2vqf: Difference between revisions

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-[[Image:2vqf.png|left|200px]]
-{{STRUCTURE_2vqf|  PDB=2vqf  |  SCENE=  }}
+==Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U-G wobble pairing during decoding==
+<StructureSection load='2vqf' size='340' side='right'caption='[[2vqf]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2vqf]] 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=2VQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VQF 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]] 2.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=TM2:5-{[(2-SULFOETHYL)AMINO]METHYL}URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>TM2</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=2vqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vqf OCA], [https://pdbe.org/2vqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vqf RCSB], [https://www.ebi.ac.uk/pdbsum/2vqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vqf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B]  Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_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/vq/2vqf_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=2vqf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Post-transcriptional modifications at the first (wobble) position of the tRNA anticodon participate in precise decoding of the genetic code. To decode codons that end in a purine (R) (i.e. NNR), tRNAs frequently utilize 5-methyluridine derivatives (xm(5)U) at the wobble position. However, the functional properties of the C5-substituents of xm(5)U in codon recognition remain elusive. We previously found that mitochondrial tRNAs(Leu(UUR)) with pathogenic point mutations isolated from MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes) patients lacked the 5-taurinomethyluridine (taum(5)U) modification and caused a decoding defect. Here, we constructed Escherichia coli tRNAs(Leu(UUR)) with or without xm(5)U modifications at the wobble position and measured their decoding activities in an in vitro translation as well as by A-site tRNA binding. In addition, the decoding properties of tRNA(Arg) lacking mnm(5)U modification in a knock-out strain of the modifying enzyme (DeltamnmE) were examined by pulse labeling using reporter constructs with consecutive AGR codons. Our results demonstrate that the xm(5)U modification plays a critical role in decoding NNG codons by stabilizing U.G pairing at the wobble position. Crystal structures of an anticodon stem-loop containing taum(5)U interacting with a UUA or UUG codon at the ribosomal A-site revealed that the taum(5)U.G base pair does not have classical U.G wobble geometry. These structures provide help to explain how the taum(5)U modification enables efficient decoding of UUG codons.
-===MODIFIED URIDINES WITH C5-METHYLENE SUBSTITUENTS AT THE FIRST POSITION OF THE TRNA ANTICODON STABILIZE U-G WOBBLE PAIRING DURING DECODING===
+Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U.G wobble pairing during decoding.,Kurata S, Weixlbaumer A, Ohtsuki T, Shimazaki T, Wada T, Kirino Y, Takai K, Watanabe K, Ramakrishnan V, Suzuki T J Biol Chem. 2008 Jul 4;283(27):18801-11. Epub 2008 May 2. PMID:18456657<ref>PMID:18456657</ref>
-{{ABSTRACT_PUBMED_18456657}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2vqf" style="background-color:#fffaf0;"></div>
-[[2vqf]] 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=2VQF 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: Kirino Y]]
-*[[Ribosomal protein S19|Ribosomal protein S19]]
+[[Category: Kurata S]]
-*[[Ribosomal protein S2|Ribosomal protein S2]]
+[[Category: Ohtsuki T]]
-*[[Ribosomal protein S20|Ribosomal protein S20]]
+[[Category: Ramakrishnan V]]
-*[[Ribosomal protein S3|Ribosomal protein S3]]
+[[Category: Shimazaki T]]
-*[[Ribosomal protein S4|Ribosomal protein S4]]
+[[Category: Suzuki T]]
-*[[Ribosomal protein S5|Ribosomal protein S5]]
+[[Category: Takai K]]
-*[[Ribosomal protein S6|Ribosomal protein S6]]
+[[Category: Wada T]]
-*[[Ribosomal protein S7|Ribosomal protein S7]]
+[[Category: Watanabe K]]
-*[[Ribosomal protein S8|Ribosomal protein S8]]
+[[Category: Weixlbaumer A]]
-*[[Ribosomal protein S9|Ribosomal protein S9]]
-*[[Ribosomal protein THX|Ribosomal protein THX]]
-==Reference==
-<ref group="xtra">PMID:018456657</ref><references group="xtra"/>
-[[Category: Thermus thermophilus]]
-[[Category: Kirino, Y.]]
-[[Category: Kurata, S.]]
-[[Category: Ohtsuki, T.]]
-[[Category: Ramakrishnan, V.]]
-[[Category: Shimazaki, T.]]
-[[Category: Suzuki, T.]]
-[[Category: Takai, K.]]
-[[Category: Wada, T.]]
-[[Category: Watanabe, K.]]
-[[Category: Weixlbaumer, A.]]
-[[Category: Cmo5u]]
-[[Category: Metal-binding]]
-[[Category: Modifiaction]]
-[[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]]