5GQW

Crystal structure of branching enzyme W610N mutant from Cyanothece sp. ATCC 51142


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1074/jbc.M116.755629
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Related Citations: 
    • Crystallization and crystallographic analysis of branching enzymes from Cyanothece sp. ATCC 51142
      Hayashi, M.,Suzuki, R.,Colleoni, C.,Ball, S.G.,Fujita, N.,Suzuki, E.
      (2015) Acta Crystallogr F Struct Biol Commun 71: 1109


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1,4-alpha-glucan branching enzyme GlgB
A
793Cyanothece sp. (strain ATCC 51142)Mutation(s): 1 
Gene Names: glgB (glgB1)
EC: 2.4.1.18
Find proteins for B1WPM8 (Cyanothece sp. (strain ATCC 51142))
Go to UniProtKB:  B1WPM8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.149 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 133.619α = 90.00
b = 133.619β = 90.00
c = 185.248γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
MOLREPphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-08-08 
  • Released Date: 2017-02-22 
  • Deposition Author(s): Suzuki, R., Suzuki, E.

Funding OrganizationLocationGrant Number
Shimadzu Science FoundationJapan120003
JSPS KAKENHIJapan15K18685
JSPS KAKENHIJapan25440193

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-04-12
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Data collection