2dfx - Revision history

OCA at 13:47, 13 March 2024

2024-03-13T13:47:27Z

←Older revision		Revision as of 13:47, 13 March 2024
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	<StructureSection load='2dfx' size='340' side='right'caption='[[2dfx]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dfx' size='340' side='right'caption='[[2dfx]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dfx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DFX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dfx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DFX FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>~~[[~~2djh~~\|~~2djh~~]]~~</div>~~</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]] 1.9Å</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=2dfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfx OCA], [https://pdbe.org/2dfx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dfx RCSB], [https://www.ebi.ac.uk/pdbsum/2dfx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dfx 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=2dfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfx OCA], [https://pdbe.org/2dfx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dfx RCSB], [https://www.ebi.ac.uk/pdbsum/2dfx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dfx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CEA5_ECOLX CEA5_ECOLX]] Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria. This colicin is an endonuclease~~. [[https://www.uniprot.org/uniprot/IMM5_ECOLX IMM5_ECOLX]] This protein is able to protect a cell, which harbors the plasmid ColE5 encoding colicin E5, against colicin E5~~.	+	[https://www.uniprot.org/uniprot/CEA5_ECOLX CEA5_ECOLX] Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria. This colicin is an endonuclease.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 19:
	</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=2dfx 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=2dfx ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Colicin E5--a tRNase toxin--specifically cleaves QUN (Q: queuosine) anticodons of the Escherichia coli tRNAs for Tyr, His, Asn and Asp. Here, we report the crystal structure of the C-terminal ribonuclease domain (CRD) of E5 complexed with a substrate analog, namely, dGpdUp, at a resolution of 1.9 A. Thisstructure is the first to reveal the substrate recognition mechanism of sequence-specific ribonucleases. E5-CRD realized the strict recognition for both the guanine and uracil bases of dGpdUp forming Watson-Crick-type hydrogen bonds and ring stacking interactions, thus mimicking the codons of mRNAs to bind to tRNA anticodons. The docking model of E5-CRD with tRNA also suggests its substrate preference for tRNA over ssRNA. In addition, the structure of E5-CRD/dGpdUp along with the mutational analysis suggests that Arg33 may play an important role in the catalytic activity, and Lys25/Lys60 may also be involved without His in E5-CRD. Finally, the comparison of the structures of E5-CRD/dGpdUp and E5-CRD/ImmE5 (an inhibitor protein) complexes suggests that the binding mode of E5-CRD and ImmE5 mimics that of mRNA and tRNA; this may represent the evolutionary pathway of these proteins from the RNA-RNA interaction through the RNA-protein interaction of tRNA/E5-CRD.
-
-	Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction.,Yajima S, Inoue S, Ogawa T, Nonaka T, Ohsawa K, Masaki H Nucleic Acids Res. 2006;34(21):6074-82. Epub 2006 Nov 11. PMID:17099236<ref>PMID:17099236</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2dfx" 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: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Inoue, S]]	+	[[Category: Inoue S]]
-	[[Category: Masaki, H]]	+	[[Category: Masaki H]]
-	[[Category: Nonaka, T]]	+	[[Category: Nonaka T]]
-	[[Category: Ogawa, T]]	+	[[Category: Ogawa T]]
-	[[Category: Ohsawa, K]]	+	[[Category: Ohsawa K]]
-	[[Category: Yajima, S]]	+	[[Category: Yajima S]]
-	~~[[Category: Alpha/beta protein]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protein-inhibitor protein complex~~]]	+

