27:47 GMT

←Older revision		Revision as of 03:27, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2gzj.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A)==
		+	<StructureSection load='2gzj' size='340' side='right' caption='[[2gzj]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2gzj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GZJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GZJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1emv\|1emv]], [[1bxi\|1bxi]], [[2gyk\|2gyk]], [[2gze\|2gze]], [[2gzf\|2gzf]], [[2gzg\|2gzg]], [[2gzi\|2gzi]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">imm, ceiE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12]), col, cei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_I Deoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1] </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=2gzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gzj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gzj RCSB], [http://www.ebi.ac.uk/pdbsum/2gzj 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/gz/2gzj_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 ==
		+	The crystal structure of the cytotoxic endonuclease domain from the bacterial toxin colicin E9 in complex with its cognate immunity protein Im9 reveals that the inhibitor does not bind at the active site, the core of which comprises the HNH motif found in intron-encoded homing endonucleases, but rather at an adjacent position leaving the active site exposed yet unable to bind DNA because of steric and electrostatic clashes with incoming substrate. Although its mode of action is unorthodox, Im9 is a remarkably effective inhibitor since it folds within milliseconds and then associates with its target endonuclease at the rate of diffusion to form an inactive complex with sub-femtomolar binding affinity. This hyperefficient mechanism of inhibition could be well suited to other toxic enzyme systems, particularly where the substrate is a polymer extending beyond the boundaries of the active site.

-	~~{{STRUCTURE_2gzj\| PDB=2gzj \| SCENE= }}~~	+	Structural and mechanistic basis of immunity toward endonuclease colicins.,Kleanthous C, Kuhlmann UC, Pommer AJ, Ferguson N, Radford SE, Moore GR, James R, Hemmings AM Nat Struct Biol. 1999 Mar;6(3):243-52. PMID:10074943<ref>PMID:10074943</ref>

-	~~===Crystal Structure~~ of the ~~E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10074943}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2gzj]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2GZJ OCA].~~	+

	==See Also==		==See Also==
	*[[Colicin\|Colicin]]		*[[Colicin\|Colicin]]
	*[[Colicin Immunity Protein\|Colicin Immunity Protein]]		*[[Colicin Immunity Protein\|Colicin Immunity Protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010074943<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Deoxyribonuclease I]]		[[Category: Deoxyribonuclease I]]
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]

OCA at 10:12, 20 October 2012

OCA — Sat, 20 Oct 2012 10:12:53 GMT

←Older revision		Revision as of 10:12, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2gzj]] is a 4 chain structure ~~of [[Colicin]] and [[Colicin Immunity Protein]]~~ with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k12~~ Escherichia coli ~~k12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GZJ OCA].	+	[[2gzj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GZJ OCA].

	==See Also==		==See Also==
Line 17:		Line 17:
	<ref group="xtra">PMID:010074943</ref><references group="xtra"/>		<ref group="xtra">PMID:010074943</ref><references group="xtra"/>
	[[Category: Deoxyribonuclease I]]		[[Category: Deoxyribonuclease I]]
-	[[Category: Escherichia coli ~~k12~~]]	+	[[Category: Escherichia coli k-12]]
	[[Category: Hemmings, A M.]]		[[Category: Hemmings, A M.]]
	[[Category: Kleanthous, C.]]		[[Category: Kleanthous, C.]]

OCA: Protected "2gzj" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 01:21:44 GMT

Protected "2gzj" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:21, 26 July 2012

OCA at 01:21, 26 July 2012

OCA — Thu, 26 Jul 2012 01:21:43 GMT

←Older revision		Revision as of 01:21, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2gzj.png\|left\|200px]]		[[Image:2gzj.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2gzj", 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_2gzj\| PDB=2gzj \| SCENE= }}		{{STRUCTURE_2gzj\| PDB=2gzj \| SCENE= }}

	===Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A)===		===Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A)===

		+	{{ABSTRACT_PUBMED_10074943}}

	==About this Structure==		==About this Structure==
-	~~2GZJ~~ is a 4 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GZJ OCA].	+	[[2gzj]] is a 4 chain structure of [[Colicin]] and [[Colicin Immunity Protein]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GZJ OCA].
		+
		+	==See Also==
		+	*[[Colicin\|Colicin]]
		+	*[[Colicin Immunity Protein\|Colicin Immunity Protein]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~10074943~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:010074943</ref><references group="xtra"/>
	[[Category: Deoxyribonuclease I]]		[[Category: Deoxyribonuclease I]]
	[[Category: Escherichia coli k12]]		[[Category: Escherichia coli k12]]
Line 30:		Line 28:
	[[Category: Hnh-motif]]		[[Category: Hnh-motif]]
	[[Category: Protein-protein complex]]		[[Category: Protein-protein complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 6 05:36:42 2010''