Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 79495.98 
• Atom Count: 5562 
• Residue Count: 686 
• Unique protein chains: 1

1D3C

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

• DOI: 10.2210/pdb1D3C/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus circulans
• Expression System: Bacillus subtilis
• Mutation(s): 2 


• Deposited: 1999-09-29 Released: 1999-12-22 
• Deposition Author(s): Uitdehaag, J.C.M., Kalk, K.H., van der Veen, B.A., Dijkhuizen, L., Dijkstra, B.W.

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Experimental Data Snapshot

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

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: 10574960 
• DOI: 10.1074/jbc.274.49.34868


• 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 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.

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Related Citations: 

• 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
• 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




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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
Molecule	Chains	Sequence Length	Organism	Details
CYCLODEXTRIN GLYCOSYLTRANSFERASE	A	686	Bacillus circulans	Mutation(s): 2  Gene Names: cgt EC: 2.4.1.19
Find proteins for P43379 (Bacillus circulans) Go to UniProtKB:  P43379

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
GLC	A	ALPHA-D-GLUCOSE C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
MPD	A	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

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 = 117.791	α = 90.00
b = 109.532	β = 90.00
c = 65.223	γ = 90.00

Software Package:

Software Name	Purpose
TNT	refinement
TNT	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-09-29 
• Released Date: 1999-12-22 
• Deposition Author(s): Uitdehaag, J.C.M., Kalk, K.H., van der Veen, B.A., Dijkhuizen, L., Dijkstra, B.W.

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