2DIJ

COMPLEX OF A Y195F MUTANT CGTASE FROM B. CIRCULANS STRAIN 251 COMPLEXED WITH A MALTONONAOSE INHIBITOR AT PH 9.8 OBTAINED AFTER SOAKING THE CRYSTAL WITH ACARBOSE AND MALTOHEXAOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

Structure of cyclodextrin glycosyltransferase complexed with a maltononaose inhibitor at 2.6 angstrom resolution. Implications for product specificity.

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

(1996) Biochemistry 35: 4241-4249

  • DOI: 10.1021/bi952339h

  • PubMed Abstract: 
  • Crystals of the Y195F mutant of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 were subjected to a double soaking procedure, in which they were first soaked in a solution containing the inhibitor acarbose and subsequently in a so ...

    Crystals of the Y195F mutant of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 were subjected to a double soaking procedure, in which they were first soaked in a solution containing the inhibitor acarbose and subsequently in a solution containing maltohexaose. The refined structure of the resulting protein-carbohydrate complex has final crystallographic and free R-factors for data in the 8-2.6 angstrom resolution range of 15.0% and 21.5%, respectively, and reveals that a new inhibitor, composed of nine saccharide residues, is bound in the active site. The first four residues correspond to acarbose and occupy the same subsites near the catalytic residues as observed in the previously reported acarbose-enzyme complex [Strokopytov et al. (1995) Biochemistry 34, 2234-2240]. An oliogosaccharide consisting of five glucose residues has been coupled to the nonreducing end of acarbose. At the fifth residue the polysaccharide chain makes a sharp turn, allowing it to interact with residues Tyr89, Phe195, and Asn193 and a flexible loop formed by residues 145-148. On the basis of the refined model of the complex an explanation is given for the product specificity of CGTases.


    Related Citations: 
    • Kinetic Evidence that Acarbose is a Transition State Analogue Inhibitor of Cyclodextrin Glycosyltransferase
      Mosi, R.,Sham, H.,Uitdehaag, J.C.M.,Ruiterkamp, R.,Dijkstra, B.W.,Withers, S.G.
      () TO BE PUBLISHED --: --
    • Site-Directed Mutations in Tyrosine 195 of Cyclodextrin Glycosyltransferase from Bacillus Circulans Strain 251 Affect Activity and Product Specificity
      Penninga, D.,Strokopytov, B.,Rozeboom, H.J.,Lawson, C.L.,Dijkstra, B.W.,Bergsma, J.,Dijkhuizen, L.
      (1995) Biochemistry 34: 3368
    • 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
    • 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
    • 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


    Organizational Affiliation

    BIOSON Research Institute and Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYCLODEXTRIN GLYCOSYLTRANSFERASE
A
686Bacillus circulansMutation(s): 1 
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
ADH
Query on ADH

Download SDF File 
Download CCD File 
A
1-AMINO-2,3-DIHYDROXY-5-HYDROXYMETHYL CYCLOHEX-5-ENE
C7 H13 N O3
BMZJPVSGERKRHP-ACZMJKKPSA-N
 Ligand Interaction
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
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: 2.6 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 119.964α = 90.00
b = 111.282β = 90.00
c = 67.977γ = 90.00
Software Package:
Software NamePurpose
TNTphasing
TNTrefinement
BIOMOLdata scaling
BIOMOLdata reduction
MADNESdata reduction
MADNESdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-12-09
    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