Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA dimethylallyltransferase, mitochondrial
Synonym: IPTase, IPPT
GI: 2507067
Orf: YOR274W
COG: COG0324
UniProt: P07884
Structures: | 3EPH | 3EPK | 3EPJ | 3EPL |
Alpha Fold Predicted Structure: AF-P07884-F1
Enzyme type: dimethylallyltransferase
Position of modification - modification: t:37 - i6A


PDB Structures:


3EPH

Structure Description:

Title: Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism
Classification: Transferase/RNA
Technique: X-Ray Diffraction
Resolution: 2.95
R value free: 0.236
R value observed:
R value work: 0.197

Abstract of the PDB Structure's related Publication:

Hypermodifications near the anticodon of tRNA are fundamental for the efficiency and fidelity of protein synthesis. Dimethylallyltransferase (DMATase) catalyzes transfer of a dimethylallyl moiety from dimethylallyl pyrophosphate to N6 of A37 in certain tRNAs. Here we present the crystal structures of Saccharomyces cerevisiae DMATase-tRNA(Cys) complex in four distinct forms, which provide snapshots of the RNA modification reaction catalyzed by DMATase. The structures reveal that the enzyme recognizes the tRNA substrate through indirect sequence readout. The targeted nucleotide A37 flips out from the anticodon loop of tRNA and flips into a channel in DMATase, where it meets its reaction partner di methylallyl pyrophosphate, which enters the channel from the opposite end. Structural changes accompanying the transfer reaction taking place in the crystal result in disengagement of DMATase-tRNA interaction near the reaction center. In addition, structural comparison of DMATase in the complex with unliganded bacterial DMATase provides a molecular basis of ordered substrate binding by DMATase.

Download RCSB-PDB Structures:

Pdb Files   3EPH.pdb   3EPJ.pdb   3EPK.pdb   3EPL.pdb  
Pdbx/mmCIF Files   3EPH.cif   3EPJ.cif   3EPK.cif   3EPL.cif  


Protein sequence:

MLKGPLKGCLNMSKKVIVIAGTTGVGKSQLSIQLAQKFNGEVINSDSMQVYKDIPIITNKHPLQEREGIPHHVMNHVDWSEEYYSHRFETECMNAIEDIHRRGKIPIVVGGTHYYLQTLFNKRVDTKSSERKLTRKQLDILESTDPDVIYNTLVKCDPDIATKYHPNDYRRVQRMLEIYYKTGKKPSETFNEQKITLKFDTLFLWLYSKPEPLFQRLDDRVDDMLERGALQEIKQLYEYYSQNKFTPEQCENGVWQVIGFKEFLPWLTGKTDDNTVKLEDCIERMKTRTRQYAKRQVKWIKKMLIPDIKGDIYLLDATDLSQWDTNASQRAIAISNDFISNRPIKQERAPKALEELLSKGETTMKKLDDWTHYTCNVCRNADGKNVVAIGEKYWKIHLGSRRHKSNLKRNTRQADFEKWKINKKETVE

Comments:

Mod5 catalyzes the transfer the delta2-isopropyl group from dimethylallyl diphosphate - a mevalonic acid derivative – to the exocyclic N6 of A36A37-containing tRNA (i6A37 formation). A single C2H2 Zn-finger-like motif present in this protein isabsent in the bacterial homolog. From a single gene MOD5, two mod5 isozymes (I, and II) are generated at the translation level (alternative translation initiation). Mod5-I is mainly located in mitochondria as well as in the cytoplasm, while Mod5-II is mainly located in the cytoplasm and in the nucleus, never in mitochondria. Sequence responsible for the subcellular distribution of the isozymes appears to reside in ‘accessory’ motifs missing from the prokaryotic counterpart (MiaA). Eukaryotic Mod5 is the ortholog of bacterial MiaA. There are no MiaA/Mod5 homologs in Archaea.





Alpha Fold Predicted Structure:




Downloading... [298746/407667]


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Protein sequence:

M L K G P L K G C L N M S K K V I V I A G T T G V G K S Q L S I Q L A Q K F N G E V I N S D S M Q V Y K D I P I I T N K H P L Q E R E G I P H H V M N H V D W S E E Y Y S H R F E T E C M N A I E D I H R R G K I P I V V G G T H Y Y L Q T L F N K R V D T K S S E R K L T R K Q L D I L E S T D P D V I Y N T L V K C D P D I A T K Y H P N D Y R R V Q R M L E I Y Y K T G K K P S E T F N E Q K I T L K F D T L F L W L Y S K P E P L F Q R L D D R V D D M L E R G A L Q E I K Q L Y E Y Y S Q N K F T P E Q C E N G V W Q V I G F K E F L P W L T G K T D D N T V K L E D C I E R M K T R T R Q Y A K R Q V K W I K K M L I P D I K G D I Y L L D A T D L S Q W D T N A S Q R A I A I S N D F I S N R P I K Q E R A P K A L E E L L S K G E T T M K K L D D W T H Y T C N V C R N A D G K N V V A I G E K Y W K I H L G S R R H K S N L K R N T R Q A D F E K W K I N K K E T V E
50100150200250300350400SequenceGHITBSN

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-P07884-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P07884-F1.cif  
DSSP Secondary Structures   P07884.dssp  





Publications:

Links:

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