2ZXU

Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe) and DMASPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon

Chimnaronk, S.Forouhar, F.Sakai, J.Yao, M.Tron, C.M.Atta, M.Fontecave, M.Hunt, J.F.Tanaka, I.

(2009) Biochemistry 48: 5057-5065

  • DOI: 10.1021/bi900337d
  • Primary Citation of Related Structures:  2ZM5

  • PubMed Abstract: 
  • 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 transl ...

    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.


    Organizational Affiliation

    Faculty of Advanced Life Sciences, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA delta(2)-isopentenylpyrophosphate transferase
A, B
316Escherichia coli (strain K12)Gene Names: miaA (trpX)
EC: 2.5.1.75
Find proteins for P16384 (Escherichia coli (strain K12))
Go to UniProtKB:  P16384
Entity ID: 2
MoleculeChainsLengthOrganism
tRNA(Phe)C,D76Escherichia coli K-12
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DST
Query on DST

Download SDF File 
Download CCD File 
A, B
DIMETHYLALLYL S-THIOLODIPHOSPHATE
C5 H14 O6 P2 S
UWSFTDFHOGCIEL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.300α = 90.00
b = 90.000β = 90.00
c = 150.500γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
LAFIREphasing
HKL-2000data scaling
LAFIREmodel building
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance