This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2a6q

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:40, 13 March 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2a6q.png|left|200px]]
 
-
<!--
+
==Crystal structure of YefM-YoeB complex==
-
The line below this paragraph, containing "STRUCTURE_2a6q", creates the "Structure Box" on the page.
+
<StructureSection load='2a6q' size='340' side='right'caption='[[2a6q]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<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>
-
or leave the SCENE parameter empty for the default display.
+
</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>
-
-->
+
<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>
-
{{STRUCTURE_2a6q| PDB=2a6q | SCENE= }}
+
</table>
-
 
+
== Function ==
-
===Crystal structure of YefM-YoeB complex===
+
[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]]
-
<!--
+
Check<jmol>
-
The line below this paragraph, {{ABSTRACT_PUBMED_16109374}}, adds the Publication Abstract to the page
+
<jmolCheckbox>
-
(as it appears on PubMed at http://www.pubmed.gov), where 16109374 is the PubMed ID number.
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a6/2a6q_consurf.spt"</scriptWhenChecked>
-
-->
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
{{ABSTRACT_PUBMED_16109374}}
+
<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 Sun Jul 27 14:39:28 2008''
+

Current revision

Crystal structure of YefM-YoeB complex

PDB ID 2a6q

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2a6q"
Personal tools