2CXG

CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED TO THE INHIBITOR ACARBOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report



Literature

X-ray structure of cyclodextrin glycosyltransferase complexed with acarbose. Implications for the catalytic mechanism of glycosidases.

Strokopytov, B.Penninga, D.Rozeboom, H.J.Kalk, K.H.Dijkhuizen, L.Dijkstra, B.W.

(1995) Biochemistry 34: 2234-2240

  • DOI: 10.1021/bi00007a018
  • Primary Citation of Related Structures:  
    2CXG

  • PubMed Abstract: 
  • Crystals of cyclodextrin glycosyltransferase (CGTase) from Bacillus circulans strain 251 were soaked in buffer solutions containing the pseudotetrasaccharide acarbose, a strong amylase- and CGTase inhibitor. The X-ray structure of the complex was elu ...

    Crystals of cyclodextrin glycosyltransferase (CGTase) from Bacillus circulans strain 251 were soaked in buffer solutions containing the pseudotetrasaccharide acarbose, a strong amylase- and CGTase inhibitor. The X-ray structure of the complex was elucidated at 2.5-A resolution with a final crystallographic R value of 15.8% for all data between 8.0 and 2.5 A. Acarbose is bound near the catalytic residues Asp229, Glu257, and Asp328. The carboxylic group of Glu257 is at hydrogen bonding distance from the glycosidic oxygen in the scissile bond between the B and C sugars (residue A is at the nonreducing end of the inhibitor). Asp328 makes hydrogen bonds with the 4-amino-4,6-dideoxyglucose (residue B), and Asp229 is in a close van der Waals contact with the C1 atom of this sugar. From this we conclude that in CGTase Glu257 acts as the proton donor and Asp229 serves as the general base or nucleophile, while Asp328 is involved in substrate binding and may be important for elevating the pKa of Glu257. On the basis of these results it appears that the absence of the C6-hydroxyl group in the B sugar is responsible for the inhibitory properties of acarbose on CGTase. This suggests that the C6-hydroxyl group of this sugar plays an essential role in the catalytic mechanism of CGTase.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • Reassessment of Acarbose as a Transition State Analogue Inhibitor of Cyclodextrin Glycosyltransferase
      Mosi, R., Sham, H., Uitdehaag, J.C.M., Ruiterkamp, R., Dijkstra, B.W., Withers, S.G.
      (1998) Biochemistry 37: 17192
    • Nucleotide Sequence and X-Ray Structure of Cyclodextrin Glycosyltransferase from Bacillus Circulans Strain 251 in a Maltose-Dependent Crystal Form
      Lawson, C.L., Van Montfort, R., Strokopytov, B., Rozeboom, H.J., Kalk, K.H., De Vries, G.E., Penninga, D., Dijkhuizen, L., Dijkstra, B.W.
      (1994) J Mol Biol 236: 590
    • Maltodextrin-Dependent Crystallization of Cyclomaltodextrin Glucanotransferase from Bacillus Circulans
      Lawson, C.L., Bergsma, J., Bruinenberg, P.M., De Vries, G., Dijkhuizen, L., Dijkstra, B.W.
      (1990) J Mol Biol 214: 807

    Organizational Affiliation

    BIOSON Research Institute, University of Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLODEXTRIN GLYCOSYLTRANSFERASEA686Bacillus circulansMutation(s): 0 
Gene Names: cgt
EC: 2.4.1.19
Find proteins for P43379 (Bacillus circulans)
Explore P43379 
Go to UniProtKB:  P43379
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B, D
2 N/A Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose
C
2 N/A Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
E
4 N/A Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC

Download CCD File 
A
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
ACI
Query on ACI

Download CCD File 
A
6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
C7 H13 N O4
XPHOBMULWMGEBA-VZFHVOOUSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
B, Dalpha-maltoseOligosaccharide /  Nutrient

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Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900010
Query on PRD_900010
Ealpha-maltotetraoseOligosaccharide /  Substrate analog

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.887α = 90
b = 111.903β = 90
c = 65.748γ = 90
Software Package:
Software NamePurpose
MADNESdata collection
BIOMOLdata reduction
TNTrefinement
MADNESdata reduction
BIOMOLdata scaling
TNTphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2017-10-25
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2018-04-18
    Changes: Data collection
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary