Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA-specific adenosine deaminase 1
Synonym: ADAT1, YGL243W
GI: 1723979
Orf: HRA400
COG: COG0590
UniProt: P53065
Alpha Fold Predicted Structure: AF-P53065-F1
Enzyme type: deaminase
Position of modification - modification: t:37 - m1I



Protein sequence:

MVSCQGTRPCIVNLLTMPSEDKLGEEISTRVINEYSKLKSACRPIIRPSGIREWTILAGVAAINRDGGANKIEILSIATGVKALPDSELQRSEGKILHDCHAEILALRGANTVLLNRIQNYNPSSGDKFIQHNDEIPARFNLKENWELALYISRLPCGDASMSFLNDNCKNDDFIKIEDSDEFQYVDRSVKTILRGRLNFNRRNVVRTKPGRYDSNITLSKSCSDKLLMKQRSSVLNCLNYELFEKPVFLKYIVIPNLEDETKHHLEQSFHTRLPNLDNEIKFLNCLKPFYDDKLDEEDVPGLMCSVKLFMDDFSTEEAILNGVRNGFYTKSSKPLRKHCQSQVSRFAQWELFKKIRPEYEGISYLEFKSRQKKRSQLIIAIKNILSPDGWIPTRTDDVK

Comments:

ADAT1 is a homodimeric enzyme and shares conserved sequence motifs with other well-characterized adenosine deaminases, including mammalian mRNA deaminases (ADARs). Also, like most members of the deaminase superfamily, a Zn2+ ion is coordinated by a conserved histidine and two cysteines. The fourth ligand is an active water molecule that acts as the nucleophile. Highly conserved glutamate then aids the reactions by shuttling a proton from water to the N1 position of inosine during the deamination reaction. These motifs constitute the canonical deaminase signature (C/H)xExnPCxxC found in most nucleotide deaminases. Tad1 (ADAT1) catalyzes the A-to-I deamination which is the first step in m1I synthesis in tRNA position 37 (Paris et al. 2011 ).




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:I RNA tRNA 37 IGC IGC tRNAAlaIGC anticodon Nucleus 22024020   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P53065-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P53065-F1.cif  
DSSP Secondary Structures   P53065.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Tad1p, a yeast tRNA-specific adenosine deaminase, is related to the mammalian pre-mRNA editing enzymes ADAR1 and ADAR2. Gerber A, Grosjean H, Melcher T, Keller W EMBO J [details] 9707437 -
A-to-I and C-to-U editing within transfer RNAs. Su AA, Randau L Biochemistry (Mosc) [details] 22022967 -
Determinants of tRNA editing and modification: Avoiding conundrums, affecting function. Paris Z, Fleming IM, Alfonzo JD Semin Cell Dev Biol [details] 22024020 -

Links:

_Wikipedia_-_RNA_editing_
_Wikipedia_-_Deamination_
_SGD_