3QO8

Crystal Structure of seryl-tRNA synthetase from Candida albicans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 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 U S A 108: 14091-14096

  • DOI: https://doi.org/10.1073/pnas.1102835108
  • Primary Citation of Related Structures:  
    3QNE, 3QO5, 3QO7, 3QO8

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Seryl-tRNA synthetase, cytoplasmic485Candida albicansMutation(s): 0 
Gene Names: SES1CaO19.7901
EC: 6.1.1.11
UniProt
Find proteins for Q9HGT6 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore Q9HGT6 
Go to UniProtKB:  Q9HGT6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HGT6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.997α = 90
b = 90.997β = 90
c = 275.767γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASESphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2011-08-24
    Changes: Database references
  • Version 1.2: 2011-08-31
    Changes: Database references
  • Version 1.3: 2011-09-14
    Changes: Database references
  • Version 1.4: 2014-09-10
    Changes: Database references
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description