3L4G

Crystal structure of Homo Sapiens cytoplasmic Phenylalanyl-tRNA synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of human cytosolic phenylalanyl-tRNA synthetase: evidence for kingdom-specific design of the active sites and tRNA binding patterns.

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

(2010) Structure 18: 343-353

  • DOI: https://doi.org/10.1016/j.str.2010.01.002
  • Primary Citation of Related Structures:  
    3L4G

  • PubMed Abstract: 

    The existence of three types of phenylalanyl-tRNA synthetase (PheRS), bacterial (alphabeta)(2), eukaryotic/archaeal cytosolic (alphabeta)(2), and mitochondrial alpha, is a prominent example of structural diversity within the aaRS family. PheRSs have considerably diverged in primary sequences, domain compositions, and subunit organizations. Loss of the anticodon-binding domain B8 in human cytosolic PheRS (hcPheRS) is indicative of variations in the tRNA(Phe) binding and recognition as compared to bacterial PheRSs. We report herein the crystal structure of hcPheRS in complex with phenylalanine at 3.3 A resolution. A novel structural module has been revealed at the N terminus of the alpha subunit. It stretches out into the solvent of approximately 80 A and is made up of three structural domains (DBDs) possessing DNA-binding fold. The dramatic reduction of aminoacylation activity for truncated N terminus variants coupled with structural data and tRNA-docking model testify that DBDs play crucial role in hcPheRS activity.


  • Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanyl-tRNA synthetase alpha chain
A, C, E, G, I
A, C, E, G, I, K, M, O
508Homo sapiensMutation(s): 0 
Gene Names: FARSAFARSFARSLFARSLA
EC: 6.1.1.20
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y285 (Homo sapiens)
Go to UniProtKB:  Q9Y285
PHAROS:  Q9Y285
GTEx:  ENSG00000179115 
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanyl-tRNA synthetase beta chain
B, D, F, H, J
B, D, F, H, J, L, N, P
589Homo sapiensMutation(s): 0 
Gene Names: FARSBFARSLBFRSBHSPC173
EC: 6.1.1.20
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NSD9 (Homo sapiens)
Go to UniProtKB:  Q9NSD9
PHAROS:  Q9NSD9
GTEx:  ENSG00000116120 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 363.338α = 90
b = 213.884β = 125.2
c = 212.957γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description