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Processive chitinase is Brownian monorail operated by fast catalysis after peeling rail from crystalline chitin

Author

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  • Akihiko Nakamura

    (National Institutes of Natural Sciences
    SOKENDAI (The Graduate University for Advanced Studies))

  • Kei-ichi Okazaki

    (National Institutes of Natural Sciences)

  • Tadaomi Furuta

    (Tokyo Institute of Technology)

  • Minoru Sakurai

    (Tokyo Institute of Technology)

  • Ryota Iino

    (National Institutes of Natural Sciences
    SOKENDAI (The Graduate University for Advanced Studies))

Abstract

Processive chitinase is a linear molecular motor which moves on the surface of crystalline chitin driven by processive hydrolysis of single chitin chain. Here, we analyse the mechanism underlying unidirectional movement of Serratia marcescens chitinase A (SmChiA) using high-precision single-molecule imaging, X-ray crystallography, and all-atom molecular dynamics simulation. SmChiA shows fast unidirectional movement of ~50 nm s−1 with 1 nm forward and backward steps, consistent with the length of reaction product chitobiose. Analysis of the kinetic isotope effect reveals fast substrate-assisted catalysis with time constant of ~3 ms. Decrystallization of the single chitin chain from crystal surface is the rate-limiting step of movement with time constant of ~17 ms, achieved by binding free energy at the product-binding site of SmChiA. Our results demonstrate that SmChiA operates as a burnt-bridge Brownian ratchet wherein the Brownian motion along the single chitin chain is rectified forward by substrate-assisted catalysis.

Suggested Citation

  • Akihiko Nakamura & Kei-ichi Okazaki & Tadaomi Furuta & Minoru Sakurai & Ryota Iino, 2018. "Processive chitinase is Brownian monorail operated by fast catalysis after peeling rail from crystalline chitin," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06362-3
    DOI: 10.1038/s41467-018-06362-3
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    Cited by:

    1. Sukanya Luang & Xavier Fernández-Luengo & Alba Nin-Hill & Victor A. Streltsov & Julian G. Schwerdt & Santiago Alonso-Gil & James R. Ketudat Cairns & Stéphanie Pradeau & Sébastien Fort & Jean-Didier Ma, 2022. "The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    2. Chapin S. Korosec & Ivan N. Unksov & Pradheebha Surendiran & Roman Lyttleton & Paul M. G. Curmi & Christopher N. Angstmann & Ralf Eichhorn & Heiner Linke & Nancy R. Forde, 2024. "Motility of an autonomous protein-based artificial motor that operates via a burnt-bridge principle," Nature Communications, Nature, vol. 15(1), pages 1-10, December.

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