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Deciphering the enzymatic mechanism of sugar ring contraction in UDP-apiose biosynthesis

Nature Catalysis volume 2, pages 1115–1123 (2019)Cite this article

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Abstract

The C-branched pentose sugar d-apiose is important for plant cell wall development. Its biosynthesis as urdine diphosphate-d-apiose (UDP-d-apiose) involves decarboxylation of the UDP-d-glucuronic acid precursor coupled with pyranosyl-to-furanosyl sugar ring contraction. This unusual multistep reaction is catalysed in a single active site by UDP-d-apiose/UDP-d-xylose synthase (UAXS). Here we decipher the UAXS catalytic mechanism on the basis of crystal structures of the enzyme (which is from Arabidopsis thaliana), molecular dynamics simulations that are expanded by hybrid quantum mechanics/molecular mechanics 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 co-enzyme with retroaldol/aldol chemistry for the sugar ring contraction. We further demonstrate that decarboxylation occurs only after the sugar ring opening and identify that the thiol group of Cys100 steers the sugar skeleton rearrangement by proton transfer to and from 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.

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Fig. 1: The proposed mechanism of UAXS.
Fig. 2: Crystallographic analysis of the three-dimensional structure of UAXS from Arabidopsis thaliana.
Fig. 3: The positioning of the UDP-GlcA substrate for catalytic oxidation and ring opening at the active site of UAXS, as revealed by QM/MM calculations.
Fig. 4: Deuterium incorporation at C3′ during the conversion of 2 by the wild-type, C100A and C100S forms of UAXS.
Fig. 5: The reaction of UAXS with 5 to study ring opening and reduction by the enzyme.
Fig. 6: The proposed enzymatic mechanism of UAXS.

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Data availability

Coordinates and structure factors have been deposited with the Protein Data Bank with accession codes 6H0N and 6H0P. All other data are available from the authors on reasonable request.

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Acknowledgements

The contributions of P. Scudieri (enzyme characterization), A. Lepak (UDP-apiose HPLC assay) and J. Coines (analysis of MD trajectories) are gratefully acknowledged. This work was supported by the Federal Ministry of Science, Research and Economy (BMWFW), the Federal Ministry of Traffic, Innovation and Technology (bmvit), the Styrian Business Promotion Agency SFG, the Standortagentur Tirol, and the Government of Lower Austrian and Business Agency Vienna through the COMET-funding programme managed by the Austrian Research Promotion Agency FFG. Funding from the Austrian Science Funds (FWF; I-3247 to B.N. and A.J.E.B.) and by the Italian Ministry of Education, University and Research (MIUR) (Dipartimenti di Eccellenza Program (2018–2022)—Department of Biology and Biotechnology ‘L. Spallanzani’ University of Pavia) is acknowledged.

Author information

Author notes

  1. These authors contributed equally: Simone Savino, Annika J. E. Borg, Alexander Dennig.

Authors and Affiliations

  1. Department of Biology and Biotechnology, University of Pavia, Pavia, Italy

    Simone Savino, Francesca De Giorgi & Andrea Mattevi

  2. Austrian Centre of Industrial Biotechnology, Graz, Austria

    Simone Savino, Alexander Dennig & Bernd Nidetzky

  3. Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria

    Annika J. E. Borg, Alexander Dennig, Martin Pfeiffer, Francesca De Giorgi & Bernd Nidetzky

  4. Institute of Organic Chemistry, Graz University of Technology, NAWI Graz, Graz, Austria

    Hansjörg Weber

  5. Organic Chemistry Section, Department of Inorganic and Organic Chemistry & Institute of Computational and Theoretical Chemistry (IQTCUB), University of Barcelona, Barcelona, Spain

    Kshatresh Dutta Dubey & Carme Rovira

  6. Catalan Institution for Advanced Studies (ICREA), Barcelona, Spain

    Carme Rovira

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Contributions

S.S. performed protein crystallization and determined the structures. K.D.D., M.P. and C.R. performed MD simulations and QM calculations, and, with A.J.E.B., analysed the data. A.D., with F. de G. and A.J.E.B., designed enzyme variants and performed biochemical characterization. A.D., A.J.E.B. and H.W. performed the NMR analyses. A.J.E.B. performed substrate synthesis and product isolation. A.J.E.B. and A.D. performed the mechanistic analyses. B.N. and A.M. designed and supervised the research. The manuscript was written with contributions from all authors. B.N., A.D., A.M. S.S. and A.J.E.B. wrote the paper.

Corresponding authors

Correspondence to Andrea Mattevi or Bernd Nidetzky.

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Supplementary information

Supplementary Information

Supplementary Methods, Table 1, Figs. 1–47 and references

Reporting Summary

Supplementary Video 1

Motions of the UAXS active site during MD simulations (replica 1)

Supplementary Video 2

Motions of the UAXS active site during MD simulations (replica 2)

Supplementary Data 1

Initial coordinates for replica 1

Supplementary Data 2

Initial coordinates for replica 2

Supplementary Data 3

Final coordinates after 300 ns of MD simulations for replica 1

Supplementary Data 4

Final coordinates after 300 ns of MD simulations for replica 2

Supplementary Data 5

QM/MM optimized geometry of the QM region of the QM/MM calculation in the XYZ file format for a snapshot taken from the MD of replica 1

Supplementary Data 6

QM/MM optimized geometry of the QM region of the QM/MM calculation in the XYZ file format, the snapshot is taken from the MD for replica 2

Supplementary Data 7

Snapshot from replica 1 used for QM/MM calculations, it represents the Michaelis complex before QM/MM optimization

Supplementary Data 8

Snapshot from replica 2 used for QM/MM calculations, it represents the complex before QM/MM optimization

Supplementary Data 9

QM/MM optimized geometry of the entire complex including the QM and MM region from the QM/MM calculation in the XYZ file format, the snapshot was taken from the MD of replica 1.

Supplementary Data 10

QM/MM optimized geometry of the entire complex including the QM and MM region of the QM/MM calculation in the XYZ file format, the snapshot was taken from the MD of replica 2

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Savino, S., Borg, A.J.E., Dennig, A. et al. Deciphering the enzymatic mechanism of sugar ring contraction in UDP-apiose biosynthesis. Nat Catal 2, 1115–1123 (2019). https://doi.org/10.1038/s41929-019-0382-8

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