3CMQ | pdb_00003cmq

Crystal structure of human mitochondrial phenylalanine tRNA synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.242 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3CMQ

Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1016/j.str.2008.03.020
  • Primary Citation Related Structures: 
    3CMQ

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 49.02 kDa 
  • Atom Count: 3,598 
  • Modeled Residue Count: 405 
  • Deposited Residue Count: 415 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phenylalanyl-tRNA synthetase, mitochondrial415Homo sapiensMutation(s): 0 
Gene Names: FARS2FARS1
EC: 6.1.1.20
UniProt & NIH Common Fund Data Resources
Find proteins for O95363 (Homo sapiens)
Explore O95363 
Go to UniProtKB:  O95363
PHAROS:  O95363
GTEx:  ENSG00000145982 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95363
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FA5

Query on FA5



Download:Ideal Coordinates CCD File
C [auth A]ADENOSINE-5'-[PHENYLALANINYL-PHOSPHATE]
C19 H23 N6 O8 P
ZFNOOEXYTZPIQS-URQYDQELSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.242 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description