Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA(Ile2) 2-agmatinylcytidine synthase TiaS
Synonym: AF_2259
GI: 74511356
COG: COG1571
UniProt: O28025
Structures: | 3AMU | 3AU7 | 3AMT |
Alpha Fold Predicted Structure: AF-O28025-F1
Enzyme type: agmatidine synthase


PDB Structures:


3AMU

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The cytidine at the first position of the anticodon (C34) in the AUA codon-specific archaeal tRNA(Ile2) is modified to 2-agmatinylcytidine (agm(2)C or agmatidine), an agmatine-conjugated cytidine derivative, which is crucial for the precise decoding of the genetic code. Agm(2)C is synthesized by tRNA(Ile)-agm(2)C synthetase (TiaS) in an ATP-dependent manner. Here we present the crystal structures of the Archaeoglobus fulgidus TiaS-tRNA(Ile2) complexed with ATP, or with AMPCPP and agmatine, revealing a previously unknown kinase module required for activating C34 by phosphorylation, and showing the molecular mechanism by which TiaS discriminates between tRNA(Ile2) and tRNA(Met). In the TiaS-tRNA(Ile2)-ATP complex, C34 is trapped within a pocket far away from the ATP-binding site. In the agmatine-containing crystals, C34 is located near the AMPCPP γ-phosphate in the kinase module, demonstrating that agmatine is essential for placing C34 in the active site. These observations also provide the structural dynamics for agm(2)C formation.

Download RCSB-PDB Structures:

Pdb Files   3AMT.pdb   3AMU.pdb   3AU7.pdb  
Pdbx/mmCIF Files   3AMT.cif   3AMU.cif   3AU7.cif  


Protein sequence:

MRVWVGIDDTDSSRGMCTTYLAVLAMERVERELGKVIGFPRLIRLNPTIPYKTRGNGAVSFLVEVDDVGELVDVVNEVIIEHAMLDDEKTNPGAVFVDEELAVKLKPFADKAIKDVLQIDEALFVIGKYFIPHLRHKKGRGLIGALAAVGAELEDFTLELIAYRYPERFGTEREYDEESFFDMDYELYPQTFDNVDWCNDVVVCIPNTPCPVLYGIRGESVEALYKAMESVKTEPVDRRMIFVTNHATDMHLIGEEEVHRLENYRSYRLRGRVTLEPYDIEGGHVFFEIDTKFGSVKCAAFEPTKQFRNVIRLLRKGDVVEVYGSMKKDTINLEKIQIVELAEIWVEKNPICPSCGRRMESAGRGQGFRCKKCRTKADEKLREKVERELQPGFYEVPPSARRHLSKPLIRMNVEGRHIFR

Comments:

Archaeal TiaS catalyzing formation of agmatidine plays the same decoding role as bacterial TilS catalyzing the formation of lysidine (k2C) in the wobble position of tRNAIle(CAU). Moreover in comparison to bacterial TilS, TiaS has an additional function (phosphorylation of C2 atom of the wobble cytidine-34 as well as autophosphorylation of Thr18 of TiaS).




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
C:C+ tRNA (t) Ile/CAU/prokaryotic cytosol 34 22002223   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-O28025-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-O28025-F1.cif  
DSSP Secondary Structures   O28025.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Ikeuchi Y, Kimura S, Numata T, Nakamura D, Yokogawa T, Ogata T, Wada T, Suzuki T, Suzuki T Nat Chem Biol [details] 20139989 -
Structural basis of tRNA agmatinylation essential for AUA codon decoding. Osawa T, Kimura S, Terasaka N, Inanaga H, Suzuki T, Numata T Nat Struct Mol Biol [details] 22002223 -
Biogenesis of 2-agmatinylcytidine catalyzed by the dual protein and RNA kinase TiaS. Terasaka N, Kimura S, Osawa T, Numata T, Suzuki T Nat Struct Mol Biol [details] 22002222 -