Crystal structure of F183L/F259L mutant cyclodextrin glucanotransferase complexed with a pseudo-maltotetraose derived from acarbose

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 2.2 of the entry. See complete history


Effects of Essential Carbohydrate/Aromatic Stacking Interaction with Tyr100 and Phe259 on Substrate Binding of Cyclodextrin Glycosyltransferase from Alkalophilic Bacillus sp. 1011

Haga, K.Kanai, R.Sakamoto, O.Aoyagi, M.Harata, K.Yamane, K.

(2003) J Biochem 134: 881-891

  • DOI: https://doi.org/10.1093/jb/mvg215
  • Primary Citation of Related Structures:  
    1UKQ, 1UKS, 1UKT

  • PubMed Abstract: 

    The stacking interaction between a tyrosine residue and the sugar ring at the catalytic subsite -1 is strictly conserved in the glycoside hydrolase family 13 enzymes. Replacing Tyr100 with leucine in cyclodextrin glycosyltransferase (CGTase) from Bacillus sp. 1011 to prevent stacking significantly decreased all CGTase activities. The adjacent stacking interaction with both Phe183 and Phe259 onto the sugar ring at subsite +2 is essentially conserved among CGTases. F183L/F259L mutant CGTase affects donor substrate binding and/or acceptor binding during transglycosylation [Nakamura et al. (1994) Biochemistry 33, 9929-9936]. To elucidate the precise role of carbohydrate/aromatic stacking interaction at subsites -1 and +2 on the substrate binding of CGTases, we analyzed the X-ray structures of wild-type (2.0 A resolution), and Y100L (2.2 A resolution) and F183L/F259L mutant (1.9 A resolution) CGTases complexed with the inhibitor, acarbose. The refined structures revealed that acarbose molecules bound to the Y100L mutant moved from the active center toward the side chain of Tyr195, and the hydrogen bonding and hydrophobic interaction between acarbose and subsites significantly diminished. The position of pseudo-tetrasaccharide binding in the F183L/F259L mutant was closer to the non-reducing end, and the torsion angles of glycosidic linkages at subsites -1 to +1 on molecule 1 and subsites -2 to -1 on molecule 2 significantly changed compared with that of each molecule of wild-type-acarbose complex to adopt the structural change of subsite +2. These structural and biochemical data suggest that substrate binding in the active site of CGTase is critically affected by the carbohydrate/aromatic stacking interaction with Tyr100 at the catalytic subsite -1 and that this effect is likely a result of cooperation between Tyr100 and Phe259 through stacking interaction with substrate at subsite +2.

  • Organizational Affiliation

    Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclomaltodextrin glucanotransferase
A, B
686Bacillus sp. 1011Mutation(s): 2 
Find proteins for P05618 (Bacillus sp. (strain 1011))
Explore P05618 
Go to UniProtKB:  P05618
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05618
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D
Glycosylation Resources
GlyTouCan:  G94251DX
GlyCosmos:  G94251DX
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GLC

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
C6 H12 O6
Query on ACI

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
C7 H13 N O4
Query on CA

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
K [auth B],
L [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.85α = 85.19
b = 74.53β = 104.86
c = 78.94γ = 101.04
Software Package:
Software NamePurpose
MADNESSdata collection
FFFEARdata reduction
X-PLORmodel building
MADNESSdata reduction
FFFEARdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-11-10
    Changes: Database references, Structure summary
  • Version 2.2: 2023-10-25
    Changes: Data collection, Refinement description