2dfx

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{{Seed}}
 
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[[Image:2dfx.png|left|200px]]
 
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==Crystal structure of the carboxy terminal domain of colicin E5 complexed with its inhibitor==
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The line below this paragraph, containing "STRUCTURE_2dfx", creates the "Structure Box" on the page.
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<StructureSection load='2dfx' size='340' side='right'caption='[[2dfx]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<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>
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{{STRUCTURE_2dfx| PDB=2dfx | SCENE= }}
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/2dfx_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2dfx ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Crystal structure of the carboxy terminal domain of colicin E5 complexed with its inhibitor===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2dfx" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_17099236}}, adds the Publication Abstract to the page
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*[[Colicin 3D structures|Colicin 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 17099236 is the PubMed ID number.
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*[[Colicin immunity protein 3D structures|Colicin immunity protein 3D structures]]
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== References ==
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{{ABSTRACT_PUBMED_17099236}}
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<references/>
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__TOC__
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==About this Structure==
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</StructureSection>
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2DFX is a 2 chains structure of sequences 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].
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==Reference==
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<ref group="xtra">PMID:17099236</ref><references group="xtra"/>
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Inoue, S.]]
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[[Category: Large Structures]]
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[[Category: Masaki, H.]]
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[[Category: Inoue S]]
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[[Category: Nonaka, T.]]
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[[Category: Masaki H]]
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[[Category: Ogawa, T.]]
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[[Category: Nonaka T]]
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[[Category: Ohsawa, K.]]
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[[Category: Ogawa T]]
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[[Category: Yajima, S.]]
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[[Category: Ohsawa K]]
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[[Category: Alpha/beta protein]]
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[[Category: Yajima S]]
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[[Category: Protein-inhibitor protein complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:01:37 2009''
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Current revision

Crystal structure of the carboxy terminal domain of colicin E5 complexed with its inhibitor

PDB ID 2dfx

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