Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.55 kDa 
• Atom Count: 6063 
• Modelled Residue Count: 686 
• Deposited Residue Count: 686 
• Unique protein chains: 1

1CXL

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

• PDB DOI: 10.2210/pdb1CXL/pdb

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


• 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 Biol 6: 432-436

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


• 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: 

• 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

• 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

• 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

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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
4-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G46685FC GlyCosmos:  G46685FC

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
4-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G32509JF GlyCosmos:  G32509JF

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
4-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranosyl fluoride	D, E	3		N/A
Glycosylation Resources
GlyTouCan:  G06043OH GlyCosmos:  G06043OH

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	H [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-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
b = 109.281	β = 90
c = 65.335	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: 1999-02-27 
• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-11-06
  Changes: Data collection, Database references, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-11-03
  Changes: Database references, Structure summary