8QNC

Crystal structure of ancestral L-galactono-1,4-lactone dehydrogenase: A113G variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history


Literature

Structure, mechanism, and evolution of the last step in vitamin C biosynthesis.

Boverio, A.Jamil, N.Mannucci, B.Mascotti, M.L.Fraaije, M.W.Mattevi, A.

(2024) Nat Commun 15: 4158-4158

  • DOI: https://doi.org/10.1038/s41467-024-48410-1
  • Primary Citation of Related Structures:  
    8QMY, 8QNB, 8QNC, 8QNR

  • PubMed Abstract: 

    Photosynthetic organisms, fungi, and animals comprise distinct pathways for vitamin C biosynthesis. Besides this diversity, the final biosynthetic step consistently involves an oxidation reaction carried out by the aldonolactone oxidoreductases. Here, we study the origin and evolution of the diversified activities and substrate preferences featured by these flavoenzymes using molecular phylogeny, kinetics, mutagenesis, and crystallographic experiments. We find clear evidence that they share a common ancestor. A flavin-interacting amino acid modulates the reactivity with the electron acceptors, including oxygen, and determines whether an enzyme functions as an oxidase or a dehydrogenase. We show that a few side chains in the catalytic cavity impart the reaction stereoselectivity. Ancestral sequence reconstruction outlines how these critical positions were affixed to specific amino acids along the evolution of the major eukaryotic clades. During Eukarya evolution, the aldonolactone oxidoreductases adapted to the varying metabolic demands while retaining their overarching vitamin C-generating function.


  • Organizational Affiliation

    Molecular Enzymology group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-galactono-1,4-lactone dehydrogenase: A113G variant511synthetic constructMutation(s): 0 
EC: 1.3.2.3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.387α = 90
b = 69.657β = 98.29
c = 67.608γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references, Structure summary