Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (uridine(54)-C5)-methyltransferase
Synonym: RumT
GI: 136247
Orf: b3965
COG: COG2265
UniProt: P23003
Structures: | 3BT7 |
Alpha Fold Predicted Structure: AF-P23003-F1
Enzyme type: methyltransferase
Position of modification - modification: t:54 - m5U


PDB Structures:


3BT7

Structure Description:

Title: Structure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide T-arm analogue
Classification: TRANSFERASE/RNA
Technique: X-Ray Diffraction
Resolution: 2.43
R value free: 0.286
R value observed: 0.23
R value work: 0.225

Abstract of the PDB Structure's related Publication:

TrmA catalyzes S-adenosylmethionine (AdoMet)-dependent methylation of U54 in most tRNAs. We solved the structure of the Escherichia coli 5-methyluridine (m(5)U) 54 tRNA methyltransferase (MTase) TrmA in a covalent complex with a 19-nt T arm analog to 2.4-A resolution. Mutation of the TrmA catalytic base Glu-358 to Gln arrested catalysis and allowed isolation of the covalent TrmA-RNA complex for crystallization. The protein-RNA interface includes 6 nt of the T loop and two proximal base pairs of the stem. U54 is flipped out of the loop into the active site. A58 occupies the space of the everted U54 and is part of a collinear base stack G53-A58-G57-C56-U55. The RNA fold is different from T loop conformations in unbound tRNA or T arm analogs, but nearly identical to the fold of the RNA loop bound at the active site of the m(5)U MTase RumA. In both enzymes, this consensus fold presents the target U and the following two bases to a conserved binding groove on the protein. Outside of this fold, the RumA and TrmA substrates have completely different structures and protein interfaces. Loop residues other than the target U54 make more than half of their hydrogen bonds to the protein via sugar-phosphate moieties, accounting, in part, for the broad consensus sequence for TrmA substrates.

Download RCSB-PDB Structures:

Pdb Files   3BT7.pdb  
Pdbx/mmCIF Files   3BT7.cif  


Protein sequence:

MTPEHLPTEQYEAQLAEKVVRLQSMMAPFSDLVPEVFRSPVSHYRMRAEFRIWHDGDDLYHIIFDQQTKSRIRVDSFPAASELINQLMTAMIAGVRNNPVLRHKLFQIDYLTTLSNQAVVSLLYHKKLDDEWRQEAEALRDALRAQNLNVHLIGRATKTKIELDQDYIDERLPVAGKEMIYRQVENSFTQPNAAMNIQMLEWALDVTKGSKGDLLELYCGNGNFSLALARNFDRVLATEIAKPSVAAAQYNIAANHIDNVQIIRMAAEEFTQAMNGVREFNRLQGIDLKSYQCETIFVDPPRSGLDSETEKMVQAYPRILYISCNPETLCKNLETLSQTHKVERLALFDQFPYTHHMECGVLLTAK

Comments:

AdoMet is the methyl group donor.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M T P E H L P T E Q Y E A Q L A E K V V R L Q S M M A P F S D L V P E V F R S P V S H Y R M R A E F R I W H D G D D L Y H I I F D Q Q T K S R I R V D S F P A A S E L I N Q L M T A M I A G V R N N P V L R H K L F Q I D Y L T T L S N Q A V V S L L Y H K K L D D E W R Q E A E A L R D A L R A Q N L N V H L I G R A T K T K I E L D Q D Y I D E R L P V A G K E M I Y R Q V E N S F T Q P N A A M N I Q M L E W A L D V T K G S K G D L L E L Y C G N G N F S L A L A R N F D R V L A T E I A K P S V A A A Q Y N I A A N H I D N V Q I I R M A A E E F T Q A M N G V R E F N R L Q G I D L K S Y Q C E T I F V D P P R S G L D S E T E K M V Q A Y P R I L Y I S C N P E T L C K N L E T L S Q T H K V E R L A L F D Q F P Y T H H M E C G V L L T A K
50100150200250300350SequenceGHTBSN

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-P23003-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P23003-F1.cif  
DSSP Secondary Structures   P23003.dssp  





Publications:

Links:

_MetaCyc_