3BC9

Alpha-amylase B in complex with acarbose

Summary for 3BC9

• Entry DOI: 10.2210/pdb3bc9/pdb
• Related: 3BCD 3BCF
• Related PRD ID: PRD_900007
• Descriptor: Alpha amylase, catalytic region, alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose, 4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose, ... (10 entities in total)
• Functional Keywords: alpha-amylase, acarbose, thermostable, halophilic, n domain, raw starch binding, hydrolase
• Biological source: Halothermothrix orenii
• Total number of polymer chains: 1
• Total formula weight: 71229.53

Authors

Tan, T.-C.,Mijts, B.N.,Swaminathan, K.,Patel, B.K.C.,Divne, C. (deposition date: 2007-11-12, release date: 2008-04-22, Last modification date: 2024-03-13)

Primary citation

Tan, T.-C.,Mijts, B.N.,Swaminathan, K.,Patel, B.K.C.,Divne, C.
Crystal Structure of the Polyextremophilic alpha-Amylase AmyB from Halothermothrix orenii: Details of a Productive Enzyme-Substrate Complex and an N Domain with a Role in Binding Raw Starch
J.Mol.Biol., 378:850-868, 2008

PubMed Abstract: The gene for a membrane-bound, halophilic, and thermostable alpha-amylase, AmyB, from Halothermothrix orenii was cloned and sequenced. The crystal structure shows that, in addition to the typical domain organization of family 13 glycoside hydrolases, AmyB carries an additional N-terminal domain (N domain) that forms a large groove--the N-C groove--some 30 A away from the active site. The structure of AmyB with the inhibitor acarbose at 1.35 A resolution shows that a nonasaccharide has been synthesized through successive transglycosylation reactions of acarbose. Unexpectedly, in a complex of wild-type AmyB with alpha-cyclodextrin and maltoheptaose at 2.2 A resolution, a maltotetraose molecule is bound in subsites -1 to +3, spanning the cleavage point at -1/+1, with the -1 glucosyl residue present as a (2)S(o) skew boat. This wild-type AmyB complex was obtained in the presence of a large excess of substrate, a condition under which it is possible to capture Michaelis complexes, which may explain the observed binding across -1/+1 and ring distortion. We observe three methionine side chains that serve as "binding platforms" for glucosyl rings in AmyB, a seemingly rare occurrence in carbohydrate-binding proteins. The structures and results from the biochemical characterization of AmyB and AmyB lacking the N domain show that the N domain increases binding of the enzyme to raw starch. Furthermore, theoretical modeling suggests that the N-C groove can accommodate, spatially and chemically, large substrates such as A-starch.

PubMed: 18387632
DOI: 10.1016/j.jmb.2008.02.041

Experimental method

X-RAY DIFFRACTION (1.35 Å)