Crystal structure of octopus S-crystallin Q108F mutant in complex with glutathione

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

Starting Model: in silico
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Structure of a Highly Active Cephalopod S-crystallin Mutant: New Molecular Evidence for Evolution from an Active Enzyme into Lens-Refractive Protein.

Tan, W.H.Cheng, S.C.Liu, Y.T.Wu, C.G.Lin, M.H.Chen, C.C.Lin, C.H.Chou, C.Y.

(2016) Sci Rep 6: 31176-31176

  • DOI: https://doi.org/10.1038/srep31176
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Crystallins are found widely in animal lenses and have important functions due to their refractive properties. In the coleoid cephalopods, a lens with a graded refractive index provides good vision and is required for survival. Cephalopod S-crystallin is thought to have evolved from glutathione S-transferase (GST) with various homologs differentially expressed in the lens. However, there is no direct structural information that helps to delineate the mechanisms by which S-crystallin could have evolved. Here we report the structural and biochemical characterization of novel S-crystallin-glutathione complex. The 2.35-Å crystal structure of a S-crystallin mutant from Octopus vulgaris reveals an active-site architecture that is different from that of GST. S-crystallin has a preference for glutathione binding, although almost lost its GST enzymatic activity. We've also identified four historical mutations that are able to produce a "GST-like" S-crystallin that has regained activity. This protein recapitulates the evolution of S-crystallin from GST. Protein stability studies suggest that S-crystallin is stabilized by glutathione binding to prevent its aggregation; this contrasts with GST-σ, which do not possess this protection. We suggest that a tradeoff between enzyme activity and the stability of the lens protein might have been one of the major driving force behind lens evolution.

  • Organizational Affiliation

    Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-crystallin OctvuS4235Octopus vulgarisMutation(s): 0 
Find proteins for A0A1C7D1H4 (Octopus vulgaris)
Explore A0A1C7D1H4 
Go to UniProtKB:  A0A1C7D1H4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C7D1H4
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.322α = 90
b = 114.322β = 90
c = 63.927γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description