4UZS

Crystal structure of Bifidobacterium bifidum beta-galactosidase

Summary for 4UZS

• Entry DOI: 10.2210/pdb4uzs/pdb
• Descriptor: BETA-GALACTOSIDASE, DI(HYDROXYETHYL)ETHER, GLYCEROL, ... (6 entities in total)
• Functional Keywords: hydrolase, lactase, family 42
• Biological source: BIFIDOBACTERIUM BIFIDUM S17
• Total number of polymer chains: 3
• Total formula weight: 233458.59

Authors

Godoy, A.S.,Murakami, M.T.,Camilo, C.M.,Bernardes, A.,Polikarpov, I. (deposition date: 2014-09-08, release date: 2015-09-30, Last modification date: 2024-05-08)

Primary citation

Godoy, A.S.,Camilo, C.M.,Kadowaki, M.A.,Muniz, H.D.S.,Santo, M.E.,Murakami, M.T.,Nascimento, A.S.,Polikarpov, I.
Crystal Structure of Beta1-6-Galactosidase from Bifidobacterium Bifidum S17: Trimeric Architecture, Molecular Determinants of the Enzymatic Activity and its Inhibition by Alpah-Galactose.
FEBS J., 283:4097-, 2016

PubMed Abstract: In a search for better comprehension of β-galactosidase function and specificity, we solved the crystal structures of the GH42 β-galactosidase BbgII from Bifidobacterium bifidum S17, a well-adapted probiotic microorganism from the human digestive tract, and its complex with d-α-galactose. BbgII is a three-domain molecule that forms barrel-shaped trimers in solution. BbgII interactions with d-α-galactose, a competitive inhibitor, showed a number of residues that are involved in the coordination of ligands. A combination of site-directed mutagenesis of these amino acid residues with enzymatic activity measurements confirmed that Glu161 and Glu320 are fundamental for catalysis and their substitution by alanines led to catalytically inactive mutants. Mutation Asn160Ala resulted in a two orders of magnitude decrease of the enzyme k without significant modification in its K , whereas mutations Tyr289Phe and His371Phe simultaneously decreased k and increased K values. Enzymatic activity of Glu368Ala mutant was too low to be detected. Our docking and molecular dynamics simulations showed that the enzyme recognizes and tightly binds substrates with β1→6 and β1→3 bonds, while binding of the substrates with β1→4 linkages is less favorable.

PubMed: 27685756
DOI: 10.1111/FEBS.13908

Experimental method

X-RAY DIFFRACTION (1.74 Å)