6GYA

Amylase in complex with branched ligand

Summary for 6GYA

• Entry DOI: 10.2210/pdb6gya/pdb
• Related PRD ID: PRD_900001
• Descriptor: A-amylase, alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, ... (8 entities in total)
• Functional Keywords: amylase glycoside hydrolase, hydrolase
• Biological source: Alicyclobacillus sp.
• Total number of polymer chains: 4
• Total formula weight: 221157.43

Authors

Agirre, J.,Moroz, O.,Meier, S.,Brask, J.,Munch, A.,Hoff, T.,Andersen, C.,Wilson, K.S.,Davies, G.J. (deposition date: 2018-06-28, release date: 2019-01-23, Last modification date: 2024-01-17)

Primary citation

Agirre, J.,Moroz, O.,Meier, S.,Brask, J.,Munch, A.,Hoff, T.,Andersen, C.,Wilson, K.S.,Davies, G.J.
The structure of the AliC GH13 alpha-amylase from Alicyclobacillus sp. reveals the accommodation of starch branching points in the alpha-amylase family.
Acta Crystallogr D Struct Biol, 75:1-7, 2019

PubMed Abstract: α-Amylases are glycoside hydrolases that break the α-1,4 bonds in starch and related glycans. The degradation of starch is rendered difficult by the presence of varying degrees of α-1,6 branch points and their possible accommodation within the active centre of α-amylase enzymes. Given the myriad industrial uses for starch and thus also for α-amylase-catalysed starch degradation and modification, there is considerable interest in how different α-amylases might accommodate these branches, thus impacting on the potential processing of highly branched post-hydrolysis remnants (known as limit dextrins) and societal applications. Here, it was sought to probe the branch-point accommodation of the Alicyclobacillus sp. CAZy family GH13 α-amylase AliC, prompted by the observation of a molecule of glucose in a position that may represent a branch point in an acarbose complex solved at 2.1 Å resolution. Limit digest analysis by two-dimensional NMR using both pullulan (a regular linear polysaccharide of α-1,4, α-1,4, α-1,6 repeating trisaccharides) and amylopectin starch showed how the Alicyclobacillus sp. enzyme could accept α-1,6 branches in at least the -2, +1 and +2 subsites, consistent with the three-dimensional structures with glucosyl moieties in the +1 and +2 subsites and the solvent-exposure of the -2 subsite 6-hydroxyl group. Together, the work provides a rare insight into branch-point acceptance in these industrial catalysts.

PubMed: 30644839
DOI: 10.1107/S2059798318014900

Experimental method

X-RAY DIFFRACTION (2.95 Å)