2uub

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[[Image:2uub.png|left|200px]]
 
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{{STRUCTURE_2uub| PDB=2uub | SCENE= }}
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==Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a Valine-ASL with cmo5U in position 34 bound to an mRNA with a GUU-codon in the A-site and paromomycin.==
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<StructureSection load='2uub' size='340' side='right'caption='[[2uub]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2uub]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UUB FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=CM0:5-(CARBOXYMETHOXY)+URIDINE-5-MONOPHOSPHATE'>CM0</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2uub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2uub OCA], [https://pdbe.org/2uub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2uub RCSB], [https://www.ebi.ac.uk/pdbsum/2uub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2uub ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RS20_THET8 RS20_THET8] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the bottom of the body of the 30S subunit, by binding to several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00500]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uu/2uub_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2uub ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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One of the most prevalent base modifications involved in decoding is uridine 5-oxyacetic acid at the wobble position of tRNA. It has been known for several decades that this modification enables a single tRNA to decode all four codons in a degenerate codon box. We have determined structures of an anticodon stem-loop of tRNA(Val) containing the modified uridine with all four valine codons in the decoding site of the 30S ribosomal subunit. An intramolecular hydrogen bond involving the modification helps to prestructure the anticodon loop. We found unusual base pairs with the three noncomplementary codon bases, including a G.U base pair in standard Watson-Crick geometry, which presumably involves an enol form for the uridine. These structures suggest how a modification in the uridine at the wobble position can expand the decoding capability of a tRNA.
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===STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH A VALINE-ASL WITH CMO5U IN POSITION 34 BOUND TO AN MRNA WITH A GUU-CODON IN THE A-SITE AND PAROMOMYCIN.===
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Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines.,Weixlbaumer A, Murphy FV 4th, Dziergowska A, Malkiewicz A, Vendeix FA, Agris PF, Ramakrishnan V Nat Struct Mol Biol. 2007 Jun;14(6):498-502. Epub 2007 May 13. PMID:17496902<ref>PMID:17496902</ref>
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{{ABSTRACT_PUBMED_17496902}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==About this Structure==
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<div class="pdbe-citations 2uub" style="background-color:#fffaf0;"></div>
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[[2uub]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UUB OCA].
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==See Also==
==See Also==
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*[[Ribosomal protein S10|Ribosomal protein S10]]
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*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
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*[[Ribosomal protein S11|Ribosomal protein S11]]
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*[[Ribosome 3D structures|Ribosome 3D structures]]
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*[[Ribosomal protein S12|Ribosomal protein S12]]
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== References ==
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*[[Ribosomal protein S13|Ribosomal protein S13]]
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<references/>
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*[[Ribosomal protein S14|Ribosomal protein S14]]
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__TOC__
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*[[Ribosomal protein S15|Ribosomal protein S15]]
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</StructureSection>
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*[[Ribosomal protein S16|Ribosomal protein S16]]
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[[Category: Large Structures]]
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*[[Ribosomal protein S17|Ribosomal protein S17]]
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[[Category: Synthetic construct]]
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*[[Ribosomal protein S18|Ribosomal protein S18]]
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[[Category: Thermus thermophilus HB8]]
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*[[Ribosomal protein S19|Ribosomal protein S19]]
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[[Category: Agris PF]]
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*[[Ribosomal protein S2|Ribosomal protein S2]]
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[[Category: Dziergowska A]]
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*[[Ribosomal protein S20|Ribosomal protein S20]]
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[[Category: Malkiewicz A]]
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*[[Ribosomal protein S3|Ribosomal protein S3]]
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[[Category: Murphy FV]]
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*[[Ribosomal protein S4|Ribosomal protein S4]]
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[[Category: Ramakrishnan V]]
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*[[Ribosomal protein S5|Ribosomal protein S5]]
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[[Category: Vendeix FAP]]
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*[[Ribosomal protein S6|Ribosomal protein S6]]
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[[Category: Weixlbaumer A]]
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*[[Ribosomal protein S7|Ribosomal protein S7]]
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*[[Ribosomal protein S8|Ribosomal protein S8]]
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*[[Ribosomal protein S9|Ribosomal protein S9]]
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*[[Ribosomal protein THX|Ribosomal protein THX]]
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==Reference==
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<ref group="xtra">PMID:017496902</ref><references group="xtra"/>
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[[Category: Thermus thermophilus]]
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[[Category: Agris, P F.]]
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[[Category: Dziergowska, A.]]
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[[Category: Malkiewicz, A.]]
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[[Category: Murphy, F V.]]
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[[Category: Ramakrishnan, V.]]
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[[Category: Vendeix, F A.P.]]
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[[Category: Weixlbaumer, A.]]
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[[Category: Cmo5u]]
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[[Category: Metal-binding]]
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[[Category: Modification]]
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[[Category: Mrna]]
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[[Category: Paromomycin]]
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[[Category: Ribonucleoprotein]]
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[[Category: Ribosomal protein]]
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[[Category: Ribosome]]
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[[Category: Rna-binding]]
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[[Category: Rrna-binding]]
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[[Category: Translation]]
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[[Category: Trna]]
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[[Category: Trna-binding]]
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[[Category: Zinc-finger]]
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Current revision

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a Valine-ASL with cmo5U in position 34 bound to an mRNA with a GUU-codon in the A-site and paromomycin.

PDB ID 2uub

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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