3ZIU

Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Leucyl-tRNA Synthetase Editing Domain Functions as a Molecular Rheostat to Control Codon Ambiguity in Mycoplasma Pathogens.

Li, L.Palencia, A.Lukk, T.Li, Z.Luthey-Schulten, Z.A.Cusack, S.Martinis, S.A.Boniecki, M.T.

(2013) Proc.Natl.Acad.Sci.USA 110: 3817

  • DOI: 10.1073/pnas.1218374110

  • PubMed Abstract: 
  • Mycoplasma leucyl-tRNA synthetases (LeuRSs) have been identified in which the connective polypeptide 1 (CP1) amino acid editing domain that clears mischarged tRNAs are missing (Mycoplasma mobile) or highly degenerate (Mycoplasma synoviae). Thus, thes ...

    Mycoplasma leucyl-tRNA synthetases (LeuRSs) have been identified in which the connective polypeptide 1 (CP1) amino acid editing domain that clears mischarged tRNAs are missing (Mycoplasma mobile) or highly degenerate (Mycoplasma synoviae). Thus, these enzymes rely on a clearance pathway called pretransfer editing, which hydrolyzes misactivated aminoacyl-adenylate intermediate via a nebulous mechanism that has been controversial for decades. Even as the sole fidelity pathway for clearing amino acid selection errors in the pathogenic M. mobile, pretransfer editing is not robust enough to completely block mischarging of tRNA(Leu), resulting in codon ambiguity and statistical proteins. A high-resolution X-ray crystal structure shows that M. mobile LeuRS structurally overlaps with other LeuRS cores. However, when CP1 domains from different aminoacyl-tRNA synthetases and origins were fused to this common LeuRS core, surprisingly, pretransfer editing was enhanced. It is hypothesized that the CP1 domain evolved as a molecular rheostat to balance multiple functions. These include distal control of specificity and enzyme activity in the ancient canonical core, as well as providing a separate hydrolytic active site for clearing mischarged tRNA.


    Organizational Affiliation

    Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEUCYL-TRNA SYNTHETASE
A, B
637Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711)Gene Names: leuS
EC: 6.1.1.4
Find proteins for Q6KHA5 (Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711))
Go to UniProtKB:  Q6KHA5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LSS
Query on LSS

Download SDF File 
Download CCD File 
A, B
5'-O-(L-leucylsulfamoyl)adenosine
5-O-N-LEUCYL-SULFAMOYLADENOSINE
C16 H25 N7 O7 S
XFEDFDTWJLGMBO-LEJQEAHTSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.160 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 202.851α = 90.00
b = 202.851β = 90.00
c = 213.922γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CCP4phasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-03-20
    Type: Database references