3FOZ | pdb_00003foz

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

• PDB DOI: https://doi.org/10.2210/pdb3FOZ/pdb
• NAKB: 3FOZ

• Classification: TRANSFERASE/RNA
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-02 Released: 2009-01-20 
• Deposition Author(s): Seif, E., Hallberg, B.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.268 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Models: experimental

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 Biological Chem 284: 6600-6604

• PubMed: 19158097 
• DOI: https://doi.org/10.1074/jbc.C800235200
• Primary Citation 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 117.21 kDa 
• Atom Count: 7,933 
• Modeled Residue Count: 751 
• Deposited Residue Count: 775 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA delta(2)-isopentenylpyrophosphate transferase	A, B	316	Escherichia coli K-12	Mutation(s): 0  Gene Names: b4171, E. coli, JW4129, miaA, trpX EC: 2.5.1.8 (PDB Primary Data), 2.5.1.75 (UniProt)
UniProt
Find proteins for P16384 (Escherichia coli (strain K12)) Explore P16384  Go to UniProtKB:  P16384

Entity ID: 2
Molecule	Chains	Length	Organism	Image
tRNA(Phe)	C	74	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
tRNA(Phe)	D	69	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	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 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.24	α = 90
b = 91.26	β = 90
c = 152.36	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): Seif, E., Hallberg, B.M.

Revision History  

• 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