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Structural insights into β-1,3-glucan cleavage by a glycoside hydrolase family

Nature Chemical Biology volume 16, pages 920–929 (2020)Cite this article

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Abstract

The fundamental and assorted roles of β-1,3-glucans in nature are underpinned on diverse chemistry and molecular structures, demanding sophisticated and intricate enzymatic systems for their processing. In this work, the selectivity and modes of action of a glycoside hydrolase family active on β-1,3-glucans were systematically investigated combining sequence similarity network, phylogeny, X-ray crystallography, enzyme kinetics, mutagenesis and molecular dynamics. This family exhibits a minimalist and versatile (α/β)-barrel scaffold, which can harbor distinguishing exo or endo modes of action, including an ancillary-binding site for the anchoring of triple-helical β-1,3-glucans. The substrate binding occurs via a hydrophobic knuckle complementary to the canonical curved conformation of β-1,3-glucans or through a substrate conformational change imposed by the active-site topology of some fungal enzymes. Together, these findings expand our understanding of the enzymatic arsenal of bacteria and fungi for the breakdown and modification of β-1,3-glucans, which can be exploited for biotechnological applications.

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Fig. 1: Clustering and phylogeny of the GH128 family.
Fig. 2: Structure, substrate recognition and bacterial subgroups.
Fig. 3: Structural determinants for β-1,3-glucan binding in subgroups III, V and VII.
Fig. 4: The unconventional substrate-binding mode of subgroups IV and VI.
Fig. 5: β-1,3-glucan recognition and cleavage by the GH128 family.

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Data availability

Structural data have been deposited in the Protein Data Bank (https://www.rcsb.org/) under accession codes 6UAQ (AmGH128_I), 6UAR (AmGH128_I, L3), 6UAS (AmGH128_I/E199A, L5+GLC), 6UFL (AmGH128_I/E199Q, L6), 6UFZ (AmGH128_I/E199Q), 6UAT (AmGH128_I/E102A, L5), 6UAU (AmGH128_I/E102A, L3 + L2), 6UAV (PvGH128_II), 6UAW (PvGH128_II, L3), 6UAX (ScGH128_II), 6UAY (BgGH128_III), 6UAZ (BgGH128_III, GLC), 6UB0 (BgGH128_III, L2), 6UB1 (BgGH128_III, L3), 6UB2 (LeGH128_IV), 6UB3 (LeGH128_IV, L2), 6UB4 (LeGH128_IV, L3(C2)), 6UB5 (LeGH128_IV, L3 (P21)), 6UB6 (LeGH128_IV, L4), 6UB7 (CnGH128_V), 6UB8 (AnGH128_VI), 6UBA (AnGH128_VI, L3), 6UBB (AnGH128_VI, exo-site), 6UBC (CnGH128_VII) and 6UBD (TgGH128_VII). All other data generated or analyzed during this study are included in this published article (and its Supplementary information files) or are available from the corresponding author on reasonable request.

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Acknowledgements

We thank M.L. Sforça and J.A. Aricetti for the support in data collection of 1H-NMR spectra and lentinan purification, respectively. We thank C.S. Farah for the access and support in the operation of the rotating anode X-ray generator available at the Chemistry Institute, University of São Paulo. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The Stanford Synchrotron Radiation Lights Structural Molecular Biology Program is supported by the Department of Energy Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (P41GM103393). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of the NIGMS or NIH. We acknowledge the LNLS for the provision of time on the MX2, SAXS1 and SAXS2 beamlines, the Brazilian Biosciences National Laboratory (LNBio) for accessibility to crystallization (Robolab), NMR and spectroscopy facilities and the Brazilian Biorenewables National Laboratory (LNBR) for the use of the characterization of macromolecules facility. LNLS, LNBio and LNBR are operated by the Brazilian Center for Research in Energy and Materials for the Brazilian Ministry for Science, Technology, Innovations and Communications. This research was supported by grants from Fundação de Amparo à Pesquisa do Estado de São Paulo (grant nos. 2015/26982-0 to M.T.M. and 2013/08293-7 to M.S.S.) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (grant no. 306135/2016-7 to M.T.M.).

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  1. Érica T. Prates

    Present address: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA

  2. These authors contributed equally: Camila R. Santos, Pedro A. C. R. Costa.

Authors and Affiliations

  1. Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil

    Camila R. Santos, Pedro A. C. R. Costa, Plínio S. Vieira, Thamy L. R. Correa, Evandro A. Lima, Fernanda Mandelli, Renan A. S. Pirolla, Mariane N. Domingues, Lucelia Cabral, Marcele P. Martins, Rosa L. Cordeiro, Atílio T. Junior, Beatriz P. Souza, Gabriela F. Persinoti & Mario T. Murakami

  2. Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil

    Pedro A. C. R. Costa

  3. Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil

    Sinkler E. T. Gonzalez, Érica T. Prates, Fabio C. Gozzo & Munir S. Skaf

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Contributions

M.T.M. initiated the study and directed the project. S.E.T.G., E.T.P. and M.S.S. devised and performed the molecular dynamic simulations. P.A.C.R.C. and G.F.P. performed the bioinformatics analyses. R.A.S.P. and F.C.G. carried out the mass spectrometry analyses. C.R.S., P.A.C.R.C., E.A.L., F.M., P.S.V., T.L.R.C., L.C., R.L.C., M.P.M., M.N.D., B.P.S. and A.T.J. expressed and purified the enzymes and performed the structural and functional characterization. C.R.S., P.S.V., G.F.P., M.S.S. and M.T.M. wrote the paper with input from P.A.C.R.C. and T.L.R.C. All authors analyzed the results and approved the final version of the manuscript.

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Correspondence to Mario T. Murakami.

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Extended data

Extended Data Fig. 1 Domain organization in the GH128 family.

Domain architecture according to PFAM annotation. Subgroups in which the modular organization is present are indicated in roman numbers. Glyco_hydro_cc (PF11790), Sig-70 (PF04542), CBM6 (PF03422), F5_F8 (PF00754), WSC (PF01822), CBM4 (PF02018), Lectin (PF00652), DUFF (PF18099), Glyco_hydro_16 (PF00722) and PDK (PF00801).

Extended Data Fig. 2 Surface-binding sites in the subgroups IV and VI.

Comparison of the surface-binding sites in the subgroups IV (a and b) and VI (c and d). Relative position of the surface-binding sites to the nearest substrate-binding site (a and c). Protein-carbohydrate interactions (b and d).

Supplementary information

Supplementary Information

Supplementary Tables 1–11 and Figs. 1–30.

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Santos, C.R., Costa, P.A.C.R., Vieira, P.S. et al. Structural insights into β-1,3-glucan cleavage by a glycoside hydrolase family. Nat Chem Biol 16, 920–929 (2020). https://doi.org/10.1038/s41589-020-0554-5

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