2UUB: 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

Citation:
Abstract
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.
PDB ID: 2UUBDownload
MMDB ID: 152764
PDB Deposition Date: 2007/3/1
Updated in MMDB: 2017/07
Experimental Method:
x-ray diffraction
Resolution: 2.8  Å
Source Organism:
Thermus thermophilus HB8
Similar Structures:
Biological Unit for 2UUB: 23-meric; determined by author and by software (PQS)
Molecular Components in 2UUB
Label Count Molecule
Proteins (20 molecules)
1
30S Ribosomal Protein S2(Gene symbol: rpsB)
Molecule annotation
1
30S Ribosomal Protein S3(Gene symbol: rpsC)
Molecule annotation
1
30S Ribosomal Protein S4(Gene symbol: rpsD)
Molecule annotation
1
30S Ribosomal Protein S5(Gene symbol: rpsE)
Molecule annotation
1
30S Ribosomal Protein S6(Gene symbol: rpsF)
Molecule annotation
1
30S Ribosomal Protein S7(Gene symbol: TTHA1696)
Molecule annotation
1
30S Ribosomal Protein S8
Molecule annotation
1
30S Ribosomal Protein S9(Gene symbol: rpsI)
Molecule annotation
1
30S Ribosomal Protein S10(Gene symbol: rpsJ)
Molecule annotation
1
30S Ribosomal Protein S11(Gene symbol: TTHA1666)
Molecule annotation
1
30S Ribosomal Protein S12(Gene symbol: rpsL)
Molecule annotation
1
30S Ribosomal Protein S13(Gene symbol: rpsM)
Molecule annotation
1
30S Ribosomal Protein S14
Molecule annotation
1
30S Ribosomal Protein S15(Gene symbol: rpsO)
Molecule annotation
1
30S Ribosomal Protein S16(Gene symbol: rpsP)
Molecule annotation
1
30S Ribosomal Protein S17
Molecule annotation
1
30S Ribosomal Protein S18(Gene symbol: rpsR)
Molecule annotation
1
30S Ribosomal Protein S19(Gene symbol: rpsS)
Molecule annotation
1
30S Ribosomal Protein S20(Gene symbol: rpsT)
Molecule annotation
1
30S Ribosomal Protein THX(Gene symbol: TTHA1396)
Molecule annotation
Nucleotides(3 molecules)
1
16S Ribosomal RNA
Molecule annotation
1
5'-r(*gp*up*up*ap*ap*ap)-3'
Molecule annotation
1
5'-r(*cp*cp*up*cp*cp*cp*up*cm0p*ap*cp*6mzp*ap *gp*gp*ap*gp*g)-3'
Molecule annotation
Chemicals (256 molecules)
1
1
2
218
3
35
4
2
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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