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: Crystal structure of the TiaS-tRNA(Ile2)-ATP complex
Classification: RNA BINDING PROTEIN/RNA
Technique: X-Ray Diffraction
Resolution: 2.9
R value free: 0.286
R value observed: 0.24
R value work: 0.24

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).





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
50100150200250300350400SequenceGHTBSN

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: