2CXG

CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED TO THE INHIBITOR ACARBOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

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


  • 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: 
    • 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
    • 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
    • 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


    Organizational Affiliation

    BIOSON Research Institute, University of Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYCLODEXTRIN GLYCOSYLTRANSFERASE
A
686Bacillus circulansMutation(s): 0 
Gene Names: cgt
EC: 2.4.1.19
Find proteins for P43379 (Bacillus circulans)
Go to UniProtKB:  P43379
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
ACI
Query on ACI

Download SDF File 
Download CCD File 
A
6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
C7 H13 N O4
XPHOBMULWMGEBA-VZFHVOOUSA-N
 Ligand Interaction
G6D
Query on G6D

Download SDF File 
Download CCD File 
A
6-DEOXY-ALPHA-D-GLUCOSE
D-Quinovose
C6 H12 O5
SHZGCJCMOBCMKK-DVKNGEFBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 120.887α = 90.00
b = 111.903β = 90.00
c = 65.748γ = 90.00
Software Package:
Software NamePurpose
MADNESdata collection
BIOMOLdata scaling
TNTphasing
TNTrefinement
BIOMOLdata reduction
MADNESdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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