1CXL

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


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

  • 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 ...

    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.


    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

    Organizational Affiliation

    BIOSON Research Institute, University of Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (CYCLODEXTRIN-GLYCOSYLTRANSFERASE)A686Niallia circulansMutation(s): 1 
Gene Names: cgt
EC: 2.4.1.19
UniProt
Find proteins for P43379 (Bacillus circulans)
Explore P43379 
Go to UniProtKB:  P43379
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
4-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseB3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G46685FC
GlyCosmos:  G46685FC
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
4-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseC2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G32509JF
GlyCosmos:  G32509JF
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
4-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranosyl fluorideD, E3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G06043OH
GlyCosmos:  G06043OH
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
H [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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 = 117.071α = 90
b = 109.281β = 90
c = 65.335γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
TNTphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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