2a6q: Difference between revisions

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[[Image:2a6q.gif|left|200px]]


{{Structure
==Crystal structure of YefM-YoeB complex==
|PDB= 2a6q |SIZE=350|CAPTION= <scene name='initialview01'>2a6q</scene>, resolution 2.05&Aring;
<StructureSection load='2a6q' size='340' side='right'caption='[[2a6q]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[2a6q]] is a 6 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=2A6Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A6Q 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]] 2.05&#8491;</td></tr>
|GENE= yefM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), yoeB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2a6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6q OCA], [https://pdbe.org/2a6q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a6q RCSB], [https://www.ebi.ac.uk/pdbsum/2a6q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a6q ProSAT]</span></td></tr>
|DOMAIN=
</table>
|RELATEDENTRY=[[2a6r|2A6R]], [[2a6s|2A6S]]
== Function ==
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6q OCA], [http://www.ebi.ac.uk/pdbsum/2a6q PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2a6q RCSB]</span>
[https://www.uniprot.org/uniprot/YOEB_ECOLI YOEB_ECOLI] Toxic component of a toxin-antitoxin (TA) module. Its mode of function is controversial; it has been proposed to be an mRNA interferase but also an inhibitor of translation initiation. When overproduced in wild-type cells, inhibits bacterial growth and translation by cleavage of mRNA molecules while it has a weak effect on colony forming ability. Overproduction of Lon protease specifically activates YoeB-dependent mRNA cleavage, leading to lethality. YefM binds to the promoter region of the yefM-yeoB operon to repress transcription, YeoB acts as a corepressor.<ref>PMID:14672926</ref> <ref>PMID:15009896</ref> <ref>PMID:17170003</ref> <ref>PMID:18854355</ref> <ref>PMID:19028895</ref> <ref>PMID:19124462</ref> <ref>PMID:19400780</ref> <ref>PMID:16109374</ref>  Shown in vitro to be an mRNA interferase that requires translation for substrate cleavage; if the mRNA is mutated so as to not be translatable it is no longer cleaved. Cleavage only occurs within translated regions. Has RNase activity and preferentially cleaves at the 3'-end of purine ribonucleotides.<ref>PMID:14672926</ref> <ref>PMID:15009896</ref> <ref>PMID:17170003</ref> <ref>PMID:18854355</ref> <ref>PMID:19028895</ref> <ref>PMID:19124462</ref> <ref>PMID:19400780</ref> <ref>PMID:16109374</ref>  Also shown in vitro to be a translation initiation blocker. Binds to the 70S ribosome and 50S ribosomal subunit; binding is inhibited by hygromycin A and tetracycline, both of which bind to the 30S subunit in the A site. Thus YoeB is located at the interface between 50S and 30S ribosomes and interacts with the A site where it cleaves mRNA, blocking translation initiation.<ref>PMID:14672926</ref> <ref>PMID:15009896</ref> <ref>PMID:17170003</ref> <ref>PMID:18854355</ref> <ref>PMID:19028895</ref> <ref>PMID:19124462</ref> <ref>PMID:19400780</ref> <ref>PMID:16109374</ref>
}}
== Evolutionary Conservation ==
 
[[Image:Consurf_key_small.gif|200px|right]]
'''Crystal structure of YefM-YoeB complex'''
Check<jmol>
 
  <jmolCheckbox>
 
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a6/2a6q_consurf.spt"</scriptWhenChecked>
==Overview==
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
The eubacterial chromosome encodes various addiction modules that control global levels of translation through RNA degradation. Crystal structures of the Escherichia coli YefM2 (antitoxin)-YoeB (toxin) complex and the free YoeB toxin have been determined. The structure of the heterotrimeric complex reveals an asymmetric disorder-to-order recognition strategy, in which one C terminus of the YefM homodimer exclusively interacts with an atypical microbial ribonuclease (RNase) fold of YoeB. Comparison with the YefM-free YoeB structure indicates a conformational rearrangement of the RNase catalytic site of YoeB, induced by interaction with YefM. Complementary biochemical experiments demonstrate that the YoeB toxin has an in vitro RNase activity that preferentially cleaves at the 3' end of purine ribonucleotides.
    <text>to colour the structure by Evolutionary Conservation</text>
 
  </jmolCheckbox>
==About this Structure==
</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=2a6q ConSurf].
2A6Q 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=2A6Q OCA].  
<div style="clear:both"></div>
 
== References ==
==Reference==
<references/>
Conformational change in the catalytic site of the ribonuclease YoeB toxin by YefM antitoxin., Kamada K, Hanaoka F, Mol Cell. 2005 Aug 19;19(4):497-509. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16109374 16109374]
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Hanaoka, F.]]
[[Category: Hanaoka F]]
[[Category: Kamada, K.]]
[[Category: Kamada K]]
[[Category: addiction module]]
[[Category: antitoxin]]
[[Category: inhibitor]]
[[Category: rnase]]
[[Category: toxin]]
[[Category: yefm]]
[[Category: yoeb]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:48:39 2008''
Retrieved from "https://proteopedia.org/2a6q"