3FOZ

Structure of E. coli Isopentenyl-tRNA transferase in complex with E. coli tRNA(Phe)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 

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This is version 1.3 of the entry. See complete history. 


Literature

RNA-Protein Mutually Induced Fit: STRUCTURE OF ESCHERICHIA COLI ISOPENTENYL-tRNA TRANSFERASE IN COMPLEX WITH tRNA(Phe).

Seif, E., Hallberg, B.M.

(2009) J Biol Chem 284: 6600-6604

  • DOI: https://doi.org/10.1074/jbc.C800235200
  • Primary Citation of Related Structures:  
    3FOZ

  • PubMed Abstract: 

    tRNAs that read codons starting with U are usually modified at their A37 by isopentenyl-tRNA transferases to minimize peptidyl-tRNA slippage in translation. The consensus substrate requirements of the isopentenyl-tRNA transferase of Escherichia coli, MiaA, have been the focus of extensive study. However, the molecular basis of tRNA-MiaA recognition remains unknown. Here we describe the 2.5A crystal structure of MiaA in complex with substrate tRNA(Phe). Comparative structural analysis reveals that the enzymatic reaction involves an RNA-protein mutually induced fit mechanism in which large domain movements in MiaA provoke the partial unfolding of the substrate tRNA anticodon loop. In addition, we show how substrate tRNAs are recognized by MiaA through a combination of direct and indirect sequence readouts.

    • Organizational Affiliation: 

    Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institutet, SE-171 77 Stockholm, Sweden.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA delta(2)-isopentenylpyrophosphate transferase
A, B
316Escherichia coli K-12Mutation(s): 0 
Gene Names: b4171, E. coli, JW4129, miaA, trpX
EC: 2.5.1.8
UniProt
Find proteins for P16384 (Escherichia coli (strain K12))
Explore P16384 
Go to UniProtKB:  P16384
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16384
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
tRNA(Phe)74N/A
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
tRNA(Phe)69N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
E [auth B]
F [auth B]
G [auth C]
H [auth C]
I [auth C]
E [auth B],
F [auth B],
G [auth C],
H [auth C],
I [auth C],
J [auth C],
K [auth C],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
P [auth D],
Q [auth D],
R [auth D],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.24α = 90
b = 91.26β = 90
c = 152.36γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-05-23
    Changes: Data collection
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description