Crystal Structure of Paenibacillus sp. 598K cycloisomaltooligosaccharide glucanotransferase complexed with cycloisomaltoheptaose

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 

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Isomaltooligosaccharide-binding structure ofPaenibacillussp. 598K cycloisomaltooligosaccharide glucanotransferase

Fujimoto, Z.Kishine, N.Suzuki, N.Suzuki, R.Mizushima, D.Momma, M.Kimura, K.Funane, K.

(2017) Biosci Rep 37

  • DOI: https://doi.org/10.1042/BSR20170253
  • Primary Citation of Related Structures:  
    5X7G, 5X7H

  • PubMed Abstract: 

    Paenibacillus sp. 598K cycloisomaltooligosaccharide glucanotransferase (CITase), a member of glycoside hydrolase family 66 (GH66), catalyses the intramolecular transglucosylation of dextran to produce CIs with seven or more degrees of polymerization. To clarify the cyclization reaction and product specificity of the enzyme, we determined the crystal structure of PsCITase. The core structure of PsCITase consists of four structural domains: a catalytic (β/α) 8 -domain and three β-domains. A family 35 carbohydrate-binding module (first CBM35 region of Paenibacillus sp. 598K CITase, (PsCBM35-1)) is inserted into and protrudes from the catalytic domain. The ligand complex structure of PsCITase prepared by soaking the crystal with cycloisomaltoheptaose yielded bound sugars at three sites: in the catalytic cleft, at the joint of the PsCBM35-1 domain and at the loop region of PsCBM35-1. In the catalytic site, soaked cycloisomaltoheptaose was observed as a linear isomaltoheptaose, presumably a hydrolysed product from cycloisomaltoheptaose by the enzyme and occupied subsites -7 to -1. Beyond subsite -7, three glucose moieties of another isomaltooiligosaccharide were observed, and these positions are considered to be distal subsites -13 to -11. The third binding site is the canonical sugar-binding site at the loop region of PsCBM35-1, where the soaked cycloisomaltoheptaose is bound. The structure indicated that the concave surface between the catalytic domain and PsCBM35-1 plays a guiding route for the long-chained substrate at the cyclization reaction.

  • Organizational Affiliation

    Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan zui@affrc.go.jp funane@affrc.go.jp.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cycloisomaltooligosaccharide glucanotransferase720Paenibacillus sp. 598KMutation(s): 0 
Gene Names: cit
Find proteins for G9MBW2 (Paenibacillus sp. 598K)
Explore G9MBW2 
Go to UniProtKB:  G9MBW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9MBW2
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
B, C
Glycosylation Resources
GlyTouCan:  G08843CO
GlyCosmos:  G08843CO
GlyGen:  G08843CO
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G02998EX
GlyCosmos:  G02998EX
GlyGen:  G02998EX
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.844α = 90
b = 112.844β = 90
c = 122.275γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Data collection
  • Version 1.2: 2017-12-06
    Changes: Database references
  • Version 1.3: 2018-05-02
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary