4ypb: Difference between revisions

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

OCA

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 4ypb is ON HOLD
+==Precleavage 70S structure of the P. vulgaris HigB DeltaH92 toxin bound to the AAA codon==
+<StructureSection load='4ypb' size='340' side='right'caption='[[4ypb]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4ypb]] 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=4YPB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YPB 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]] 3.4&#8491;</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=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=4ypb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ypb OCA], [https://pdbe.org/4ypb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ypb RCSB], [https://www.ebi.ac.uk/pdbsum/4ypb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ypb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RL24_THET8 RL24_THET8] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_B]  One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_B]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Bacteria contain multiple type II toxins that selectively degrade mRNAs bound to the ribosome to regulate translation and growth and facilitate survival during the stringent response. Ribosome-dependent toxins recognize a variety of three-nucleotide codons within the aminoacyl (A) site, but how these endonucleases achieve substrate specificity remains poorly understood. Here, we identify the critical features for how the host inhibition of growth B (HigB) toxin recognizes each of the three A-site nucleotides for cleavage. X-ray crystal structures of HigB bound to two different codons on the ribosome illustrate how HigB uses a microbial RNase-like nucleotide recognition loop to recognize either cytosine or adenosine at the second A-site position. Strikingly, a single HigB residue and 16S rRNA residue C1054 form an adenosine-specific pocket at the third A-site nucleotide, in contrast to how tRNAs decode mRNA. Our results demonstrate that the most important determinant for mRNA cleavage by ribosome-dependent toxins is interaction with the third A-site nucleotide.
-Authors: Schureck, M.A., Maehigashi, T., Dunkle, J.A., Dunham, C.M.
+Defining the mRNA recognition signature of a bacterial toxin protein.,Schureck MA, Dunkle JA, Maehigashi T, Miles SJ, Dunham CM Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):13862-7. doi:, 10.1073/pnas.1512959112. Epub 2015 Oct 27. PMID:26508639<ref>PMID:26508639</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Maehigashi, T]]
+<div class="pdbe-citations 4ypb" style="background-color:#fffaf0;"></div>
-[[Category: Schureck, M.A]]
-[[Category: Dunham, C.M]]
+==See Also==
-[[Category: Dunkle, J.A]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Thermus thermophilus HB8]]
+[[Category: Dunham CM]]
+[[Category: Dunkle JA]]
+[[Category: Maehigashi T]]
+[[Category: Schureck MA]]