Crystal Structure of the Starch-Binding Domain from Rhizopus oryzae Glucoamylase in Complex with isomaltotriose

Experimental Data Snapshot

  • Resolution: 1.18 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

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Crystal Structures of Starch Binding Domain from Rhizopus Oryzae Glucoamylase in Complex with Isomaltooligosaccharide: Insights Into Polysaccharide Binding Mechanism of Cbm21 Family.

Chu, C.Li, K.Lin, S.Chang, M.D.Jiang, T.Sun, Y.

(2014) Proteins 82: 1079

  • DOI: https://doi.org/10.1002/prot.24446
  • Primary Citation of Related Structures:  
    4BFN, 4BFO

  • PubMed Abstract: 

    Glucoamylases are responsible for hydrolysis of starch and polysaccharides to yield β-D-glucose. Rhizopus oryzae glucoamylase (RoGA) is composed of an N-terminal starch binding domain (SBD) and a C-terminal catalytic domain connected by an O-glycosylated linker. Two carbohydrate binding sites in RoSBD have been identified, site I is created by three highly conserved aromatic residues, Trp47, Tyr83, and Tyr94, and site II is built up by Tyr32 and Phe58. Here, the two crystal structures of RoSBD in complex with only α-(1,6)-linked isomaltotriose (RoSBD-isoG3) and isomaltotetraose (RoSBD-isoG4) have been determined at 1.2 and 1.3 Å, respectively. Interestingly, site II binding is observed in both complexes, while site I binding is only found in the RoSBD-isoG4 complex. Hence, site II acts as the recognition binding site for carbohydrate and site I accommodates site II to bind isoG4. Site I participates in sugar binding only when the number of glucosyl units of oligosaccharides is more than three. Taken together, two carbohydrate binding sites in RoSBD cooperate to reinforce binding mode of glucoamylase with polysaccharides as well as the starch.

  • Organizational Affiliation

    Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan, Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUCOAMYLASE106Rhizopus arrhizusMutation(s): 0 
Find proteins for Q2VC81 (Rhizopus oryzae)
Explore Q2VC81 
Go to UniProtKB:  Q2VC81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2VC81
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G02998EX
GlyCosmos:  G02998EX
GlyGen:  G02998EX
Experimental Data & Validation

Experimental Data

  • Resolution: 1.18 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.529α = 90
b = 25.866β = 124.01
c = 61.085γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2014-05-28
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary