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 
  • R-Value Observed: 0.245 

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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
  • Primary Citation of Related Structures:  
    3TUP

  • 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 cytosolic ...

    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

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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phenylalanyl-tRNA synthetase, mitochondrial A415Homo sapiensMutation(s): 0 
Gene Names: FARS2, FARS1, HSPC320
EC: 6.1.1.20
Find proteins for O95363 (Homo sapiens)
Explore O95363 
Go to UniProtKB:  O95363
NIH Common Fund Data Resources
PHAROS:  O95363
GTEx:  ENSG00000145982
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
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 
  • R-Value Observed: 0.245 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.041α = 90
b = 116.041β = 90
c = 123.276γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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