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[[Image: | ==STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH A VALINE-ASL WITH CMO5U IN POSITION 34 BOUND TO AN MRNA WITH A GUG-CODON IN THE A-SITE AND PAROMOMYCIN.== | ||
<StructureSection load='2uu9' size='340' side='right' caption='[[2uu9]], [[Resolution|resolution]] 3.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2uu9]] 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=2UU9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2UU9 FirstGlance]. <br> | |||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><br> | |||
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=CM0:5-(CARBOXYMETHOXY)+URIDINE-5-MONOPHOSPHATE'>CM0</scene></td></tr> | |||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fjg|1fjg]], [[1gix|1gix]], [[1i94|1i94]], [[1i95|1i95]], [[1i96|1i96]], [[1i97|1i97]], [[1ibk|1ibk]], [[1ibl|1ibl]], [[1ibm|1ibm]], [[1j5e|1j5e]], [[1jgo|1jgo]], [[1jgp|1jgp]], [[1jgq|1jgq]], [[1l1u|1l1u]], [[1n32|1n32]], [[1n33|1n33]], [[1n34|1n34]], [[1n36|1n36]], [[1pns|1pns]], [[1pnx|1pnx]], [[1xmo|1xmo]], [[1xmq|1xmq]], [[1xnq|1xnq]], [[1xnr|1xnr]], [[1yl4|1yl4]], [[2b64|2b64]], [[2b9m|2b9m]], [[2b9o|2b9o]], [[2f4v|2f4v]], [[2j00|2j00]], [[2j02|2j02]], [[2uua|2uua]], [[2uub|2uub]], [[2uuc|2uuc]]</td></tr> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2uu9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2uu9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2uu9 RCSB], [http://www.ebi.ac.uk/pdbsum/2uu9 PDBsum]</span></td></tr> | |||
<table> | |||
== 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/2uu9_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/chain_selection.php?pdb_ID=2ata 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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | ==See Also== | ||
*[[Ribosomal protein THX|Ribosomal protein THX]] | *[[Ribosomal protein THX|Ribosomal protein THX]] | ||
*[[Ribosome 3D structures|Ribosome 3D structures]] | |||
== | == References == | ||
< | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Thermus thermophilus]] | [[Category: Thermus thermophilus]] | ||
[[Category: Agris, P F.]] | [[Category: Agris, P F.]] | ||
Revision as of 10:13, 29 September 2014
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH A VALINE-ASL WITH CMO5U IN POSITION 34 BOUND TO AN MRNA WITH A GUG-CODON IN THE A-SITE AND PAROMOMYCIN.STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH A VALINE-ASL WITH CMO5U IN POSITION 34 BOUND TO AN MRNA WITH A GUG-CODON IN THE A-SITE AND PAROMOMYCIN.
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedOne 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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