Mechanism and biomass association of glucuronoyl esterase: an α/β hydrolase with potential in biomass conversion
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Glucuronoyl esterases (GEs) are α/β serine hydrolases and a relatively new addition in the toolbox to reduce the recalcitrance of lignocellulose, the biggest obstacle in cost-effective utilization of this important renewable resource. While biochemical and structural characterization of GEs have progressed greatly recently, there have yet been no mechanistic studies shedding light onto the rate-limiting steps relevant for biomass conversion. The bacterial GE OtCE15A possesses a classical yet distinctive catalytic machinery, with easily identifiable catalytic Ser/His completed by two acidic residues (Glu and Asp) rather than one as in the classical triad, and an Arg side chain participating in the oxyanion hole. By QM/MM calculations, we identified deacylation as the decisive step in catalysis, and quantified the role of Asp, Glu and Arg, showing the latter to be particularly important. The results agree well with experimental and structural data. We further calculated the free-energy barrier of post-catalysis dissociation from a complex natural substrate, suggesting that in industrial settings non-catalytic processes may constitute the rate-limiting step, and pointing to future directions for enzyme engineering in biomass utilization.
| Original language | English |
|---|---|
| Article number | 1449 |
| Journal | Nature Communications |
| Volume | 13 |
| Issue number | 1 |
| Number of pages | 10 |
| ISSN | 2041-1723 |
| DOIs | |
| Publication status | Published - Dec 2022 |
Bibliographical note
Funding Information:
The authors thank Prof. Paul Dupree, University of Cambridge, for useful discussion of the biomass model and Jens-Christian N. Poulsen and Mohannad Aloula for technical help with crystallization. This study was supported by Novo Nordisk Foundation grants NNF17OC0027698 and NNF21OC0071611?to L.L.L. and J.L. We acknowledge MAX IV Laboratory for time on Beamline Biomax under Proposal 20190334 to L.L.L. Research conducted at MAX IV, a Swedish national user facility, is supported by the Swedish Research council under contract 2018-07152, the Swedish Governmental Agency for Innovation Systems under contract 2018-04969, and Formas under contract 2019-02496. L.L.L. and Z.Z. are members of ISBUC, Integrative Structural Biology at the University of Copenhagen (www.isbuc.ku.dk). Travel to synchrotrons was supported by the Danish Ministry of Higher Education and Science through the Instrument Center DANSCATT. Computations were mainly carried out on Computerome 2.0 (Danish National Supercomputer for Life Sciences installed at the DTU National Lifescience Center at the Technical University of Denmark (DTU), Lyngby, Danmark, with access funded by the University of Copenhagen. Furthermore, partial computations in this study were supported by National Natural Science Foundation of China (22005157 to Z.Z.). M.S.S. and C.S.P. thank the support from FAPESP (grant # 2013/08293-7 and 15/25031-1).
Funding Information:
The authors thank Prof. Paul Dupree, University of Cambridge, for useful discussion of the biomass model and Jens-Christian N. Poulsen and Mohannad Aloula for technical help with crystallization. This study was supported by Novo Nordisk Foundation grants NNF17OC0027698 and NNF21OC0071611 to L.L.L. and J.L. We acknowledge MAX IV Laboratory for time on Beamline Biomax under Proposal 20190334 to L.L.L. Research conducted at MAX IV, a Swedish national user facility, is supported by the Swedish Research council under contract 2018-07152, the Swedish Governmental Agency for Innovation Systems under contract 2018-04969, and Formas under contract 2019-02496. L.L.L. and Z.Z. are members of ISBUC, Integrative Structural Biology at the University of Copenhagen ( www.isbuc.ku.dk ). Travel to synchrotrons was supported by the Danish Ministry of Higher Education and Science through the Instrument Center DANSCATT. Computations were mainly carried out on Computerome 2.0 (Danish National Supercomputer for Life Sciences installed at the DTU National Lifescience Center at the Technical University of Denmark (DTU), Lyngby, Danmark, with access funded by the University of Copenhagen. Furthermore, partial computations in this study were supported by National Natural Science Foundation of China (22005157 to Z.Z.). M.S.S. and C.S.P. thank the support from FAPESP (grant # 2013/08293-7 and 15/25031-1).
Publisher Copyright:
© 2022, The Author(s).
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