Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 79.10 kDa 
• Atom Count: 6201 
• Modelled Residue Count: 686 
• Deposited 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): Niallia circulans
• Expression System: Bacillus subtilis
• Mutation(s): Yes 


• 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 
• R-Value Observed: 0.222 

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
• Primary Citation of Related Structures:  
  1D3C


• 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 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLODEXTRIN GLYCOSYLTRANSFERASE	A	686	Niallia circulans	Mutation(s): 2  Gene Names: cgt EC: 2.4.1.19
UniProt
Find proteins for P43379 (Bacillus circulans) Explore P43379  Go to UniProtKB:  P43379

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
Cyclooctakis-(1-4)-(alpha-D-glucopyranose)	C, D, E	8		N/A
Glycosylation Resources
GlyTouCan:  G28503YQ GlyCosmos:  G28503YQ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	I [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide /  Nutrient		Ligand Interaction

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900042	C, D, E	gamma-cyclodextrin	Oligosaccharide /  Drug delivery		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 
• R-Value Observed: 0.222 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.791	α = 90
b = 109.532	β = 90
c = 65.223	γ = 90

Software Package:

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

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
  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: Atomic model, Data collection, Derived calculations, Structure summary