Crystal structure of branching enzyme from Cyanothece sp. ATCC 51142

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

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This is version 1.3 of the entry. See complete history


Bound Substrate in the Structure of Cyanobacterial Branching Enzyme Supports a New Mechanistic Model

Hayashi, M.Suzuki, R.Colleoni, C.Ball, S.G.Fujita, N.Suzuki, E.

(2017) J Biol Chem 292: 5465-5475

  • DOI: https://doi.org/10.1074/jbc.M116.755629
  • Primary Citation of Related Structures:  
    5GQU, 5GQV, 5GQW, 5GQX

  • 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, Cyanothece 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) 8 -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.

  • Organizational Affiliation

    From the Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Shimoshinjyo-Nakano, Akita 010-0195, Japan and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1,4-alpha-glucan branching enzyme GlgB793Crocosphaera subtropica ATCC 51142Mutation(s): 0 
Gene Names: glgBglgB1cce_2248
Find proteins for B1WPM8 (Crocosphaera subtropica (strain ATCC 51142 / BH68))
Explore B1WPM8 
Go to UniProtKB:  B1WPM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1WPM8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
C3 H8 O3
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.75α = 90
b = 133.75β = 90
c = 185.902γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Shimadzu Science FoundationJapan120003
JSPS KAKENHIJapan25440193

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description