8S6D | pdb_00008s6d

Fumonisin B1 esterase

• PDB DOI: https://doi.org/10.2210/pdb8S6D/pdb

• Classification: HYDROLASE
• Organism(s): Caulobacter sp.
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2024-02-27 Released: 2025-02-12 
• Deposition Author(s): Nagy, G.N., Incze, D.J., Bata, Z., Molnar, Z., Leveles, I., Vertessy, B.G., Poppe, L.
• Funding Organization(s): National Research Development and Innovation Office (NKFIH)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.211 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: in silico

Literature

Understanding the molecular mechanism of fumonisin esterases by kinetic and structural studies.

Incze, D.J., Molnar, Z., Nagy, G.N., Leveles, I., Vertessy, B.G., Poppe, L., Bata, Z.

(2025) Food Chem 473: 143110-143110

• PubMed: 39892340 
• DOI: https://doi.org/10.1016/j.foodchem.2025.143110
• Primary Citation of Related Structures:  
  8S6D


• PubMed Abstract: 
  

  Fumonisins are sphingolipid-like mycotoxins that cause serious damage by contaminating food and feed. The tricarballylic acid (TCA) units of fumonisin B ₁ (FB ₁ ; accounting for 70 % of fumonisin contamination) can be removed by fumonisin B ₁ esterase (FE, EC 3.1.1.87) providing a biotechnological FB ₁ detoxification possibility. Here, we report the regioselective cleavage of the TCA ester at C6 in the first step of FB ₁ hydrolysis and kinetic characterization for two FEs. The low K _M values (4.76-44.3 μM) are comparable to concentrations of environmental contaminations, and the high catalytic efficiencies are promising for practical applications. The X-ray structure of one of the FEs enabled the understanding of the FB ₁ hydrolysis at molecular level and revealed an arginine pocket key for substrate binding, and the catalytic role of the glutamate preceding the catalytic serine. Computations showed that this FE is likely capable of detoxifying any fumonisin indicating its potential applicability in food and feed products.

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Organizational Affiliation: 
• Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, Budapest 1111, Hungary; Dr. Bata Ltd., Research and Development Laboratory, Bajcsy-Zsilinszky u. 139, Ócsa 2364, Hungary.
Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, Budapest 1111, Hungary; Institute of Molecular Life Sciences, HUN-REN, Research Centre for Natural Sciences, Magyar Tudósok krt. 2, Budapest 1117, Hungary.
Institute of Molecular Life Sciences, HUN-REN, Research Centre for Natural Sciences, Magyar Tudósok krt. 2, Budapest 1117, Hungary; Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, Budapest 1111, Hungary.
Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, Budapest 1111, Hungary; Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University of Cluj-Napoca, Arany János str. 11, Cluj-Napoca 400028, Romania. Electronic address: [e-mail].
Dr. Bata Ltd., Research and Development Laboratory, Bajcsy-Zsilinszky u. 139, Ócsa 2364, Hungary. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.22 kDa 
• Atom Count: 3,921 
• Modeled Residue Count: 485 
• Deposited Residue Count: 499 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fumonisin B1 esterase	A	499	Caulobacter sp.	Mutation(s): 0  EC: 3.1.1.87
UniProt
Find proteins for D2D3B6 (Sphingopyxis macrogoltabida) Explore D2D3B6  Go to UniProtKB:  D2D3B6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.211 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.308	α = 90
b = 106.217	β = 90
c = 117.75	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
autoPROC	data scaling
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Nagy, G.N., Incze, D.J., Bata, Z., Molnar, Z., Leveles, I., Vertessy, B.G., Poppe, L.

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Funding Organization	Location	Grant Number
National Research Development and Innovation Office (NKFIH)	Hungary	TKP2021-EGA-02
National Research Development and Innovation Office (NKFIH)	Hungary	C1341189

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release