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==Structure of the E. coli colicin D bound to its immunity protein ImmD== | |||
<StructureSection load='1v74' size='340' side='right'caption='[[1v74]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1v74]] 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=1V74 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V74 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]] 2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</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=1v74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v74 OCA], [https://pdbe.org/1v74 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v74 RCSB], [https://www.ebi.ac.uk/pdbsum/1v74 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v74 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CEAD_ECOLX CEAD_ECOLX] Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria. Colicin D inhibits protein synthesis. | |||
== 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/v7/1v74_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/main_output.php?pdb_ID=1v74 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Colicins are toxins secreted by Escherichia coli in order to kill their competitors. Colicin D is a 75 kDa protein that consists of a translocation domain, a receptor-binding domain and a cytotoxic domain, which specifically cleaves the anticodon loop of all four tRNA(Arg) isoacceptors, thereby inactivating protein synthesis and leading to cell death. Here we report the 2.0 A resolution crystal structure of the complex between the toxic domain and its immunity protein ImmD. Neither component shows structural homology to known RNases or their inhibitors. In contrast to other characterized colicin nuclease-Imm complexes, the colicin D active site pocket is completely blocked by ImmD, which, by bringing a negatively charged cluster in opposition to a positively charged cluster on the surface of colicin D, appears to mimic the tRNA substrate backbone. Site-directed mutations affecting either the catalytic domain or the ImmD protein have led to the identification of the residues vital for catalytic activity and for the tight colicin D/ImmD interaction that inhibits colicin D toxicity and tRNase catalytic activity. | |||
Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein.,Graille M, Mora L, Buckingham RH, van Tilbeurgh H, de Zamaroczy M EMBO J. 2004 Apr 7;23(7):1474-82. Epub 2004 Mar 11. PMID:15014439<ref>PMID:15014439</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1v74" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Colicin 3D structures|Colicin 3D structures]] | |||
*[[Colicin immunity protein 3D structures|Colicin immunity protein 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Buckingham | [[Category: Buckingham RH]] | ||
[[Category: Graille | [[Category: Graille M]] | ||
[[Category: Mora | [[Category: Mora L]] | ||
[[Category: De Zamaroczy M]] | |||
[[Category: Zamaroczy | [[Category: Van Tilbeurgh H]] | ||
[[Category: | |||
Latest revision as of 02:58, 28 December 2023
Structure of the E. coli colicin D bound to its immunity protein ImmDStructure of the E. coli colicin D bound to its immunity protein ImmD
Structural highlights
FunctionCEAD_ECOLX Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria. Colicin D inhibits protein synthesis. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedColicins are toxins secreted by Escherichia coli in order to kill their competitors. Colicin D is a 75 kDa protein that consists of a translocation domain, a receptor-binding domain and a cytotoxic domain, which specifically cleaves the anticodon loop of all four tRNA(Arg) isoacceptors, thereby inactivating protein synthesis and leading to cell death. Here we report the 2.0 A resolution crystal structure of the complex between the toxic domain and its immunity protein ImmD. Neither component shows structural homology to known RNases or their inhibitors. In contrast to other characterized colicin nuclease-Imm complexes, the colicin D active site pocket is completely blocked by ImmD, which, by bringing a negatively charged cluster in opposition to a positively charged cluster on the surface of colicin D, appears to mimic the tRNA substrate backbone. Site-directed mutations affecting either the catalytic domain or the ImmD protein have led to the identification of the residues vital for catalytic activity and for the tight colicin D/ImmD interaction that inhibits colicin D toxicity and tRNase catalytic activity. Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein.,Graille M, Mora L, Buckingham RH, van Tilbeurgh H, de Zamaroczy M EMBO J. 2004 Apr 7;23(7):1474-82. Epub 2004 Mar 11. PMID:15014439[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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