Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA-specific adenosine deaminase
Synonym: aq_903
GI: 6226405
COG: COG0590
UniProt: O67050
Structures: | 1WWR |
Alpha Fold Predicted Structure: AF-O67050-F1
Enzyme type: deaminase predicted
Position of modification - modification: t:34 - I


PDB Structures:


1WWR

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

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.

Download RCSB-PDB Structures:

Pdb Files   1WWR.pdb  
Pdbx/mmCIF Files   1WWR.cif  


Protein sequence:

MGKEYFLKVALREAKRAFEKGEVPVGAIIVKEGEIISKAHNSVEELKDPTAHAEMLAIKEACRRLNTKYLEGCELYVTLEPCIMCSYALVLSRIEKVIFSALDKKHGGVVSVFNILDEPTLNHRVKWEYYPLEEASELLSEFFKKLRNNII

Comments:

Works as a homodimer. The homologue from E. coli was biochemically characterized.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M G K E Y F L K V A L R E A K R A F E K G E V P V G A I I V K E G E I I S K A H N S V E E L K D P T A H A E M L A I K E A C R R L N T K Y L E G C E L Y V T L E P C I M C S Y A L V L S R I E K V I F S A L D K K H G G V V S V F N I L D E P T L N H R V K W E Y Y P L E E A S E L L S E F F K K L R N N I I

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-O67050-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-O67050-F1.cif  
DSSP Secondary Structures   O67050.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus. Kuratani M, Ishii R, Bessho Y, Fukunaga R, Sengoku T, Shirouzu M, Sekine S, Yokoyama S J Biol Chem [details] 15677468 -