3QO8

Crystal Structure of seryl-tRNA synthetase from Candida albicans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Unveiling the structural basis for translational ambiguity tolerance in a human fungal pathogen.

Rocha, R.Pereira, P.J.Santos, M.A.Macedo-Ribeiro, S.

(2011) Proc.Natl.Acad.Sci.USA 108: 14091-14096

  • DOI: 10.1073/pnas.1102835108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In a restricted group of opportunistic fungal pathogens the universal leucine CUG codon is translated both as serine (97%) and leucine (3%), challenging the concept that translational ambiguity has a negative impact in living organisms. To elucidate ...

    In a restricted group of opportunistic fungal pathogens the universal leucine CUG codon is translated both as serine (97%) and leucine (3%), challenging the concept that translational ambiguity has a negative impact in living organisms. To elucidate the molecular mechanisms underlying the in vivo tolerance to a nonconserved genetic code alteration, we have undertaken an extensive structural analysis of proteins containing CUG-encoded residues and solved the crystal structures of the two natural isoforms of Candida albicans seryl-tRNA synthetase. We show that codon reassignment resulted in a nonrandom genome-wide CUG redistribution tailored to minimize protein misfolding events induced by the large-scale leucine-to-serine replacement within the CTG clade. Leucine or serine incorporation at the CUG position in C. albicans seryl-tRNA synthetase induces only local structural changes and, although both isoforms display tRNA serylation activity, the leucine-containing isoform is more active. Similarly, codon ambiguity is predicted to shape the function of C. albicans proteins containing CUG-encoded residues in functionally relevant positions, some of which have a key role in signaling cascades associated with morphological changes and pathogenesis. This study provides a first detailed analysis on natural reassignment of codon identity, unveiling a highly dynamic evolutionary pattern of thousands of fungal CUG codons to confer an optimized balance between protein structural robustness and functional plasticity.


    Related Citations: 
    • Purification, crystallization and preliminary X-ray diffraction analysis of the seryl-tRNA synthetase from Candida albicans.
      Rocha, R.,Barbosa Pereira, P.J.,Santos, M.A.,Macedo-Ribeiro, S.
      (2011) Acta Crystallogr.,Sect.F 67: 153


    Organizational Affiliation

    Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Seryl-tRNA synthetase, cytoplasmic
A
485Candida albicans (strain SC5314 / ATCC MYA-2876)Mutation(s): 0 
Gene Names: SES1
EC: 6.1.1.11
Find proteins for Q9HGT6 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Go to UniProtKB:  Q9HGT6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SSA
Query on SSA

Download SDF File 
Download CCD File 
A
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
C13 H19 N7 O8 S
HQXFJGONGJPTLZ-YTMOPEAISA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.181 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 90.997α = 90.00
b = 90.997β = 90.00
c = 275.767γ = 120.00
Software Package:
Software NamePurpose
PHASESphasing
PHENIXrefinement
MOSFLMdata reduction
ADSCdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2011-08-24
    Type: Database references
  • Version 1.2: 2011-08-31
    Type: Database references
  • Version 1.3: 2011-09-14
    Type: Database references
  • Version 1.4: 2014-09-10
    Type: Database references