2DIJ

COMPLEX OF A Y195F MUTANT CGTASE FROM B. CIRCULANS STRAIN 251 COMPLEXED WITH A MALTONONAOSE INHIBITOR AT PH 9.8 OBTAINED AFTER SOAKING THE CRYSTAL WITH ACARBOSE AND MALTOHEXAOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å

wwPDB Validation   3D Report Full Report


This is version 3.1 of the entry. See complete history


Literature

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: 4241-4249

  • DOI: 10.1021/bi952339h
  • Primary Citation of Related Structures:  
    2DIJ

  • PubMed Abstract: 
  • Crystals of the Y195F mutant of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 were subjected to a double soaking procedure, in which they were first soaked in a solution containing the inhibitor acarbose and subsequently in a solution containing maltohexaose ...

    Crystals of the Y195F mutant of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 were subjected to a double soaking procedure, in which they were first soaked in a solution containing the inhibitor acarbose and subsequently in a solution containing maltohexaose. The refined structure of the resulting protein-carbohydrate complex has final crystallographic and free R-factors for data in the 8-2.6 angstrom resolution range of 15.0% and 21.5%, respectively, and reveals that a new inhibitor, composed of nine saccharide residues, is bound in the active site. The first four residues correspond to acarbose and occupy the same subsites near the catalytic residues as observed in the previously reported acarbose-enzyme complex [Strokopytov et al. (1995) Biochemistry 34, 2234-2240]. An oliogosaccharide consisting of five glucose residues has been coupled to the nonreducing end of acarbose. At the fifth residue the polysaccharide chain makes a sharp turn, allowing it to interact with residues Tyr89, Phe195, and Asn193 and a flexible loop formed by residues 145-148. On the basis of the refined model of the complex an explanation is given for the product specificity of CGTases.


    Related Citations: 
    • Reassessment of Acarbose as a Transition State Analogue Inhibitor of Cyclodextrin Glycosyltransferase
      Mosi, R., Sham, H., Uitdehaag, J.C.M., Ruiterkamp, R., Dijkstra, B.W., Withers, S.G.
      (1998) Biochemistry 37: 17192
    • Kinetic Evidence that Acarbose is a Transition State Analogue Inhibitor of Cyclodextrin Glycosyltransferase
      Mosi, R., Sham, H., Uitdehaag, J.C.M., Ruiterkamp, R., Dijkstra, B.W., Withers, S.G.
      () To be published --: --
    • X-Ray Structure of Cyclodextrin Glycosyltransferase Complexed with Acarbose. Implications for the Catalytic Mechanism of Glycosidases
      Strokopytov, B., Penninga, D., Rozeboom, H.J., Kalk, K.H., Dijkhuizen, L., Dijkstra, B.W.
      (1995) Biochemistry 34: 2234
    • Site-Directed Mutations in Tyrosine 195 of Cyclodextrin Glycosyltransferase from Bacillus Circulans Strain 251 Affect Activity and Product Specificity
      Penninga, D., Strokopytov, B., Rozeboom, H.J., Lawson, C.L., Dijkstra, B.W., Bergsma, J., Dijkhuizen, L.
      (1995) Biochemistry 34: 3368
    • 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
    • Maltodextrin-Dependent Crystallization of Cyclomaltodextrin Glucanotransferase from Bacillus Circulans
      Lawson, C.L., Bergsma, J., Bruinenberg, P.M., De Vries, G., Dijkhuizen, L., Dijkstra, B.W.
      (1990) J Mol Biol 214: 807

    Organizational Affiliation

    BIOSON Research Institute and Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLODEXTRIN GLYCOSYLTRANSFERASEA686Niallia circulansMutation(s): 1 
Gene Names: cgt
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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseB 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseC 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G96370VA
GlyCosmos:  G96370VA
GlyGen:  G96370VA
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseD 5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G50146AM
GlyCosmos:  G50146AM
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranoseE 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G96906VH
GlyCosmos:  G96906VH
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseF 6N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G91368RN
GlyCosmos:  G91368RN
GlyGen:  G91368RN
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADH
Query on ADH

Download Ideal Coordinates CCD File 
I [auth A]1-AMINO-2,3-DIHYDROXY-5-HYDROXYMETHYL CYCLOHEX-5-ENE
C7 H13 N O3
BMZJPVSGERKRHP-ACZMJKKPSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 4 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
Balpha-maltoseOligosaccharide / Nutrient Ligand Interaction
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900009
Query on PRD_900009
Calpha-maltotrioseOligosaccharide / Nutrient Ligand Interaction
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900030
Query on PRD_900030
Dalpha-maltopentaoseOligosaccharide / Substrate analog Ligand Interaction
Entity ID: 6
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900035
Query on PRD_900035
Falpha-maltohexaoseOligosaccharide / Substrate analog Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.964α = 90
b = 111.282β = 90
c = 67.977γ = 90
Software Package:
Software NamePurpose
MADNESdata collection
BIOMOLdata reduction
TNTrefinement
MADNESdata reduction
BIOMOLdata scaling
TNTphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-12-09
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2017-10-25
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2018-04-18
    Changes: Data collection
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2021-11-03
    Changes: Database references, Structure summary