9EGA | pdb_00009ega

Crystal Structure of a CE20 carbohydrate acetylesterase from Pedobacter psychrotolerans (PpCE20_II), with ancillary domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.192 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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Literature

Insights into a water-mediated catalytic triad architecture in CE20 carbohydrate esterases.

Teune, M.Vieira, P.S.Dohler, T.Palm, G.J.Dutschei, T.Bartosik, D.Berndt, L.Persinoti, G.F.Maass, S.Becher, D.Schweder, T.Murakami, M.T.Lammers, M.Bornscheuer, U.T.

(2025) Nat Commun 16: 7034-7034

  • DOI: https://doi.org/10.1038/s41467-025-62387-5
  • Primary Citation of Related Structures:  
    9EGA

  • PubMed Abstract: 

    Carbohydrate esterases modify polysaccharides by removing different ester moieties thereby affecting their physicochemical properties and their accessibility by glycoside hydrolases. We determined the full-length structures of two members (Fl8CE20_II and PpCE20_II) from the carbohydrate esterase family 20 (CE20) by X-ray crystallography that feature an ancillary domain, inserted into the catalytic SGNH-hydrolase domain. Detailed structural analysis identifies a so far undescribed catalytic triad architecture which lacks the typical aspartate for polarization of the histidine but instead reveals a precisely coordinated water molecule mediating contact between the His and Asp. This coordinated water in the Ser-His-(H 2 O-Asp/Asn) motif, as further confirmed by mutational studies and by determination of kinetic constants, is crucial for catalytic activity. We therefore term this active site architecture a water-mediated catalytic triad.


  • Organizational Affiliation

    Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sialate O-acetylesterase
A, B
644Pedobacter psychrotoleransMutation(s): 0 
Gene Names: EV200_102244
UniProt
Find proteins for A0A4R2HIK5 (Pedobacter psychrotolerans)
Explore A0A4R2HIK5 
Go to UniProtKB:  A0A4R2HIK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4R2HIK5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.192 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.134α = 90
b = 125.135β = 104.71
c = 108.688γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil16/06509-0
Sao Paulo Research Foundation (FAPESP)Brazil15/26982-0

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release