3AMK

Structure of the Starch Branching Enzyme I (BEI) from Oryza sativa L

Summary for 3AMK

• Entry DOI: 10.2210/pdb3amk/pdb
• Descriptor: Os06g0726400 protein, PHOSPHATE ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: starch-branching, transferase
• Biological source: Oryza sativa Japonica Group (Japanese rice)
• Total number of polymer chains: 1
• Total formula weight: 81945.07

Authors

Kakuta, Y.,Chaen, K.,Noguchi, J.,Vu, N.,Kimura, M. (deposition date: 2010-08-20, release date: 2011-09-28, Last modification date: 2024-03-13)

Primary citation

Noguchi, J.,Chaen, K.,Vu, N.T.,Akasaka, T.,Shimada, H.,Nakashima, T.,Nishi, A.,Satoh, H.,Omori, T.,Kakuta, Y.,Kimura, M.
Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.
Glycobiology, 21:1108-1116, 2011

PubMed Abstract: Starch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase.

PubMed: 21493662
DOI: 10.1093/glycob/cwr049

Experimental method

X-RAY DIFFRACTION (1.9 Å)