OCA at 10:31, 8 December 2021

2021-12-08T10:31:12Z

←Older revision		Revision as of 10:31, 8 December 2021
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	<StructureSection load='2dfx' size='340' side='right'caption='[[2dfx]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dfx' size='340' side='right'caption='[[2dfx]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dfx]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DFX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dfx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DFX FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2djh\|2djh]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2djh\|2djh]]</div></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=2dfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfx OCA], [~~http~~://pdbe.org/2dfx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dfx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dfx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dfx 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=2dfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfx OCA], [https://pdbe.org/2dfx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dfx RCSB], [https://www.ebi.ac.uk/pdbsum/2dfx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dfx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CEA5_ECOLX CEA5_ECOLX]] Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria. This colicin is an endonuclease. [[~~http~~://www.uniprot.org/uniprot/IMM5_ECOLX IMM5_ECOLX]] This protein is able to protect a cell, which harbors the plasmid ColE5 encoding colicin E5, against colicin E5.	+	[[https://www.uniprot.org/uniprot/CEA5_ECOLX CEA5_ECOLX]] Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria. This colicin is an endonuclease. [[https://www.uniprot.org/uniprot/IMM5_ECOLX IMM5_ECOLX]] This protein is able to protect a cell, which harbors the plasmid ColE5 encoding colicin E5, against colicin E5.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:52, 4 March 2020

2020-03-04T07:52:07Z

←Older revision		Revision as of 07:52, 4 March 2020
Line 1:		Line 1:

	==Crystal structure of the carboxy terminal domain of colicin E5 complexed with its inhibitor==		==Crystal structure of the carboxy terminal domain of colicin E5 complexed with its inhibitor==
-	<StructureSection load='2dfx' size='340' side='right' caption='[[2dfx]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='2dfx' size='340' side='right'caption='[[2dfx]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFX FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFX FirstGlance]. <br>
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Colicin\|Colicin]]	+	*[[Colicin 3D structures\|Colicin 3D structures]]
-	*[[Colicin ~~Immunity Protein~~\|Colicin ~~Immunity Protein~~]]	+	*[[Colicin immunity protein 3D structures\|Colicin immunity protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Inoue, S]]		[[Category: Inoue, S]]
	[[Category: Masaki, H]]		[[Category: Masaki, H]]

OCA at 06:42, 30 May 2018

2018-05-30T06:42:19Z

←Older revision		Revision as of 06:42, 30 May 2018
Line 1:		Line 1:
		+
	==Crystal structure of the carboxy terminal domain of colicin E5 complexed with its inhibitor==		==Crystal structure of the carboxy terminal domain of colicin E5 complexed with its inhibitor==
	<StructureSection load='2dfx' size='340' side='right' caption='[[2dfx]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dfx' size='340' side='right' caption='[[2dfx]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2dfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFX FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFX FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2djh\|2djh]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2djh\|2djh]]</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=2dfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfx OCA], [http://pdbe.org/2dfx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dfx RCSB], [http://www.ebi.ac.uk/pdbsum/2dfx 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=2dfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfx OCA], [http://pdbe.org/2dfx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dfx RCSB], [http://www.ebi.ac.uk/pdbsum/2dfx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dfx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/2dfx_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/2dfx_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>

OCA at 03:16, 9 February 2016

2016-02-09T03:16:13Z

←Older revision		Revision as of 03:16, 9 February 2016
Line 16:		Line 16:
	<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=2dfx ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 18:04, 10 September 2015

2015-09-10T18:04:26Z

←Older revision		Revision as of 18:04, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2dfx' size='340' side='right' caption='[[2dfx]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dfx' size='340' side='right' caption='[[2dfx]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFX FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2djh\|2djh]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2djh\|2djh]]</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=2dfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dfx RCSB], [http://www.ebi.ac.uk/pdbsum/2dfx 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=2dfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfx OCA], [http://pdbe.org/2dfx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dfx RCSB], [http://www.ebi.ac.uk/pdbsum/2dfx PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CEA5_ECOLX CEA5_ECOLX]] Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria. This colicin is an endonuclease. [[http://www.uniprot.org/uniprot/IMM5_ECOLX IMM5_ECOLX]] This protein is able to protect a cell, which harbors the plasmid ColE5 encoding colicin E5, against colicin E5.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 24:		Line 26:
	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 2dfx" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Inoue, S]]		[[Category: Inoue, S]]
	[[Category: Masaki, H]]		[[Category: Masaki, H]]

