3TUP

Crystal structure of human mitochondrial PheRS complexed with tRNAPhe in the active open state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Human Mitochondrial PheRS Complexed with tRNA(Phe) in the Active "Open" State.

Klipcan, L.Moor, N.Finarov, I.Kessler, N.Sukhanova, M.Safro, M.G.

(2012) J.Mol.Biol. 415: 527-537

  • DOI: 10.1016/j.jmb.2011.11.029

  • PubMed Abstract: 
  • Monomeric human mitochondrial phenylalanyl-tRNA synthetase (PheRS), or hmPheRS, is the smallest known enzyme exhibiting aminoacylation activity. HmPheRS consists of only two structural domains and differs markedly from heterodimeric eukaryotic cytoso ...

    Monomeric human mitochondrial phenylalanyl-tRNA synthetase (PheRS), or hmPheRS, is the smallest known enzyme exhibiting aminoacylation activity. HmPheRS consists of only two structural domains and differs markedly from heterodimeric eukaryotic cytosolic and bacterial analogs both in the domain organization and in the mode of tRNA binding. Here, we describe the first crystal structure of mitochondrial aminoacyl-tRNA synthetase (aaRS) complexed with tRNA at a resolution of 3.0 Å. Unlike bacterial PheRSs, the hmPheRS recognizes C74, the G1-C72 base pair, and the "discriminator" base A73, proposed to contribute to tRNA(Phe) identity in the yeast mitochondrial enzyme. An interaction of the tRNA acceptor stem with the signature motif 2 residues of hmPheRS is of critical importance for the stabilization of the CCA-extended conformation and its correct placement in the synthetic site of the enzyme. The crystal structure of hmPheRS-tRNA(Phe) provides direct evidence that the formation of the complex with tRNA requires a significant rearrangement of the anticodon-binding domain from the "closed" to the productive "open" state. Global repositioning of the domain is tRNA modulated and governed by long-range electrostatic interactions.


    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Hertzel Street, Rehovot 76100, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenylalanyl-tRNA synthetase, mitochondrial
A
415Homo sapiensMutation(s): 0 
Gene Names: FARS2 (FARS1)
EC: 6.1.1.20
Find proteins for O95363 (Homo sapiens)
Go to Gene View: FARS2
Go to UniProtKB:  O95363
Entity ID: 2
MoleculeChainsLengthOrganism
Thermus thermophilus tRNAPheT76Thermus thermophilus
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.245 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 116.041α = 90.00
b = 116.041β = 90.00
c = 123.276γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXmodel building
HKL-2000data reduction
PHENIXphasing
HKL-2000data collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2011-12-28
    Type: Database references
  • Version 1.2: 2012-02-01
    Type: Database references