Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (adenosine(37)-N6)-dimethylallyltransferase
Synonym: TrpX
GI: 127087
Orf: b4171
COG: COG0324
UniProt: P16384
Structures: | 3FOZ | 2ZM5 | 2ZXU |
Alpha Fold Predicted Structure: AF-P16384-F1
Enzyme type: dimethylallyltransferase
Position of modification - modification: t:37 - i6A


PDB Structures:


3FOZ

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Bacterial and eukaryotic tRNAs that decode codons starting with uridine have a hydrophobically hypermodified adenosine at position 37 (A(37)) adjacent to the 3'-end of the anticodon, which is essential for efficient and highly accurate protein translation by the ribosome. However, it remains unclear as to how the corresponding tRNAs are selected to be modified by alkylation at the correct position of the adenosine base. We have determined a series of crystal structures of bacterial tRNA isopentenyltransferase (MiaA) in apo- and tRNA-bound forms, which completely render snapshots of substrate selections during the modification of RNA. A compact evolutionary inserted domain (herein swinging domain) in MiaA that exhibits as a highly mobile entity moves around the catalytic domain as likely to reach and trap the tRNA substrate. Thereby, MiaA clamps the anticodon stem loop of the tRNA substrate between the catalytic and swinging domains, where the two conserved elongated residues from the swinging domain pinch the two flanking A(36) and A(38) together to squeeze out A(37) into the reaction tunnel. The site-specific isopentenylation of RNA is thus ensured by a characteristic pinch-and-flip mechanism and by a reaction tunnel to confine the substrate selection. Furthermore, combining information from soaking experiments with structural comparisons, we propose a mechanism for the ordered substrate binding of MiaA.

Download RCSB-PDB Structures:

Pdb Files   2ZM5.pdb   2ZXU.pdb   3FOZ.pdb  
Pdbx/mmCIF Files   2ZM5.cif   2ZXU.cif   3FOZ.cif  


Protein sequence:

MSDISKASLPKAIFLMGPTASGKTALAIELRKILPVELISVDSALIYKGMDIGTAKPNAEELLAAPHRLLDIRDPSQAYSAADFRRDALAEMADITAAGRIPLLVGGTMLYFKALLEGLSPLPSADPEVRARIEQQAAEQGWESLHRQLQEVDPVAAARIHPNDPQRLSRALEVFFISGKTLTELTQTSGDALPYQVHQFAIAPASRELLHQRIEQRFHQMLASGFEAEVRALFARGDLHTDLPSIRCVGYRQMWSYLEGEISYDEMVYRGVCATRQLAKRQITWLRGWEGVHWLDSEKPEQARDEVLQVVGAIAG

Comments:

Bacterial MiaA, initially called dimethylallyl diphosphate:tRNA dimethylallyltransferase, belongs to the IPP transferase superfamily including eukaryotic Mod5. It catalyzes the transfer of isopentenyl group on N6 of A37 in most A36A37-containing tRNA. Isopentenyl originates from ispentenyl-pyrophosphate (IPP). MiaA-like proteins are totally absent in Archaea.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:i6A RNA tRNA 37 Prokaryotic Cytosol

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P16384-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P16384-F1.cif  
DSSP Secondary Structures   P16384.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Molecular cloning of the Escherichia coli miaA gene involved in the formation of delta 2-isopentenyl adenosine in tRNA. Caillet J, Droogmans L J Bacteriol [details] 3045085 -
Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms(2)io(6)A37 in tRNA. Kaminska KH, Baraniak U, Boniecki M, Nowaczyk K, Czerwoniec A, Bujnicki JM Proteins [details] 17910062 -
Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon. Chimnaronk S, Forouhar F, Sakai J, Yao M, Tron CM, Atta M, Fontecave M, Hunt JF, Tanaka I Biochemistry [details] 19435325 -
RNA-protein mutually induced fit: structure of Escherichia coli isopentenyl-tRNA transferase in complex with tRNA(Phe). Seif E, Hallberg BM J Biol Chem [details] 19158097 -
Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: a binding mechanism for recombinant enzyme. Moore JA, Poulter CD Biochemistry [details] 9012675 -

Links:

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