5Y0T

Crystal structure of Thermotoga maritima TmcAL bound with alpha-thio ATP(Form II)

Summary for 5Y0T

• Entry DOI: 10.2210/pdb5y0t/pdb
• Descriptor: Thermotoga maritima TmcAL, ADENOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: acetate ligase, ligase
• Biological source: Thermotoga maritima
• Total number of polymer chains: 4
• Total formula weight: 200757.61

Authors

Yamashita, S.,Tomita, K. (deposition date: 2017-07-18, release date: 2018-07-18, Last modification date: 2024-10-16)

Primary citation

Taniguchi, T.,Miyauchi, K.,Sakaguchi, Y.,Yamashita, S.,Soma, A.,Tomita, K.,Suzuki, T.
Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis.
Nat. Chem. Biol., 14:1010-1020, 2018

PubMed Abstract: Modification of tRNA anticodons plays a critical role in ensuring accurate translation. N-acetylcytidine (acC) is present at the anticodon first position (position 34) of bacterial elongator tRNA. Herein, we identified Bacillus subtilis ylbM (renamed tmcAL) as a novel gene responsible for acC34 formation. Unlike general acetyltransferases that use acetyl-CoA, TmcAL activates an acetate ion to form acetyladenylate and then catalyzes acC34 formation through a mechanism similar to tRNA aminoacylation. The crystal structure of TmcAL with an ATP analog reveals the molecular basis of acC34 formation. The ΔtmcAL strain displayed a cold-sensitive phenotype and a strong genetic interaction with tilS that encodes the enzyme responsible for synthesizing lysidine (L) at position 34 of tRNA to facilitate AUA decoding. Mistranslation of the AUA codon as Met in the ΔtmcAL strain upon tilS repression suggests that acC34 modification of tRNA and L34 modification of tRNA act cooperatively to prevent misdecoding of the AUA codon.

PubMed: 30150682
DOI: 10.1038/s41589-018-0119-z

Experimental method

X-RAY DIFFRACTION (1.9 Å)