OCA at 16:57, 15 January 2015

2015-01-15T16:57:40Z

←Older revision		Revision as of 16:57, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFX FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFX FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2djh\|2djh]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2djh\|2djh]]</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=2dfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dfx RCSB], [http://www.ebi.ac.uk/pdbsum/2dfx 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=2dfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dfx RCSB], [http://www.ebi.ac.uk/pdbsum/2dfx 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 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Inoue, S.]]	+	[[Category: Inoue, S]]
-	[[Category: Masaki, H.]]	+	[[Category: Masaki, H]]
-	[[Category: Nonaka, T.]]	+	[[Category: Nonaka, T]]
-	[[Category: Ogawa, T.]]	+	[[Category: Ogawa, T]]
-	[[Category: Ohsawa, K.]]	+	[[Category: Ohsawa, K]]
-	[[Category: Yajima, S.]]	+	[[Category: Yajima, S]]
	[[Category: Alpha/beta protein]]		[[Category: Alpha/beta protein]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Protein-inhibitor protein complex]]		[[Category: Protein-inhibitor protein complex]]

OCA at 03:40, 29 September 2014

2014-09-29T03:40:40Z

←Older revision		Revision as of 03:40, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2dfx.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the carboxy terminal domain of colicin E5 complexed with its inhibitor==
		+	<StructureSection load='2dfx' size='340' side='right' caption='[[2dfx]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2dfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFX FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2djh\|2djh]]</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=2dfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dfx RCSB], [http://www.ebi.ac.uk/pdbsum/2dfx 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/df/2dfx_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 ==
		+	Colicin E5--a tRNase toxin--specifically cleaves QUN (Q: queuosine) anticodons of the Escherichia coli tRNAs for Tyr, His, Asn and Asp. Here, we report the crystal structure of the C-terminal ribonuclease domain (CRD) of E5 complexed with a substrate analog, namely, dGpdUp, at a resolution of 1.9 A. Thisstructure is the first to reveal the substrate recognition mechanism of sequence-specific ribonucleases. E5-CRD realized the strict recognition for both the guanine and uracil bases of dGpdUp forming Watson-Crick-type hydrogen bonds and ring stacking interactions, thus mimicking the codons of mRNAs to bind to tRNA anticodons. The docking model of E5-CRD with tRNA also suggests its substrate preference for tRNA over ssRNA. In addition, the structure of E5-CRD/dGpdUp along with the mutational analysis suggests that Arg33 may play an important role in the catalytic activity, and Lys25/Lys60 may also be involved without His in E5-CRD. Finally, the comparison of the structures of E5-CRD/dGpdUp and E5-CRD/ImmE5 (an inhibitor protein) complexes suggests that the binding mode of E5-CRD and ImmE5 mimics that of mRNA and tRNA; this may represent the evolutionary pathway of these proteins from the RNA-RNA interaction through the RNA-protein interaction of tRNA/E5-CRD.

-	~~{{STRUCTURE_2dfx\| PDB=2dfx \| SCENE= }}~~	+	Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction.,Yajima S, Inoue S, Ogawa T, Nonaka T, Ohsawa K, Masaki H Nucleic Acids Res. 2006;34(21):6074-82. Epub 2006 Nov 11. PMID:17099236<ref>PMID:17099236</ref>

-	~~===Crystal structure~~ of the ~~carboxy terminal domain of colicin E5 complexed with its inhibitor===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17099236}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2dfx]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX 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:017099236<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Inoue, S.]]		[[Category: Inoue, S.]]

OCA at 12:27, 20 October 2012

2012-10-20T12:27:19Z

←Older revision		Revision as of 12:27, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[2dfx]] is a 2 chain structure ~~of [[Colicin]] and [[Colicin Immunity Protein]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA].	+	[[2dfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFX OCA].

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

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

2012-07-26T08:46:18Z

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

←Older revision

Revision as of 08:46, 26 July 2012