Crystal Structure of tRNA Adenosine Deaminase (TadA) from Aquifex aeolicus

Mitsuo Kuratani,Ryohei Ishii,Yoshitaka Bessho,Ryuya Fukunaga,Toru Sengoku,Mikako Shirouzu,Shun-Ichi Sekine,Shigeyuki Yokoyama

doi:10.1074/jbc.m414541200

Abstract

The bacterial tRNA adenosine deaminase (TadA) generates inosine by deaminating the adenosine residue at the wobble position of tRNA(Arg-2). This modification is essential for the decoding system. In this study, we determined the crystal structure of Aquifex aeolicus TadA at a 1.8-A resolution. This is the first structure of a deaminase acting on tRNA. A. aeolicus TadA has an alpha/beta/alpha three-layered fold and forms a homodimer. The A. aeolicus TadA dimeric structure is completely different from the tetrameric structure of yeast CDD1, which deaminates mRNA and cytidine, but is similar to the dimeric structure of yeast cytosine deaminase. However, in the A. aeolicus TadA structure, the shapes of the C-terminal helix and the regions between the beta4 and beta5 strands are quite distinct from those of yeast cytosine deaminase and a large cavity is produced. This cavity contains many conserved amino acid residues that are likely to be involved in either catalysis or tRNA binding. We made a docking model of TadA with the tRNA anticodon stem loop.

Highlights

Inosine (Fig. 1A) was found at the first (“wobble”) position of the tRNA anticodon 40 years ago [1]
The wobble positions of eight cytoplasmic tRNAs bear inosine [4], which is generated by the posttranscriptional hydrolytic deamination of adenosine [5]
tRNA adenosine deaminase (TadA) contains the consensus motif (C/H)XEXnPCXXC of the cytidine deaminase (CDA) superfamily, which includes diverse deaminases acting on bases, nucleosides, nucleotides, and nucleic acids (8 –16)

Summary

Introduction

Inosine (Fig. 1A) was found at the first (“wobble”) position of the tRNA anticodon 40 years ago [1]. The initial model was the N-terminal 94 amino acid residues of yeast cytosine deaminase (CD) (Protein Data Bank code 1UAQ), and its sequence was replaced by the sequence of A. aeolicus TadA by the 3D-PSSM server.

Results

Conclusion