6SAO

Structural and functional characterisation of three novel fungal amylases with enhanced stability and pH tolerance


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.110 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Functional Characterization of Three Novel Fungal Amylases with Enhanced Stability and pH Tolerance.

Roth, C.Moroz, O.V.Turkenburg, J.P.Blagova, E.Waterman, J.Ariza, A.Ming, L.Tianqi, S.Andersen, C.Davies, G.J.Wilson, K.S.

(2019) Int J Mol Sci 20: --

  • DOI: 10.3390/ijms20194902
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Amylases are probably the best studied glycoside hydrolases and have a huge biotechnological value for industrial processes on starch. Multiple amylases from fungi and microbes are currently in use. Whereas bacterial amylases are well suited for many ...

    Amylases are probably the best studied glycoside hydrolases and have a huge biotechnological value for industrial processes on starch. Multiple amylases from fungi and microbes are currently in use. Whereas bacterial amylases are well suited for many industrial processes due to their high stability, fungal amylases are recognized as safe and are preferred in the food industry, although they lack the pH tolerance and stability of their bacterial counterparts. Here, we describe three amylases, two of which have a broad pH spectrum extending to pH 8 and higher stability well suited for a broad set of industrial applications. These enzymes have the characteristic GH13 α-amylase fold with a central (β/α) 8 -domain, an insertion domain with the canonical calcium binding site and a C-terminal β-sandwich domain. The active site was identified based on the binding of the inhibitor acarbose in form of a transglycosylation product, in the amylases from Thamnidium elegans and Cordyceps farinosa . The three amylases have shortened loops flanking the nonreducing end of the substrate binding cleft, creating a more open crevice. Moreover, a potential novel binding site in the C-terminal domain of the Cordyceps enzyme was identified, which might be part of a starch interaction site. In addition, Cordyceps farinosa amylase presented a successful example of using the microseed matrix screening technique to significantly speed-up crystallization.


    Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK. antonio.ariza@path.ox.ac.uk.,York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK. Christian.Roth@mpikg.mpg.de.,York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK. Johan.turkenburg@york.ac.uk.,York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK. gideon.davies@york.ac.uk.,Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK. jitka.waterman@diamond.ac.uk.,York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK. lena.blagova@york.ac.uk.,York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK. olga.moroz@york.ac.uk.,York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK. antonio.ariza@path.ox.ac.uk.,Novozymes (China) Investment Co. Ltd., 14 Xinli Road, Haidian District, Beijing 100085, China. TQSU@novozymes.com.,Novozymes (China) Investment Co. Ltd., 14 Xinli Road, Haidian District, Beijing 100085, China. MLIX@novozymes.com.,Novozymes (Denmark), Krogshojvej 36, DK-2880 Bagsvaerd, Denmark. CarA@novozymes.com.,Carbohydrates: Structure and Function, Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14195 Berlin, Germany. Christian.Roth@mpikg.mpg.de.,York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK. keith.wilson@york.ac.uk.,York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK. jitka.waterman@diamond.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
amylase
A
439N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AC1
Query on AC1

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A
6-METHYL-5-(4,5,6-TRIHYDROXY-3-HYDROXYMETHYL-CYCLOHEX-2-ENYLAMINO)-TETRAHYDRO-PYRAN-2,3,4-TRIOL
N-[4-HYDROXYMETHYL-CYCLOHEXAN-6-YL-1,2,3-TRIOL]-4,6-DIDEOXY-4-AMINOGLUCOPYRANOSIDE
C13 H23 N O8
RBZIIHWPZWOIDU-ZCGMLSCUSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

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Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
GLC
Query on GLC

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Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.110 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.015α = 90.00
b = 56.633β = 90.00
c = 166.012γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-10-30
    Type: Data collection, Database references