3CMQ

Crystal structure of human mitochondrial phenylalanine tRNA synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The tRNA-Induced Conformational Activation of Human Mitochondrial Phenylalanyl-tRNA Synthetase.

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

(2008) Structure 16: 1095-1104

  • DOI: 10.1016/j.str.2008.03.020
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • All class II aminoacyl-tRNA synthetases (aaRSs) are known to be active as functional homodimers, homotetramers, or heterotetramers. However, multimeric organization is not a prerequisite for phenylalanylation activity, as monomeric mitochondrial phen ...

    All class II aminoacyl-tRNA synthetases (aaRSs) are known to be active as functional homodimers, homotetramers, or heterotetramers. However, multimeric organization is not a prerequisite for phenylalanylation activity, as monomeric mitochondrial phenylalanyl-tRNA synthetase (PheRS) is also active. We herein report the structure, at 2.2 A resolution, of a human monomeric mitPheRS complexed with Phe-AMP. The smallest known aaRS, which is, in fact, 1/5 of a cytoplasmic analog, is a chimera of the catalytic module of the alpha and anticodon binding domain (ABD) of the bacterial beta subunit of (alphabeta)2 PheRS. We demonstrate that the ABD located at the C terminus of mitPheRS overlaps with the acceptor stem of phenylalanine transfer RNA (tRNAPhe) if the substrate is positioned in a manner similar to that seen in the binary Thermus thermophilus complex. Thus, formation of the PheRS-tRNAPhe complex in human mitochondria must be accompanied by considerable rearrangement (hinge-type rotation through approximately 160 degrees) of the ABD upon tRNA binding.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenylalanyl-tRNA synthetase, mitochondrialA415N/AMutation(s): 0 
Gene Names: FARS2FARS1
EC: 6.1.1.20
Find proteins for O95363 (Homo sapiens)
Explore O95363 
Go to UniProtKB:  O95363
NIH Common Fund Data Resources
PHAROS  O95363
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FA5
Query on FA5

Download CCD File 
A
ADENOSINE-5'-[PHENYLALANINYL-PHOSPHATE]
C19 H23 N6 O8 P
ZFNOOEXYTZPIQS-URQYDQELSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.888α = 90
b = 90.168β = 90
c = 95.84γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description