3HXX

Crystal Structure of catalytic fragment of E. coli AlaRS in complex with AMPPCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma.

Guo, M.Chong, Y.E.Shapiro, R.Beebe, K.Yang, X.L.Schimmel, P.

(2009) Nature 462: 808-812

  • DOI: 10.1038/nature08612
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mistranslation arising from confusion of serine for alanine by alanyl-tRNA synthetases (AlaRSs) has profound functional consequences. Throughout evolution, two editing checkpoints prevent disease-causing mistranslation from confusing glycine or serin ...

    Mistranslation arising from confusion of serine for alanine by alanyl-tRNA synthetases (AlaRSs) has profound functional consequences. Throughout evolution, two editing checkpoints prevent disease-causing mistranslation from confusing glycine or serine for alanine at the active site of AlaRS. In both bacteria and mice, Ser poses a bigger challenge than Gly. One checkpoint is the AlaRS editing centre, and the other is from widely distributed AlaXps-free-standing, genome-encoded editing proteins that clear Ser-tRNA(Ala). The paradox of misincorporating both a smaller (glycine) and a larger (serine) amino acid suggests a deep conflict for nature-designed AlaRS. Here we show the chemical basis for this conflict. Nine crystal structures, together with kinetic and mutational analysis, provided snapshots of adenylate formation for each amino acid. An inherent dilemma is posed by constraints of a structural design that pins down the alpha-amino group of the bound amino acid by using an acidic residue. This design, dating back more than 3 billion years, creates a serendipitous interaction with the serine OH that is difficult to avoid. Apparently because no better architecture for the recognition of alanine could be found, the serine misactivation problem was solved through free-standing AlaXps, which appeared contemporaneously with early AlaRSs. The results reveal unconventional problems and solutions arising from the historical design of the protein synthesis machinery.


    Organizational Affiliation

    The Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alanyl-tRNA synthetase
A
441Escherichia coli (strain K12)Mutation(s): 3 
Gene Names: alaS (lovB)
EC: 6.1.1.7
Find proteins for P00957 (Escherichia coli (strain K12))
Go to UniProtKB:  P00957
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ACP
Query on ACP

Download SDF File 
Download CCD File 
A
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.823α = 90.00
b = 111.393β = 90.00
c = 118.538γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-02-15
    Type: Non-polymer description
  • Version 1.3: 2017-11-01
    Type: Refinement description