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.
6oxa
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 6oxa is ON HOLD Authors: Hoffer, E.D., Pavelich, I.P., Maehigashi, T., Dunham, C.M. Description: Dimeric E.coli YoeB bound to Thermus thermophilus ...) |
|||
| (4 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==Dimeric E.coli YoeB bound to Thermus thermophilus 70S pre-cleavage (AAU)== | |
| + | <StructureSection load='6oxa' size='340' side='right'caption='[[6oxa]], [[Resolution|resolution]] 3.25Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6oxa]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OXA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OXA 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]] 3.25Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PPU:PUROMYCIN-5-MONOPHOSPHATE'>PPU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6oxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oxa OCA], [https://pdbe.org/6oxa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6oxa RCSB], [https://www.ebi.ac.uk/pdbsum/6oxa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6oxa ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Chromosomally-encoded toxin-antitoxin complexes are ubiquitous in bacteria and regulate growth through the release of the toxin component typically in a stress-dependent manner. Type II ribosome-dependent toxins adopt a RelE-family RNase fold and inhibit translation by degrading mRNAs while bound to the ribosome. Here, we present biochemical and structural studies of the Escherichia coli YoeB toxin interacting with both a UAA stop and an AAU sense codon in pre- and post-mRNA cleavage states to provide insights into possible mRNA substrate selection. Both mRNAs undergo minimal changes during the cleavage event in contrast to type II ribosome-dependent RelE toxin. Further, the 16S rRNA decoding site nucleotides that monitor the mRNA in the aminoacyl(A) site adopt different orientations depending upon which toxin is present. Although YoeB is a RelE family member, it is the sole ribosome-dependent toxin that is dimeric. We show that engineered monomeric YoeB is active against mRNAs bound to both the small and large subunit. However, the stability of monomeric YoeB is reduced approximately 20 degrees C, consistent with potential YoeB activation during heat shock in E. coli as previously demonstrated. These data provide a molecular basis for the ability of YoeB to function in response to thermal stress. | ||
| - | + | Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability.,Pavelich IJ, Maehigashi T, Hoffer ED, Ruangprasert A, Miles SJ, Dunham CM Nucleic Acids Res. 2019 Sep 10. pii: 5566584. doi: 10.1093/nar/gkz760. PMID:31501867<ref>PMID:31501867</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 6oxa" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | |
| - | [[Category: Hoffer | + | ==See Also== |
| - | [[Category: | + | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Thermus thermophilus HB8]] | ||
| + | [[Category: Dunham CM]] | ||
| + | [[Category: Hoffer ED]] | ||
| + | [[Category: Maehigashi T]] | ||
| + | [[Category: Pavelich IJ]] | ||
Current revision
Dimeric E.coli YoeB bound to Thermus thermophilus 70S pre-cleavage (AAU)
| |||||||||||
