5Z7N

SmChiA sliding-intermediate with chitopentaose

Summary for 5Z7N

• Entry DOI: 10.2210/pdb5z7n/pdb
• Descriptor: Chitinase A, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: chitinase, complex, intermediate, hydrolase
• Biological source: Serratia marcescens
• Total number of polymer chains: 1
• Total formula weight: 61634.67

Authors

Nakamura, A.,Iino, R. (deposition date: 2018-01-30, release date: 2018-09-26, Last modification date: 2024-11-20)

Primary citation

Nakamura, A.,Okazaki, K.I.,Furuta, T.,Sakurai, M.,Iino, R.
Processive chitinase is Brownian monorail operated by fast catalysis after peeling rail from crystalline chitin.
Nat Commun, 9:3814-3814, 2018

PubMed 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 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.

PubMed: 30232340
DOI: 10.1038/s41467-018-06362-3

Experimental method

X-RAY DIFFRACTION (1.7 Å)