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

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

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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 U S A 110: 3817

  • DOI: https://doi.org/10.1073/pnas.1218374110
  • Primary Citation of Related Structures:  

  • 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, 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
637[Mycoplasma] mobileMutation(s): 0 
Find proteins for Q6KHA5 (Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711))
Explore Q6KHA5 
Go to UniProtKB:  Q6KHA5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6KHA5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LSS

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
C16 H25 N7 O7 S
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.851α = 90
b = 202.851β = 90
c = 213.922γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-03-20
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description