3BMW

Cyclodextrin glycosyl transferase from Thermoanerobacterium thermosulfurigenes EM1 mutant S77P complexed with a maltoheptaose inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

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Ligand Structure Quality Assessment 


This is version 3.1 of the entry. See complete history


Literature

Elimination of competing hydrolysis and coupling side reactions of a cyclodextrin glucanotransferase by directed evolution.

Kelly, R.M.Leemhuis, H.Rozeboom, H.J.van Oosterwijk, N.Dijkstra, B.W.Dijkhuizen, L.

(2008) Biochem J 413: 517-525

  • DOI: 10.1042/BJ20080353
  • Primary Citation of Related Structures:  
    3BMV, 3BMW

  • PubMed Abstract: 
  • Thermoanaerobacterium thermosulfurigenes cyclodextrin glucanotransferase primarily catalyses the formation of cyclic alpha-(1,4)-linked oligosaccharides (cyclodextrins) from starch. This enzyme also possesses unusually high hydrolytic activity as a side reaction, thought to be due to partial retention of ancestral enzyme function ...

    Thermoanaerobacterium thermosulfurigenes cyclodextrin glucanotransferase primarily catalyses the formation of cyclic alpha-(1,4)-linked oligosaccharides (cyclodextrins) from starch. This enzyme also possesses unusually high hydrolytic activity as a side reaction, thought to be due to partial retention of ancestral enzyme function. This side reaction is undesirable, since it produces short saccharides that are responsible for the breakdown of the cyclodextrins formed, thus limiting the yield of cyclodextrins produced. To reduce the competing hydrolysis reaction, while maintaining the cyclization activity, we applied directed evolution, introducing random mutations throughout the cgt gene by error-prone PCR. Mutations in two residues, Ser-77 and Trp-239, on the outer region of the active site, lowered the hydrolytic activity up to 15-fold with retention of cyclization activity. In contrast, mutations within the active site could not lower hydrolytic rates, indicating an evolutionary optimized role for cyclodextrin formation by residues within this region. The crystal structure of the most effective mutant, S77P, showed no alterations to the peptide backbone. However, subtle conformational changes to the side chains of active-site residues had occurred, which may explain the increased cyclization/hydrolysis ratio. This indicates that secondary effects of mutations located on the outer regions of the catalytic site are required to lower the rates of competing side reactions, while maintaining the primary catalytic function. Subsequent functional analysis of various glucanotransferases from the superfamily of glycoside hydrolases also suggests a gradual evolutionary progression of these enzymes from a common 'intermediate-like' ancestor towards specific transglycosylation activity.


    Related Citations: 
    • Engineering of cyclodextrin product specificity and pH optima of the thermostable cyclodextrin glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1
      Wind, R.D., Uitdehaag, J.C.M., Buitelaar, R.M., Dijkstra, B.W., Dijkhuizen, L.
      (1998) J Biol Chem 273: 5771
    • Crystal structure at 2.3 A resolution and revised nucleotide sequence of the thermostable cyclodextrin glycosyltransferase from Thermonanaerobacterium thermosulfurigenes EM1
      Knegtel, R.M.A., Wind, R.D., Rozeboom, H.J., Kalk, K.H., Buitelaar, R.M., Dijkhuizen, L., Dijkstra, B.W.
      (1996) J Mol Biol 256: 611

    Organizational Affiliation

    Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclomaltodextrin glucanotransferaseA683Thermoanaerobacterium thermosulfurigenesMutation(s): 1 
Gene Names: amyA
EC: 2.4.1.19
UniProt
Find proteins for P26827 (Thermoanaerobacterium thermosulfurigenes)
Explore P26827 
Go to UniProtKB:  P26827
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26827
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

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-quinovopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseC 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G31885RT
GlyCosmos:  G31885RT
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseD 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G96370VA
GlyCosmos:  G96370VA
GlyGen:  G96370VA
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACI
Query on ACI

Download Ideal Coordinates CCD File 
E [auth A]6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
C7 H13 N O4
XPHOBMULWMGEBA-VZFHVOOUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-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
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
Balpha-maltoseOligosaccharide / Nutrient Ligand Interaction
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900009
Query on PRD_900009
Dalpha-maltotrioseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.791α = 90
b = 96.582β = 90
c = 115.241γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2017-10-25
    Changes: Advisory, Atomic model, Derived calculations, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2021-11-10
    Changes: Database references, Structure summary