3vj7: Difference between revisions
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==Crystal structure of the carboxy-terminal ribonuclease domain of Colicin E5 R33Q mutant== | |||
<StructureSection load='3vj7' size='340' side='right'caption='[[3vj7]], [[Resolution|resolution]] 2.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3vj7]] is a 1 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=3VJ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VJ7 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PD:2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>3PD</scene>, <scene name='pdbligand=UM3:2-DEOXYURIDINE+3-MONOPHOSPHATE'>UM3</scene></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=3vj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vj7 OCA], [https://pdbe.org/3vj7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vj7 RCSB], [https://www.ebi.ac.uk/pdbsum/3vj7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vj7 ProSAT]</span></td></tr> | |||
</table> | |||
== 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. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Colicin E5 cleaves tRNAs for Tyr, His, Asn and Asp in their anticodons to abolish protein synthesis in Escherichia coli. We previously showed how its C-terminal RNase domain, E5-CRD, recognizes the anticodon bases but the catalytic mechanism remained to be elucidated. Although the reaction products with 5'-OH and 2',3'-cyclic phosphate ends suggested a similar mechanism to those of RNases A and T1, E5-CRD does not have the His residues necessary as a catalyst in usual RNases. To identify residues important for the catalytic reaction, mutants as to all residues within 5 A from the central phosphorus of the scissile phosphodiester bond were prepared. Evaluation of the killing activities of the mutant colicins and the RNase activities of the mutant E5-CRDs suggested direct involvement of Arg33, Lys25, Gln29 and Lys60 in the reaction. Particularly, Arg33 plays a critical role and Ile94 provides a structural support of Arg33. Crystal structure of the complex of E5-CRD(R33Q)/dGpdUp showed structural and binding functional integrity of this mutant protein, suggesting involvement of Arg33 in the catalytic reaction. The structure of the free E5-CRD, we also determined, showed great flexibility of a flap region, which facilitates the access of Lys60 to the substrate in an induced-fit manner. | |||
Identification of the catalytic residues of sequence-specific and histidine-free ribonuclease colicin E5.,Inoue-Ito S, Yajima S, Fushinobu S, Nakamura S, Ogawa T, Hidaka M, Masaki H J Biochem. 2012 Oct;152(4):365-72. Epub 2012 Jul 18. PMID:22815490<ref>PMID:22815490</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3vj7" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Colicin|Colicin]] | *[[Colicin 3D structures|Colicin 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Fushinobu | [[Category: Large Structures]] | ||
[[Category: Hidaka | [[Category: Fushinobu S]] | ||
[[Category: Inoue | [[Category: Hidaka M]] | ||
[[Category: Masaki | [[Category: Inoue S]] | ||
[[Category: Ogawa | [[Category: Masaki H]] | ||
[[Category: Yajima | [[Category: Ogawa T]] | ||
[[Category: Yajima S]] | |||
Latest revision as of 12:23, 8 November 2023
Crystal structure of the carboxy-terminal ribonuclease domain of Colicin E5 R33Q mutant
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