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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 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 ...

    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.


    Related Citations: 
    • Crystallization and X-ray analysis of human cytoplasmic phenylalanyl-tRNA synthetase
      Finarov, I., Moor, N., Kessler, N., Safro, M.G.
      (2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 93

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phenylalanyl-tRNA synthetase alpha chainACEGIKMO508Homo sapiensMutation(s): 0 
Gene Names: FARSAFARSFARSLFARSLA
EC: 6.1.1.20
Find proteins for Q9Y285 (Homo sapiens)
Explore Q9Y285 
Go to UniProtKB:  Q9Y285
NIH Common Fund Data Resources
PHAROS  Q9Y285
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phenylalanyl-tRNA synthetase beta chainBDFHJLNP589Homo sapiensMutation(s): 0 
Gene Names: FARSBFARSLBFRSBHSPC173
EC: 6.1.1.20
Find proteins for Q9NSD9 (Homo sapiens)
Explore Q9NSD9 
Go to UniProtKB:  Q9NSD9
NIH Common Fund Data Resources
PHAROS  Q9NSD9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PHE
Query on PHE

Download CCD File 
A, C, E, G, I, K, M, O
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance