View source for 6mpf


==Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a 2-thiocytidine (s2C32) and inosine (I34) modified anticodon stem loop (ASL) of Escherichia coli transfer RNA Arginine 1 (TRNAARG1) bound to an mRNA with an CGC-codon in the A-site and paromomycin==
<StructureSection load='6mpf' size='340' side='right'caption='[[6mpf]], [[Resolution|resolution]] 3.33&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6mpf]] is a 10 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=6MPF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MPF 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]] 3.33&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=RSP:4-AMINO-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)PYRIMIDINE-2(1H)-THIONE'>RSP</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=6mpf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mpf OCA], [https://pdbe.org/6mpf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mpf RCSB], [https://www.ebi.ac.uk/pdbsum/6mpf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mpf ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]
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== Publication Abstract from PubMed ==
Three of six arginine codons (CGU, CGC and CGA) are decoded by two Escherichia coli tRNA(Arg) isoacceptors. The anticodon stem and loop (ASL) domains of tRNA(Arg1) and tRNA(Arg2) both contain inosine and 2-methyladenosine modifications at positions 34 (I34) and 37 (m(2)A37). tRNA(Arg1) is also modified from cytidine to 2-thiocytidine at position 32 (s(2)C32). The s(2)C32 modification is known to negate wobble codon recognition of the rare CGA codon by an unknown mechanism, while still allowing decoding of CGU and CGC. Substitution of s(2)C32 for C32 in the Saccharomyces cerevisiae tRNA(Ile)IAU anticodon stem and loop domain (ASL) negates wobble decoding of its synonymous A-ending codon, suggesting that this function of s(2)C at position 32 is a generalizable property. X-ray crystal structures of variously modified ASL(Arg1)ICG and ASL(Arg2)ICG constructs bound to cognate and wobble codons on the ribosome revealed the disruption of a C32-A38 cross-loop interaction, but failed to fully explain the means by which s(2)C32 restricts I34 wobbling. Computational studies revealed that the adoption of a spatially broad inosine-adenosine base pair at the wobble position of the codon cannot be maintained simultaneously with the canonical ASL U-turn motif. C32-A38 cross-loop interactions are required for stability of the anticodon/codon interaction in the ribosomal A-site.

A structural basis for restricted codon recognition mediated by 2-thiocytidine in tRNA containing a wobble position inosine.,Vangaveti S, Cantara WA, Spears JL, DeMirci H, Murphy FV 4th, Ranganathan SV, Sarachan KL, Agris PF J Mol Biol. 2020 Jan 13. pii: S0022-2836(19)30716-8. doi:, 10.1016/j.jmb.2019.12.016. PMID:31945376<ref>PMID:31945376</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 6mpf" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Thermus thermophilus HB8]]
[[Category: Agris PF]]
[[Category: Cantara WA]]
[[Category: DeMirci H]]