Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76678.47 
• Atom Count: 5394 
• Residue Count: 686 
• Unique protein chains: 1

1CXL

COMPLEX BETWEEN A COVALENT INTERMEDIATE AND BACILLUS CIRCULANS STRAIN 251 CGTASE E257Q

• DOI: 10.2210/pdb1CXL/pdb

• Classification: GLYCOSYLTRANSFERASE
• Organism(s): Bacillus circulans
• Expression System: Bacillus subtilis
• Mutation(s): 1 


• Deposited: 1999-02-27 Released: 1999-05-03 
• Deposition Author(s): Uitdehaag, J.C.M., Dijkstra, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.190 
• R-Value Work: 0.155 

Literature

X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the alpha-amylase family.

Uitdehaag, J.C., Mosi, R., Kalk, K.H., van der Veen, B.A., Dijkhuizen, L., Withers, S.G., Dijkstra, B.W.

(1999) Nat.Struct.Mol.Biol. 6: 432-436

• PubMed: 10331869 
• DOI: 10.1038/8235
• Primary Citation of Related Structures:  
  1CXK


• PubMed Abstract: 
  

Cyclodextrin glycosyltransferase (CGTase) is an enzyme of the alpha-amylase family, which uses a double displacement mechanism to process alpha-linked glucose polymers. We have determined two X-ray structures of CGTase complexes, one with an intact substrate at 2.1 A resolution, and the other with a covalently bound reaction intermediate at 1.8 A resolution. These structures give evidence for substrate distortion and the covalent character of the intermediate and for the first time show, in atomic detail, how catalysis in the alpha-amylase family proceeds by the concerted action of all active site residues.

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Related Citations: 

• 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
• 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
• Reassessment of acarbose as a transition state analogue inhibitor of cyclodextrin glycosyltransferase.
  Mosi, R.,Sham, H.,Uitdehaag, J.C.,Ruiterkamp, R.,Dijkstra, B.W.,Withers, S.G.
  (1998) Biochemistry 37: 17192
• 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




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Organizational Affiliation: 

BIOSON Research Institute, University of Groningen, The Netherlands.

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GLF	A	1-FLUORO-ALPHA-1-DEOXY-D-GLUCOSE C6 H11 F O5 ATMYEINZLWEOQU-DVKNGEFBSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
GLC	A	ALPHA-D-GLUCOSE C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
G4D	A	4-DEOXY-ALPHA-D-GLUCOSE C6 H12 O5 HDEMQQHXNOJATE-AZGQCCRYSA-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: 1.81 Å
• R-Value Free: 0.190 
• R-Value Work: 0.155 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 117.071	α = 90.00
b = 109.281	β = 90.00
c = 65.335	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-02-27 
• Released Date: 1999-05-03 
• Deposition Author(s): Uitdehaag, J.C.M., Dijkstra, B.W.

Revision History 

• Version 1.0: 1999-05-03
  Type: Initial release
• Version 1.1: 2007-10-16
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2019-11-06
  Type: Data collection, Database references, Derived calculations