2uuc: Difference between revisions

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-[[Image:2uuc.png|left|200px]]
-{{STRUCTURE_2uuc|  PDB=2uuc  |  SCENE=  }}
+==Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a Valine-ASL with cmo5U in position 34 bound to an mRNA with a GUA-codon in the A-site and paromomycin.==
+<StructureSection load='2uuc' size='340' side='right'caption='[[2uuc]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2uuc]] 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=2UUC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UUC 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]] 3.1&#8491;</td></tr>
+<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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2uuc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2uuc OCA], [https://pdbe.org/2uuc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2uuc RCSB], [https://www.ebi.ac.uk/pdbsum/2uuc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2uuc 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]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uu/2uuc_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2uuc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-===STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH A VALINE-ASL WITH CMO5U IN POSITION 34 BOUND TO AN MRNA WITH A GUA-CODON IN THE A-SITE AND PAROMOMYCIN.===
+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>
-{{ABSTRACT_PUBMED_17496902}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2uuc" style="background-color:#fffaf0;"></div>
-[[2uuc]] is a 23 chain structure of [[Ribosomal protein S10]], [[Ribosomal protein S11]], [[Ribosomal protein S12]], [[Ribosomal protein S13]], [[Ribosomal protein S14]], [[Ribosomal protein S15]], [[Ribosomal protein S16]], [[Ribosomal protein S17]], [[Ribosomal protein S18]], [[Ribosomal protein S19]], [[Ribosomal protein S2]], [[Ribosomal protein S20]], [[Ribosomal protein S3]], [[Ribosomal protein S4]], [[Ribosomal protein S5]], [[Ribosomal protein S6]], [[Ribosomal protein S7]], [[Ribosomal protein S8]], [[Ribosomal protein S9]] and [[Ribosomal protein THX]] 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=2UUC OCA].
 ==See Also==
-*[[Ribosomal protein S10|Ribosomal protein S10]]
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
-*[[Ribosomal protein S11|Ribosomal protein S11]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-*[[Ribosomal protein S12|Ribosomal protein S12]]
+== References ==
-*[[Ribosomal protein S13|Ribosomal protein S13]]
+<references/>
-*[[Ribosomal protein S14|Ribosomal protein S14]]
+__TOC__
-*[[Ribosomal protein S15|Ribosomal protein S15]]
+</StructureSection>
-*[[Ribosomal protein S16|Ribosomal protein S16]]
+[[Category: Large Structures]]
-*[[Ribosomal protein S17|Ribosomal protein S17]]
+[[Category: Thermus thermophilus HB8]]
-*[[Ribosomal protein S18|Ribosomal protein S18]]
+[[Category: Agris PF]]
-*[[Ribosomal protein S19|Ribosomal protein S19]]
+[[Category: Dziergowska A]]
-*[[Ribosomal protein S2|Ribosomal protein S2]]
+[[Category: Malkiewicz A]]
-*[[Ribosomal protein S20|Ribosomal protein S20]]
+[[Category: Murphy FV]]
-*[[Ribosomal protein S3|Ribosomal protein S3]]
+[[Category: Ramakrishnan V]]
-*[[Ribosomal protein S4|Ribosomal protein S4]]
+[[Category: Vendeix FAP]]
-*[[Ribosomal protein S5|Ribosomal protein S5]]
+[[Category: Weixlbaumer A]]
-*[[Ribosomal protein S6|Ribosomal protein S6]]
-*[[Ribosomal protein S7|Ribosomal protein S7]]
-*[[Ribosomal protein S8|Ribosomal protein S8]]
-*[[Ribosomal protein S9|Ribosomal protein S9]]
-*[[Ribosomal protein THX|Ribosomal protein THX]]
-==Reference==
-<ref group="xtra">PMID:017496902</ref><references group="xtra"/>
-[[Category: Thermus thermophilus]]
-[[Category: Agris, P F.]]
-[[Category: Dziergowska, A.]]
-[[Category: Malkiewicz, A.]]
-[[Category: Murphy, F V.]]
-[[Category: Ramakrishnan, V.]]
-[[Category: Vendeix, F A.P.]]
-[[Category: Weixlbaumer, A.]]
-[[Category: Cmo5u]]
-[[Category: Decoding]]
-[[Category: Metal-binding]]
-[[Category: Modification]]
-[[Category: Mrna]]
-[[Category: Paromomycin]]
-[[Category: Ribonucleoprotein]]
-[[Category: Ribosomal protein]]
-[[Category: Ribosome]]
-[[Category: Rna-binding]]
-[[Category: Rrna-binding]]
-[[Category: Translation]]
-[[Category: Trna]]
-[[Category: Trna-binding]]
-[[Category: Zinc-finger]]