9P28

Crystal structure of GH158(Pro) soaked with laminaritriose at 1.30 angstrom resolution.

Summary for 9P28

• Entry DOI: 10.2210/pdb9p28/pdb
• Related PRD ID: PRD_900024
• Descriptor: GH158(Pro), beta-D-glucopyranose-(1-3)-beta-D-glucopyranose, beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: enzyme, glycoside hydrolase, glucanase, hydrolase
• Biological source: metagenome
• Total number of polymer chains: 1
• Total formula weight: 47057.89

Authors

Martins, M.P.,Spadeto, J.P.M.,Araujo, E.A.,Mandelli, F.,Domingues, M.N.,Morais, M.A.B.,Murakami, M.T. (deposition date: 2025-06-11, release date: 2026-03-11, Last modification date: 2026-09-30)

Primary citation

Gimenis, G.H.B.,Spadeto, J.P.M.,Colombari, F.M.,Miyamoto, R.Y.,Higasi, P.M.R.,Santos, C.A.,Mandelli, F.,Martins, M.P.,Araujo, E.A.,Domingues, M.N.,Fuzita, F.J.,Oliveira, A.M.,Gazolla, M.C.,Santos, C.R.,Persinoti, G.F.,Brumer, H.,Rovira, C.,Ramos, C.H.I.,Morais, M.A.B.,Murakami, M.T.
Conformational gating mechanism for processive catalysis of beta (1,3)-glucans.
Nat Commun, 17:-, 2026

PubMed Abstract: Processive catalysis is a fundamental molecular mechanism to build and dismantle complex biopolymers such as nucleic acids, proteins and carbohydrates, underpinning a myriad of biotechnological applications. Here, we uncover a processive mechanism for the breakdown of β(1,3)-glucans, a widespread carbohydrate class. This mechanism involves a dynamic active site, which adopts a tunnel-like conformation upon substrate binding. For product release, the disruption of a salt bridge triggers an open conformation that interacts with the remnant substrate, essential for subsequent catalytic cycles. Molecular simulations reveal that this processive cleavage involves a non-canonical sugar conformation, a characteristic hitherto limited to exo-acting enzymes. Together, these findings establish the mechanistic basis for β(1,3)-glucan processive catalysis, from substrate recognition to tunnel formation, nucleophilic attack, intermediate state stabilization, product release and translocation. Ultimately, this work broadens the knowledge of β(1,3)-glucan breakdown, demonstrating that enzymatic processive catalysis is a conserved evolutionary strategy across all major classes of β-glucans.

PubMed: 41896250
DOI: 10.1038/s41467-026-71224-2

Experimental method

X-RAY DIFFRACTION (1.3 Å)