8QNC | pdb_00008qnc

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

• PDB DOI: https://doi.org/10.2210/pdb8QNC/pdb

• Classification: FLAVOPROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-26 Released: 2024-05-01 
• Deposition Author(s): Boverio, A., Mattevi, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.212 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: in silico

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

• PubMed: 38755143 
• DOI: https://doi.org/10.1038/s41467-024-48410-1
• Primary Citation 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.

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Organizational Affiliation: 
• Molecular Enzymology group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands.
Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
Centro Grandi Strumenti, University of Pavia, Via Bassi 21, 27100, Pavia, Italy.
Molecular Enzymology group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands. [e-mail].
IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina. [e-mail].
Instituto de Histología y Embriología de Mendoza (IHEM)-CONICET-Universidad Nacional de Cuyo, 5500, Mendoza, Argentina. [e-mail].
Molecular Enzymology group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands. [e-mail].
Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 58.32 kDa 
• Atom Count: 4,201 
• Modeled Residue Count: 486 
• Deposited Residue Count: 511 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-galactono-1,4-lactone dehydrogenase: A113G variant	A	511	synthetic construct	Mutation(s): 0  EC: 1.3.2.3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.212 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.387	α = 90
b = 69.657	β = 98.29
c = 67.608	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Boverio, A., Mattevi, A.

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Funding Organization	Location	Grant Number
Not funded	Italy	--

Revision History  

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