2dfx: Difference between revisions

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<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 ==
== 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]] 1.9&#8491;</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]]
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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].
</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&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==
==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]]

Latest revision as of 16:47, 13 March 2024

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

Structural highlights

2dfx is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CEA5_ECOLX Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria. This colicin is an endonuclease.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2dfx, resolution 1.90Å

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