5GQV

Crystal structure of branching enzyme from Cyanothece sp. ATCC 51142 in complex with maltohexaose

Summary for 5GQV

• Entry DOI: 10.2210/pdb5gqv/pdb
• Related: 5GQU 5GQW 5GQX 5GQY 5GQZ 5GR0 5GR1 5GR2 5GR3 5GR4 5GR5 5GR6
• Related PRD ID: PRD_900009 PRD_900010 PRD_900035
• Descriptor: 1,4-alpha-glucan branching enzyme GlgB, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, ... (8 entities in total)
• Functional Keywords: branching enzyme, glycoside hydrolase family 13, cyanobacteria, starch, transferase
• Biological source: Cyanothece sp. (strain ATCC 51142)
• Total number of polymer chains: 1
• Total formula weight: 99038.25

Authors

Suzuki, R.,Suzuki, E. (deposition date: 2016-08-08, release date: 2017-02-22, Last modification date: 2023-11-08)

Primary citation

Hayashi, M.,Suzuki, R.,Colleoni, C.,Ball, S.G.,Fujita, N.,Suzuki, E.
Bound Substrate in the Structure of Cyanobacterial Branching Enzyme Supports a New Mechanistic Model
J. Biol. Chem., 292:5465-5475, 2017

PubMed Abstract: Branching enzyme (BE) catalyzes the formation of α-1,6-glucosidic linkages in amylopectin and glycogen. The reaction products are variable, depending on the organism sources, and the mechanistic basis for these different outcomes is unclear. Although most cyanobacteria have only one BE isoform belonging to glycoside hydrolase family 13, sp. ATCC 51142 has three isoforms (BE1, BE2, and BE3) with distinct enzymatic properties, suggesting that investigations of these enzymes might provide unique insights into this system. Here, we report the crystal structure of ligand-free wild-type BE1 (residues 5-759 of 1-773) at 1.85 Å resolution. The enzyme consists of four domains, including domain N, carbohydrate-binding module family 48 (CBM48), domain A containing the catalytic site, and domain C. The central domain A displays a (β/α)-barrel fold, whereas the other domains adopt β-sandwich folds. Domain N was found in a new location at the back of the protein, forming hydrogen bonds and hydrophobic interactions with CBM48 and domain A. Site-directed mutational analysis identified a mutant (W610N) that bound maltoheptaose with sufficient affinity to enable structure determination at 2.30 Å resolution. In this structure, maltoheptaose was bound in the active site cleft, allowing us to assign subsites -7 to -1. Moreover, seven oligosaccharide-binding sites were identified on the protein surface, and we postulated that two of these in domain A served as the entrance and exit of the donor/acceptor glucan chains, respectively. Based on these structures, we propose a substrate binding model explaining the mechanism of glycosylation/deglycosylation reactions catalyzed by BE.

PubMed: 28193843
DOI: 10.1074/jbc.M116.755629

Experimental method

X-RAY DIFFRACTION (3 Å)