The structure of C100A mutant of Arabidopsis thaliana UDP-apiose/UDP-xylose synthase in complex with NADH and UDP-D-glucuronic acid

Experimental Data Snapshot

  • Resolution: 3.47 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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Deciphering the enzymatic mechanism of sugar ring contraction in UDP-apiose biosynthesis.

Savino, S.Borg, A.J.E.Dennig, A.Pfeiffer, M.de Giorgi, F.Weber, H.Dubey, K.D.Rovira, C.Mattevi, A.Nidetzky, B.

(2019) Nat Catal 2: 1115-1123

  • DOI: https://doi.org/10.1038/s41929-019-0382-8
  • Primary Citation of Related Structures:  
    6H0N, 6H0P

  • PubMed Abstract: 

    D-Apiose is a C -branched pentose sugar important for plant cell wall development. Its biosynthesis as UDP-D-apiose involves decarboxylation of the UDP-D-glucuronic acid precursor coupled to pyranosyl-to-furanosyl sugar ring contraction. This unusual multistep reaction is catalyzed within a single active site by UDP-D-apiose/UDP-D-xylose synthase (UAXS). Here, we decipher the UAXS catalytic mechanism based on crystal structures of the enzyme from Arabidopsis thaliana , molecular dynamics simulations expanded by QM/MM calculations, and mutational-mechanistic analyses. Our studies show how UAXS uniquely integrates a classical catalytic cycle of oxidation and reduction by a tightly bound nicotinamide coenzyme with retro-aldol/aldol chemistry for the sugar ring contraction. They further demonstrate that decarboxylation occurs only after the sugar ring opening and identify the thiol group of Cys100 in steering the sugar skeleton rearrangement by proton transfer to and from the C3'. The mechanistic features of UAXS highlight the evolutionary expansion of the basic catalytic apparatus of short-chain dehydrogenases/reductases for functional versatility in sugar biosynthesis.

  • Organizational Affiliation

    Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-D-apiose/UDP-D-xylose synthase 1
A, B
389Arabidopsis thalianaMutation(s): 1 
Gene Names: AXS1At2g27860F15K20.4
Find proteins for Q9ZUY6 (Arabidopsis thaliana)
Explore Q9ZUY6 
Go to UniProtKB:  Q9ZUY6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZUY6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.47 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.564α = 90
b = 144.564β = 90
c = 130.519γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description