7DIF

GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with beta-L-arabinofuranose-configured cyclophellitol at 1.75-angstrom resolution

Summary for 7DIF

• Entry DOI: 10.2210/pdb7dif/pdb
• Descriptor: Non-reducing end beta-L-arabinofuranosidase, ZINC ION, (1S,2S,3R,4R)-3-(hydroxymethyl)cyclopentane-1,2,4-triol, ... (5 entities in total)
• Functional Keywords: (alpha/alpha)6 barrel, glycoside hydrolase family 127, hydrolase
• Biological source: Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b)
• Total number of polymer chains: 1
• Total formula weight: 74710.57

Authors

Amaki, S.,McGregor, N.G.S.,Arakawa, T.,Yamada, C.,Borlandelli, V.,Overkleeft, H.S.,Davies, G.J.,Fushinobu, S. (deposition date: 2020-11-19, release date: 2021-01-27, Last modification date: 2024-10-23)

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 (1.75 Å)