Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with sophorose, isofagomine, sulfate ion

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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This is version 2.1 of the entry. See complete history


Mechanistic insight into the substrate specificity of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans

Nakajima, M.Tanaka, N.Furukawa, N.Nihira, T.Kodutsumi, Y.Takahashi, Y.Sugimoto, N.Miyanaga, A.Fushinobu, S.Taguchi, H.Nakai, H.

(2017) Sci Rep 7: 42671-42671

  • DOI: https://doi.org/10.1038/srep42671
  • Primary Citation of Related Structures:  
    5H3Z, 5H40, 5H41, 5H42

  • PubMed Abstract: 

    Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates. Recently, we found a novel phosphorylase acting on β-1,2-glucooligosaccharides with degrees of polymerization of 3 or more (1,2-β-oligoglucan phosphorylase, SOGP) in glycoside hydrolase family (GH) 94. Here, we characterized SOGP from Lachnoclostridium phytofermentans (LpSOGP) and determined its crystal structure. LpSOGP is a monomeric enzyme that contains a unique β-sandwich domain (Ndom1) at its N-terminus. Unlike the dimeric GH94 enzymes possessing catalytic pockets at their dimer interface, LpSOGP has a catalytic pocket between Ndom1 and the catalytic domain. In the complex structure of LpSOGP with sophorose, sophorose binds at subsites +1 to +2. Notably, the Glc moiety at subsite +1 is flipped compared with the corresponding ligands in other GH94 enzymes. This inversion suggests the great distortion of the glycosidic bond between subsites -1 and +1, which is likely unfavorable for substrate binding. Compensation for this disadvantage at subsite +2 can be accounted for by the small distortion of the glycosidic bond in the sophorose molecule. Therefore, the binding mode at subsites +1 and +2 defines the substrate specificity of LpSOGP, which provides mechanistic insights into the substrate specificity of a phosphorylase acting on β-1,2-glucooligosaccharides.

  • Organizational Affiliation

    Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
1,122Lachnoclostridium phytofermentans ISDgMutation(s): 0 
Gene Names: Cphy_0694
Find proteins for A9KJS6 (Lachnoclostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg))
Explore A9KJS6 
Go to UniProtKB:  A9KJS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9KJS6
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D
Glycosylation Resources
GlyTouCan:  G71571NA
GlyCosmos:  G71571NA
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.692α = 90
b = 94.877β = 100.81
c = 157.357γ = 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: 2017-03-01
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary