6TOZ

Crystal structure of Bacillus paralicheniformis alpha-amylase in complex with acarbose

Summary for 6TOZ

• Entry DOI: 10.2210/pdb6toz/pdb
• Related PRD ID: PRD_900007
• Descriptor: Amylase, 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, CALCIUM ION, ... (6 entities in total)
• Functional Keywords: amylase, starch binding site, hydrolase
• Biological source: Bacillus licheniformis
• Total number of polymer chains: 1
• Total formula weight: 56911.37

Authors

Rozeboom, H.J.,Janssen, D.B. (deposition date: 2019-12-12, release date: 2020-10-14, Last modification date: 2024-01-24)

Primary citation

Bozic, N.,Rozeboom, H.J.,Loncar, N.,Slavic, M.S.,Janssen, D.B.,Vujcic, Z.
Characterization of the starch surface binding site on Bacillus paralicheniformis alpha-amylase.
Int.J.Biol.Macromol., 165:1529-1539, 2020

PubMed Abstract: α-Amylase from Bacillus paralicheniformis (BliAmy), belonging to GH13_5 subfamily of glycoside hydrolases, was proven to be a highly efficient raw starch digesting enzyme. The ability of some α-amylases to hydrolyze raw starch is related to the existence of surface binding sites (SBSs) for polysaccharides that can be distant from the active site. Crystallographic studies performed on BliAmy in the apo form and of enzyme bound with different oligosaccharides and oligosaccharide precursors revealed binding of these ligands to one SBS with two amino acids F257 and Y358 mainly involved in complex formation. The role of this SBS in starch binding and degradation was probed by designing enzyme variants mutated in this region (F257A and Y358A). Kinetic studies with different substrates show that starch binding through the SBS is disrupted in the mutants and that F257 and Y358 contributed cumulatively to binding and hydrolysis. Mutation of both sites (F257A/Y358A) resulted in a 5-fold lower efficacy with raw starch as substrate and at least 5.5-fold weaker binding compared to the wild type BliAmy, suggesting that the ability of BliAmy to hydrolyze raw starch with high efficiency is related to the level of its adsorption onto starch granules.

PubMed: 33058974
DOI: 10.1016/j.ijbiomac.2020.10.025

Experimental method

X-RAY DIFFRACTION (1.94 Å)