1UAL

Crystal structure of tRNA(m1G37)methyltransferase: Insight into tRNA recognition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of tRNA(m(1)G37)methyltransferase: insights into tRNA recognition

Ahn, H.J.Kim, H.-W.Yoon, H.-J.Lee, B.I.Suh, S.W.Yang, J.K.

(2003) EMBO J 22: 2593-2603

  • DOI: 10.1093/emboj/cdg269
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • tRNA(m(1)G37)methyltransferase (TrmD) catalyzes the transfer of a methyl group from S-adenosyl-L- methionine (AdoMet) to G(37) within a subset of bacterial tRNA species, which have a G residue at the 36th position. The modified guanosine is adjacent ...

    tRNA(m(1)G37)methyltransferase (TrmD) catalyzes the transfer of a methyl group from S-adenosyl-L- methionine (AdoMet) to G(37) within a subset of bacterial tRNA species, which have a G residue at the 36th position. The modified guanosine is adjacent to and 3' of the anticodon and is essential for the maintenance of the correct reading frame during translation. Here we report four crystal structures of TrmD from Haemophilus influenzae, as binary complexes with either AdoMet or S-adenosyl-L-homocysteine (AdoHcy), as a ternary complex with AdoHcy and phosphate, and as an apo form. This first structure of TrmD indicates that it functions as a dimer. It also suggests the binding mode of G(36)G(37) in the active site of TrmD and the catalytic mechanism. The N-terminal domain has a trefoil knot, in which AdoMet or AdoHcy is bound in a novel, bent conformation. The C-terminal domain shows structural similarity to trp repressor. We propose a plausible model for the TrmD(2)-tRNA(2) complex, which provides insights into recognition of the general tRNA structure by TrmD.


    Organizational Affiliation

    Structural Proteomics Laboratory, School of Chemistry and Molecular Engineering, Seoul National University, Seoul 151-742, Korea.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA (Guanine-N(1)-)-methyltransferaseA274Haemophilus influenzaeMutation(s): 0 
EC: 2.1.1.31 (PDB Primary Data), 2.1.1.228 (UniProt)
Find proteins for P43912 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P43912 
Go to UniProtKB:  P43912
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.688α = 90
b = 93.688β = 90
c = 177.667γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance