Proteopedia

1v74: Difference between revisions

← Older edit
No edit summary
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1v74.gif|left|200px]]


{{Structure
==Structure of the E. coli colicin D bound to its immunity protein ImmD==
|PDB= 1v74 |SIZE=350|CAPTION= <scene name='initialview01'>1v74</scene>, resolution 2.0&Aring;
<StructureSection load='1v74' size='340' side='right'caption='[[1v74]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=1PE:PENTAETHYLENE GLYCOL'>1PE</scene>
<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>
|ACTIVITY=  
</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&#8491;</td></tr>
|GENE=  
<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.


'''ribonuclease-inhibitor complex'''
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1v74" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
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.
*[[Colicin 3D structures|Colicin 3D structures]]
 
*[[Colicin immunity protein 3D structures|Colicin immunity protein 3D structures]]
==About this Structure==
== References ==
1V74 is a [[Protein complex]] 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=1V74 OCA].
<references/>
 
__TOC__
==Reference==
</StructureSection>
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:[http://www.ncbi.nlm.nih.gov/pubmed/15014439 15014439]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Buckingham, R H.]]
[[Category: Buckingham RH]]
[[Category: Graille, M.]]
[[Category: Graille M]]
[[Category: Mora, L.]]
[[Category: Mora L]]
[[Category: Tilbeurgh, H van.]]
[[Category: De Zamaroczy M]]
[[Category: Zamaroczy, M de.]]
[[Category: Van Tilbeurgh H]]
[[Category: 1PE]]
[[Category: colicin d - immd complex]]
[[Category: cytotoxicity]]
[[Category: protein-protein inhibition]]
[[Category: transfer rnase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:41:43 2008''

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/w/1v74"