1EO7

BACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN GLYCOSYLTRANSFERASE IN COMPLEX WITH MALTOHEXAOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report



Literature

Structures of maltohexaose and maltoheptaose bound at the donor sites of cyclodextrin glycosyltransferase give insight into the mechanisms of transglycosylation activity and cyclodextrin size specificity.

Uitdehaag, J.C.van Alebeek, G.J.van Der Veen, B.A.Dijkhuizen, L.Dijkstra, B.W.

(2000) Biochemistry 39: 7772-7780

  • DOI: 10.1021/bi000340x
  • Primary Citation of Related Structures:  
    1EO7, 1EO5

  • PubMed Abstract: 
  • The enzymes from the alpha-amylase family all share a similar alpha-retaining catalytic mechanism but can have different reaction and product specificities. One family member, cyclodextrin glycosyltransferase (CGTase), has an uncommonly high transgly ...

    The enzymes from the alpha-amylase family all share a similar alpha-retaining catalytic mechanism but can have different reaction and product specificities. One family member, cyclodextrin glycosyltransferase (CGTase), has an uncommonly high transglycosylation activity and is able to form cyclodextrins. We have determined the 2.0 and 2.5 A X-ray structures of E257A/D229A CGTase in complex with maltoheptaose and maltohexaose. Both sugars are bound at the donor subsites of the active site and the acceptor subsites are empty. These structures mimic a reaction stage in which a covalent enzyme-sugar intermediate awaits binding of an acceptor molecule. Comparison of these structures with CGTase-substrate and CGTase-product complexes reveals three different conformational states for the CGTase active site that are characterized by different orientations of the centrally located residue Tyr 195. In the maltoheptaose and maltohexaose-complexed conformation, CGTase hinders binding of an acceptor sugar at subsite +1, which suggests an induced-fit mechanism that could explain the transglycosylation activity of CGTase. In addition, the maltoheptaose and maltohexaose complexes give insight into the cyclodextrin size specificity of CGTases, since they precede alpha-cyclodextrin (six glucoses) and beta-cyclodextrin (seven glucoses) formation, respectively. Both ligands show conformational differences at specific sugar binding subsites, suggesting that these determine cyclodextrin product size specificity, which is confirmed by site-directed mutagenesis experiments.


    Related Citations: 
    • The Cyclization Mechanism of Cyclodextrin Glycosyltransferase (CGTase) as Revealed by a Gamma-Cyclodextrin-Cgtase Complex at 1.8 Angstrom Resolution
      Uitdehaag, J.C.M., Kalk, K.H., Van Der Veen, B.A., Dijkhuizen, L., Dijkstra, B.W.
      (1999) J Biol Chem 274: 34868
    • 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 Biol 6: 432
    • Crystallographic Studies of the Interaction of Cyclodextrin Glycosyltransferase from Bacillus Circulans Strain 251 with Natural Substrates and Products
      Knegtel, R.M.A., 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.A., Penninga, D., Rozeboom, H.J., Kalk, K.H., Dijkhuizen, L., Dijkstra, B.W.
      (1996) Biochemistry 35: 4241

    Organizational Affiliation

    Center for Carbohydrate Bioengineering and Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (CYCLODEXTRIN GLYCOSYLTRANSFERASE)A686Bacillus circulansMutation(s): 2 
Gene Names: cgt
EC: 2.4.1.19
Find proteins for P43379 (Bacillus circulans)
Explore P43379 
Go to UniProtKB:  P43379
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

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

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 3 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900035
Query on PRD_900035
Balpha-maltohexaoseOligosaccharide /  Substrate analog

--

Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900009
Query on PRD_900009
C, Ealpha-maltotrioseOligosaccharide /  Nutrient

--

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

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.648α = 90
b = 109.022β = 90
c = 64.677γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
TNTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary