6YQH

GH146 beta-L-arabinofuranosidase bound to covalent inhibitor

This is a non-PDB format compatible entry.

Summary for 6YQH

• Entry DOI: 10.2210/pdb6yqh/pdb
• Descriptor: Acetyl-CoA carboxylase, biotin carboxylase, DI(HYDROXYETHYL)ETHER, TRIETHYLENE GLYCOL, ... (8 entities in total)
• Functional Keywords: arabinofuranosidse, glycosidase, gh146, hydrolase
• Biological source: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)
• Total number of polymer chains: 1
• Total formula weight: 92878.11

Authors

McGregor, N.G.S.,Davies, G.J. (deposition date: 2020-04-17, release date: 2021-01-27, Last modification date: 2024-11-20)

Primary citation

McGregor, N.G.S.,Coines, J.,Borlandelli, V.,Amaki, S.,Artola, M.,Nin-Hill, A.,Linzel, D.,Yamada, C.,Arakawa, T.,Ishiwata, A.,Ito, Y.,van der Marel, G.A.,Codee, J.D.C.,Fushinobu, S.,Overkleeft, H.S.,Rovira, C.,Davies, G.J.
Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent beta-l-Arabinofuranosidase Inhibitor.
Angew.Chem.Int.Ed.Engl., 60:5754-5758, 2021

PubMed Abstract: The recent discovery of zinc-dependent retaining glycoside hydrolases (GHs), with active sites built around a Zn(Cys) (Glu) coordination complex, has presented unresolved mechanistic questions. In particular, the proposed mechanism, depending on a Zn-coordinated cysteine nucleophile and passing through a thioglycosyl enzyme intermediate, remains controversial. This is primarily due to the expected stability of the intermediate C-S bond. To facilitate the study of this atypical mechanism, we report the synthesis of a cyclophellitol-derived β-l-arabinofuranosidase inhibitor, hypothesised to react with the catalytic nucleophile to form a non-hydrolysable adduct analogous to the mechanistic covalent intermediate. This β-l-arabinofuranosidase inhibitor reacts exclusively with the proposed cysteine thiol catalytic nucleophiles of representatives of GH families 127 and 146. X-ray crystal structures determined for the resulting adducts enable MD and QM/MM simulations, which provide insight into the mechanism of thioglycosyl enzyme intermediate breakdown. Leveraging the unique chemistry of cyclophellitol derivatives, the structures and simulations presented here support the assignment of a zinc-coordinated cysteine as the catalytic nucleophile and illuminate the finely tuned energetics of this remarkable metalloenzyme clan.

PubMed: 33528085
DOI: 10.1002/anie.202013920

Experimental method

X-RAY DIFFRACTION (1.41 Å)