1A47

CGTASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES EM1 IN COMPLEX WITH A MALTOHEXAOSE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Engineering of cyclodextrin product specificity and pH optima of the thermostable cyclodextrin glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1.

Wind, R.D.Uitdehaag, J.C.Buitelaar, R.M.Dijkstra, B.W.Dijkhuizen, L.

(1998) J Biol Chem 273: 5771-5779

  • DOI: 10.1074/jbc.273.10.5771
  • Primary Citation of Related Structures:  
    1A47

  • PubMed Abstract: 
  • The product specificity and pH optimum of the thermostable cyclodextrin glycosyltransferase (CGTase) from Thermoanaerobacterium thermosulfurigenes EM1 was engineered using a combination of x-ray crystallography and site-directed mutagenesis. Previously, a crystal soaking experiment with the Bacillus circulans strain 251 beta-CGTase had revealed a maltononaose inhibitor bound to the enzyme in an extended conformation ...

    The product specificity and pH optimum of the thermostable cyclodextrin glycosyltransferase (CGTase) from Thermoanaerobacterium thermosulfurigenes EM1 was engineered using a combination of x-ray crystallography and site-directed mutagenesis. Previously, a crystal soaking experiment with the Bacillus circulans strain 251 beta-CGTase had revealed a maltononaose inhibitor bound to the enzyme in an extended conformation. An identical experiment with the CGTase from T. thermosulfurigenes EM1 resulted in a 2.6-A resolution x-ray structure of a complex with a maltohexaose inhibitor, bound in a different conformation. We hypothesize that the new maltohexaose conformation is related to the enhanced alpha-cyclodextrin production of the CGTase. The detailed structural information subsequently allowed engineering of the cyclodextrin product specificity of the CGTase from T. thermosulfurigenes EM1 by site-directed mutagenesis. Mutation D371R was aimed at hindering the maltohexaose conformation and resulted in enhanced production of larger size cyclodextrins (beta- and gamma-CD). Mutation D197H was aimed at stabilization of the new maltohexaose conformation and resulted in increased production of alpha-CD. Glu258 is involved in catalysis in CGTases as well as alpha-amylases, and is the proton donor in the first step of the cyclization reaction. Amino acids close to Glu258 in the CGTase from T. thermosulfurigenes EM1 were changed. Phe284 was replaced by Lys and Asn327 by Asp. The mutants showed changes in both the high and low pH slopes of the optimum curve for cyclization and hydrolysis when compared with the wild-type enzyme. This suggests that the pH optimum curve of CGTase is determined only by residue Glu258.


    Related Citations: 
    • Crystal Structure at 2.3 A Resolution and Revised Nucleotide Sequence of the Thermostable Cyclodextrin Glycosyltransferase from Thermoanaerobacterium Thermosulfurigenes Em1
      Knegtel, R.M., Wind, R.D., Rozeboom, H.J., Kalk, K.H., Buitelaar, R.M., Dijkhuizen, L., Dijkstra, B.W.
      (1996) J Mol Biol 256: 611
    • 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

    Organizational Affiliation

    Agrotechnological Research Institute, P. O. Box 17, 6700 AA Wageningen, The Netherlands. r.d.wind@ato.dlo.nl



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLODEXTRIN GLYCOSYLTRANSFERASEA683Thermoanaerobacterium thermosulfurigenesMutation(s): 0 
Gene Names: amyA
EC: 2.4.1.19
UniProt
Find proteins for P26827 (Thermoanaerobacterium thermosulfurigenes)
Explore P26827 
Go to UniProtKB:  P26827
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseB3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G96370VA
GlyCosmos:  G96370VA
GlyGen:  G96370VA
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseC3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G31885RT
GlyCosmos:  G31885RT
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseD2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADH (Subject of Investigation/LOI)
Query on ADH

Download Ideal Coordinates CCD File 
E [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 
F [auth A], G [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900009
Query on PRD_900009
Balpha-maltotrioseOligosaccharide / Nutrient Ligand Interaction
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
Dalpha-maltoseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.996α = 90
b = 97.789β = 90
c = 116.263γ = 90
Software Package:
Software NamePurpose
BIOMOLmodel building
TNTrefinement
XDSdata reduction
BIOMOLdata scaling
BIOMOLphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-06-17
    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, Non-polymer description, Other, Structure summary
  • Version 2.1: 2019-11-20
    Changes: Data collection, Derived calculations
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary