2uu9: Difference between revisions

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{{Seed}}
[[Image:2uu9.png|left|200px]]


<!--
==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.==
The line below this paragraph, containing "STRUCTURE_2uu9", creates the "Structure Box" on the page.
<StructureSection load='2uu9' size='340' side='right'caption='[[2uu9]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2uu9]] 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=2UU9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UU9 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</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>
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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>
{{STRUCTURE_2uu9|  PDB=2uu9  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2uu9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2uu9 OCA], [https://pdbe.org/2uu9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2uu9 RCSB], [https://www.ebi.ac.uk/pdbsum/2uu9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2uu9 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/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/main_output.php?pdb_ID=2uu9 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 GUG-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>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2uu9" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_17496902}}, adds the Publication Abstract to the page
*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 17496902 is the PubMed ID number.
*[[Ribosome 3D structures|Ribosome 3D structures]]
-->
== References ==
{{ABSTRACT_PUBMED_17496902}}
<references/>
 
__TOC__
==About this Structure==
</StructureSection>
2UU9 is a 23 chains structure of sequences 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].
[[Category: Large Structures]]
 
[[Category: Thermus thermophilus HB8]]
==Reference==
[[Category: Agris PF]]
<ref group="xtra">PMID:17496902</ref><references group="xtra"/>
[[Category: Dziergowska A]]
[[Category: Thermus thermophilus]]
[[Category: Malkiewicz A]]
[[Category: Agris, P F.]]
[[Category: Murphy FV]]
[[Category: Dziergowska, A.]]
[[Category: Ramakrishnan V]]
[[Category: Malkiewicz, A.]]
[[Category: Vendeix FAP]]
[[Category: Murphy, F V.]]
[[Category: Weixlbaumer A]]
[[Category: Ramakrishnan, V.]]
[[Category: Vendeix, F A.P.]]
[[Category: Weixlbaumer, A.]]
[[Category: Cmo5u]]
[[Category: Coiled coil]]
[[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]]
[[Category: Zinc-finger]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 20:35:45 2009''

Latest revision as of 17:54, 13 December 2023

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

2uu9 is a 10 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.1Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Weixlbaumer A, Murphy FV 4th, Dziergowska A, Malkiewicz A, Vendeix FA, Agris PF, Ramakrishnan V. Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. Nat Struct Mol Biol. 2007 Jun;14(6):498-502. Epub 2007 May 13. PMID:17496902 doi:10.1038/nsmb1242

2uu9, resolution 3.10Å

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