8SG0

Crystal Structure of GDP-manose 3,5 epimerase de Myrciaria dubia in complex with substrate, product and NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

Starting Model: in silico
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Literature

Structural insights into the Smirnoff-Wheeler pathway for vitamin C production in the Amazon fruit camu-camu.

Vargas, J.A.Sculaccio, S.A.Pinto, A.P.A.Pereira, H.D.Mendes, L.F.S.Flores, J.F.Cobos, M.Castro, J.C.Garratt, R.C.Leonardo, D.A.

(2024) J Exp Bot 75: 2754-2771

  • DOI: https://doi.org/10.1093/jxb/erae016
  • Primary Citation of Related Structures:  
    7SML, 8SCC, 8SG0, 8SKB, 8USU

  • PubMed Abstract: 

    l-Ascorbic acid (AsA, vitamin C) is a pivotal dietary nutrient with multifaceted importance in living organisms. In plants, the Smirnoff-Wheeler pathway is the primary route for AsA biosynthesis, and understanding the mechanistic details behind its component enzymes has implications for plant biology, nutritional science, and biotechnology. As part of an initiative to determine the structures of all six core enzymes of the pathway, the present study focuses on three of them in the model species Myrciaria dubia (camu-camu): GDP-d-mannose 3',5'-epimerase (GME), l-galactose dehydrogenase (l-GalDH), and l-galactono-1,4-lactone dehydrogenase (l-GalLDH). We provide insights into substrate and cofactor binding and the conformational changes they induce. The MdGME structure reveals a distorted substrate in the active site, pertinent to the catalytic mechanism. Mdl-GalDH shows that the way in which NAD+ association affects loop structure over the active site is not conserved when compared with its homologue in spinach. Finally, the structure of Mdl-GalLDH is described for the first time. This allows for the rationalization of previously identified residues which play important roles in the active site or in the formation of the covalent bond with FAD. In conclusion, this study enhances our understanding of AsA biosynthesis in plants, and the information provided should prove useful for biotechnological applications.


  • Organizational Affiliation

    São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-120, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GDP-mannose 3,5-epimerase
A, B
409Myrciaria dubiaMutation(s): 0 
EC: 5.1.3.18
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
GDC (Subject of Investigation/LOI)
Query on GDC

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
GUANOSINE-5'-DIPHOSPHATE-BETA-L-GALACTOSE
C16 H25 N5 O16 P2
MVMSCBBUIHUTGJ-JGQUBWHWSA-N
GDD (Subject of Investigation/LOI)
Query on GDD

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
C16 H25 N5 O16 P2
MVMSCBBUIHUTGJ-GDJBGNAASA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.799α = 90
b = 60.839β = 105.86
c = 133.999γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
GDAdata collection
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentPeru380-2019-BM-INIA-PNIA-PASANTIA
Other governmentBrazilCAPES 88887.505769/2020-00
Other governmentPeru069-2019-FONDECYT

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references