2VQF

Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U-G wobble pairing during decoding

Summary for 2VQF

• Entry DOI: 10.2210/pdb2vqf/pdb
• Related: 1DV4 1EG0 1EMI 1FJG 1FKA 1G1X 1GIX 1HNW 1HNX 1HNZ 1HR0 1I94 1I95 1I96 1I97 1IBK 1IBL 1IBM 1J5E 1JGO 1JGP 1JGQ 1L1U 1MVR 1N32 1N33 1N34 1N36 1PN7 1PN8 1PNS 1PNX 1QD7 1QZC 1RSS 1TWT 1XMO 1XMQ 1XNQ 1XNR 1YL4 2B64 2B9M 2B9O 2F4V 2J00 2J02 2UU9 2UUA 2UUB 2UUC 2UXB 2UXC 2UXD 2V46 2V48 2VQE
• Descriptor: 16S RRNA, 30S RIBOSOMAL PROTEIN S10, 30S RIBOSOMAL PROTEIN S11, ... (27 entities in total)
• Functional Keywords: trna-binding, rrna-binding, metal-binding, zinc-finger, translation, coiled coil, paromomycin, trna, zinc, mrna, cmo5u, ribosome, rna-binding, modifiactions, ribosomal protein, ribonucleoprotein
• Biological source: THERMUS THERMOPHILUS; More
• Total number of polymer chains: 23
• Total formula weight: 799918.51

Authors

Kurata, S.,Weixlbaumer, A.,Ohtsuki, T.,Shimazaki, T.,Wada, T.,Kirino, Y.,Takai, K.,Watanabe, K.,Ramakrishnan, V.,Suzuki, T. (deposition date: 2008-03-14, release date: 2008-04-29, Last modification date: 2023-12-13)

Primary citation

Kurata, S.,Weixlbaumer, A.,Ohtsuki, T.,Shimazaki, T.,Wada, T.,Kirino, Y.,Takai, K.,Watanabe, K.,Ramakrishnan, V.,Suzuki, T.
Modified Uridines with C5-Methylene Substituents at the First Position of the tRNA Anticodon Stabilize U.G Wobble Pairing During Decoding.
J.Biol.Chem., 283:18801-, 2008

PubMed Abstract: 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.

PubMed: 18456657
DOI: 10.1074/JBC.M800233200

Experimental method

X-RAY DIFFRACTION (2.9 Å)