5B7C | pdb_00005b7c

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.250 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

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 Related Structures: 
    5B7C

  • 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.

Macromolecule Content 

  • Total Structure Weight: 28.43 kDa 
  • Atom Count: 1,782 
  • Modeled Residue Count: 206 
  • Deposited Residue Count: 235 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
S-crystallin OctvuS4235Octopus vulgarisMutation(s): 0 
UniProt
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
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Reference Sequence

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.250 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
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
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NSCTaiwan101-2320-B-010-061
MOSTTaiwan103-2320-B-010-025
MOSTTaiwan104-2320-B-010-034

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