3BT7

Structure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide T-arm analogue

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases.

Alian, A., Lee, T.T., Griner, S.L., Stroud, R.M., Finer-Moore, J.

(2008) Proc.Natl.Acad.Sci.Usa 105: 6876-6881

  • DOI: 10.1073/pnas.0802247105

  • PubMed Abstract: 

    • 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 ...

    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.

    Organizational Affiliation: 

    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517, USA.




Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA (uracil-5-)-methyltransferase
A, B
369Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: trmA
EC: 2.1.1.-, 2.1.1.35
Find proteins for P23003 (Escherichia coli (strain K12))
Go to UniProtKB:  P23003
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*GP*C)-3')C,D19N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5MU
Query on 5MU
C, D
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 184.407α = 90.00
b = 70.131β = 120.88
c = 107.950γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DMphasing
ADSCdata collection
SOLVEphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-09-25
    Type: Derived calculations