9EGA | pdb_00009ega

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

• PDB DOI: https://doi.org/10.2210/pdb9EGA/pdb

• Classification: HYDROLASE
• Organism(s): Pedobacter psychrotolerans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-21 Released: 2025-08-13 
• Deposition Author(s): Vieira, P.S., Morais, M.A.B., Murakami, M.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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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

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

• PubMed: 40745183 
• DOI: https://doi.org/10.1038/s41467-025-62387-5
• Primary Citation Related Structures: 
  9EGA, 9H4U


• 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.

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Organizational Affiliation: 
• Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany.
Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil.
Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany.
Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany.
Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany.
Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil. [e-mail].
Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany. [e-mail].
Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 145.8 kDa 
• Atom Count: 11,893 
• Modeled Residue Count: 1,249 
• Deposited Residue Count: 1,288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialate O-acetylesterase	A, B	644	Pedobacter psychrotolerans	Mutation(s): 0  Gene Names: EV200_102244
UniProt
Find proteins for A0A4R2HIK5 (Pedobacter psychrotolerans) Explore A0A4R2HIK5  Go to UniProtKB:  A0A4R2HIK5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMS	E [auth A], G [auth B]	phenylmethanesulfonic acid C7 H8 O3 S NIXKBAZVOQAHGC-UHFFFAOYSA-N
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 56.134	α = 90
b = 125.135	β = 104.71
c = 108.688	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Vieira, P.S., Morais, M.A.B., Murakami, M.T.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	16/06509-0
Sao Paulo Research Foundation (FAPESP)	Brazil	15/26982-0

Revision History  

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