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Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate.

Xie W, Liu X, Huang RH
Nat Struct Biol 10 781-8 (2003)
Cited: 66 times
EuropePMC logo PMID: 12949492

Abstract

Prokaryotic tRNA guanine transglycosylase (TGT) catalyzes replacement of guanine (G) by 7-aminomethyl-7-deazaguanine (PreQ1) at the wobble position of four specific tRNAs. Addition of 9-deazaguanine (9dzG) to a reaction mixture of Zymomonas mobilis TGT and an RNA substrate allowed us to trap, purify and crystallize a chemically competent covalent intermediate of the TGT-catalyzed reaction. The crystal structure of the TGT-RNA-9dzG ternary complex at a resolution of 2.9 A reveals, unexpectedly, that RNA is tethered to TGT through the side chain of Asp280. Thus, Asp280, instead of the previously proposed Asp102, acts as the nucleophile for the reaction. The RNA substrate adopts an unusual conformation, with four out of seven nucleotides in the loop region flipped out. Interactions between TGT and RNA revealed by the structure provide the molecular basis of the RNA substrate requirements by TGT. Furthermore, reaction of PreQ1 with the crystallized covalent intermediate provides insight into the necessary structural changes required for the TGT-catalyzed reaction to occur.

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  1. A nonredundant structure dataset for benchmarking protein-RNA computational docking. Huang SY, Zou X. J Comput Chem 34 311-318 (2013)
  2. Combining specificity determining and conserved residues improves functional site prediction. Kalinina OV, Gelfand MS, Russell RB, Russell RB. BMC Bioinformatics 10 174 (2009)
  3. Identification of the rate-determining step of tRNA-guanine transglycosylase from Escherichia coli. Garcia GA, Chervin SM, Kittendorf JD. Biochemistry 48 11243-11251 (2009)


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  10. Mechanisms of the tRNA wobble cytidine modification essential for AUA codon decoding in prokaryotes. Numata T. Biosci Biotechnol Biochem 79 347-353 (2015)
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