2dfx: Difference between revisions

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 ==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]] 1.90&Aring;' scene=''>
+<StructureSection load='2dfx' size='340' side='right'caption='[[2dfx]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == 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/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">[[2djh|2djh]]</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]] 1.9&#8491;</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>
 == 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.
 == Evolutionary Conservation ==
 [[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].
 <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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2dfx" style="background-color:#fffaf0;"></div>
 ==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/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Inoue, S]]
+[[Category: Large Structures]]
-[[Category: Masaki, H]]
+[[Category: Inoue S]]
-[[Category: Nonaka, T]]
+[[Category: Masaki H]]
-[[Category: Ogawa, T]]
+[[Category: Nonaka T]]
-[[Category: Ohsawa, K]]
+[[Category: Ogawa T]]
-[[Category: Yajima, S]]
+[[Category: Ohsawa K]]
-[[Category: Alpha/beta protein]]
+[[Category: Yajima S]]
-[[Category: Hydrolase]]
-[[Category: Protein-inhibitor protein complex]]