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 

Starting Model: experimental
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This is version 2.3 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: https://doi.org/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.

    • Organizational Affiliation: 

    BIOSON Research Institute, University of Groningen, The Netherlands.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (CYCLODEXTRIN-GLYCOSYLTRANSFERASE)686Niallia circulansMutation(s): 1 
EC: 2.4.1.19
UniProt
Find proteins for P43379 (Niallia circulans)
Explore P43379 
Go to UniProtKB:  P43379
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43379
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
3N/A
Glycosylation Resources
GlyTouCan:  G46685FC
GlyCosmos:  G46685FC
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G32509JF
GlyCosmos:  G32509JF
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranosyl fluoride
D, E
3N/AN/A
Glycosylation Resources
GlyTouCan:  G06043OH
GlyCosmos:  G06043OH
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

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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
  • Version 2.1: 2021-11-03
    Changes: Database references, Structure summary
  • Version 2.2: 2023-08-09
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-11-13
    Changes: Structure summary