1D3C

MICHAELIS COMPLEX OF BACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN GLYCOSYLTRANSFERASE WITH GAMMA-CYCLODEXTRIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The cyclization mechanism of cyclodextrin glycosyltransferase (CGTase) as revealed by a gamma-cyclodextrin-CGTase complex at 1.8-A resolution.

Uitdehaag, J.C.Kalk, K.H.van Der Veen, B.A.Dijkhuizen, L.Dijkstra, B.W.

(1999) J.Biol.Chem. 274: 34868-34876


  • PubMed Abstract: 
  • The enzyme cyclodextrin glycosyltransferase is closely related to alpha-amylases but has the unique ability to produce cyclodextrins (circular alpha(1-->4)-linked glucoses) from starch. To characterize this specificity we determined a 1.8-A structure ...

    The enzyme cyclodextrin glycosyltransferase is closely related to alpha-amylases but has the unique ability to produce cyclodextrins (circular alpha(1-->4)-linked glucoses) from starch. To characterize this specificity we determined a 1.8-A structure of an E257Q/D229N mutant cyclodextrin glycosyltransferase in complex with its product gamma-cyclodextrin, which reveals for the first time how cyclodextrin is competently bound. Across subsites -2, -1, and +1, the cyclodextrin ring binds in a twisted mode similar to linear sugars, giving rise to deformation of its circular symmetry. At subsites -3 and +2, the cyclodextrin binds in a manner different from linear sugars. Sequence comparisons and site-directed mutagenesis experiments support the conclusion that subsites -3 and +2 confer the cyclization activity in addition to subsite -6 and Tyr-195. On this basis, a role of the individual residues during the cyclization reaction cycle is proposed.


    Related Citations: 
    • Crystallographic Studies of the Interaction of Cyclodextrin Glycosyltransferase from Bacillus Circulans Strain 251 with Natural Substrates and Products
      Knegtel, R.M.,Strokopytov, B.,Penninga, D.,Faber, O.G.,Rozeboom, H.J.,Kalk, K.H.,Dijkhuizen, L.,Dijkstra, B.W.
      (1995) J.Biol.Chem. 270: 29256
    • 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
    • X-ray Structures Along the Reaction Pathway of Cyclodextrin Glycosyltransferase Elucidate Catalysis in the Alpha-amylase Family
      Uitdehaag, J.C.M.,Mosi, R.,Kalk, K.H.,van der Veen, B.A.,Dijkhuizen, L.,Withers, S.G.,Dijkstra, B.W.
      (1999) Nat.Struct.Mol.Biol. 6: 432


    Organizational Affiliation

    BIOSON Research Institute, Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences, University of Groningen, Nijenborgh 4, 9747AG Groningen, the Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYCLODEXTRIN GLYCOSYLTRANSFERASE
A
686Bacillus circulansGene Names: cgt
EC: 2.4.1.19
Find proteins for P43379 (Bacillus circulans)
Go to UniProtKB:  P43379
Small Molecules
Ligands 3 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
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 117.791α = 90.00
b = 109.532β = 90.00
c = 65.223γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
TNTphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance