8B30 | pdb_00008b30

Structure of the Reconstructed Ancestor of Phenolic Acid Decarboxylase AncPAD31

• PDB DOI: https://doi.org/10.2210/pdb8B30/pdb

• Classification: LYASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-15 Released: 2023-09-27 
• Deposition Author(s): Mokos, D., Schruefer, A., Gruber, K., Daniel, B.
• Funding Organization(s): H2020 Marie Curie Actions of the European Commission, Austrian Research Promotion Agency, Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.284 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

Stability Increase of Phenolic Acid Decarboxylase by a Combination of Protein and Solvent Engineering Unlocks Applications at Elevated Temperatures.

Myrtollari, K., Calderini, E., Kracher, D., Schongassner, T., Galusic, S., Slavica, A., Taden, A., Mokos, D., Schrufer, A., Wirnsberger, G., Gruber, K., Daniel, B., Kourist, R.

(2024) ACS Sustain Chem Eng 12: 3575-3584

• PubMed: 38456190 
• DOI: https://doi.org/10.1021/acssuschemeng.3c06513
• Primary Citation Related Structures: 
  8A85, 8ADX, 8B30, 8C66


• PubMed Abstract: 
  

  Enzymatic decarboxylation of biobased hydroxycinnamic acids gives access to phenolic styrenes for adhesive production. Phenolic acid decarboxylases are proficient enzymes that have been applied in aqueous systems, organic solvents, biphasic systems, and deep eutectic solvents, which makes stability a key feature. Stabilization of the enzyme would increase the total turnover number and thus reduce the energy consumption and waste accumulation associated with biocatalyst production. In this study, we used ancestral sequence reconstruction to generate thermostable decarboxylases. Investigation of a set of 16 ancestors resulted in the identification of a variant with an unfolding temperature of 78.1 °C and a half-life time of 45 h at 60 °C. Crystal structures were determined for three selected ancestors. Structural attributes were calculated to fit different regression models for predicting the thermal stability of variants that have not yet been experimentally explored. The models rely on hydrophobic clusters, salt bridges, hydrogen bonds, and surface properties and can identify more stable proteins out of a pool of candidates. Further stabilization was achieved by the application of mixtures of natural deep eutectic solvents and buffers. Our approach is a straightforward option for enhancing the industrial application of the decarboxylation process.

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Organizational Affiliation: 
• Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.
Austrian Centre of Industrial Biotechnology, ACIB GmbH, Petersgasse 14/1, 8010 Graz, Austria.
Adhesive Technologies, Henkel AG & Co. KGaA, Henkelstr. 67, 40191 Düsseldorf, Germany.
BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria.
Faculty of Food Technology and Biotechnology, Department of Biochemical Engineering, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia.
Institute of Molecular Biosciences, University of Graz, NAWI Graz, Humboldtstraße 50/3, 8010 Graz, Austria.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.8 kDa 
• Atom Count: 2,624 
• Modeled Residue Count: 317 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenolic acid decarboxylase N31	A, B	190	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.284 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.069	α = 90
b = 59.971	β = 90
c = 105.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
PROTEUM	data reduction
PROTEUM	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-27 
Deposition Author(s): Mokos, D., Schruefer, A., Gruber, K., Daniel, B.

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Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	860414
Austrian Research Promotion Agency	Austria	870454
Austrian Science Fund	Austria	P 34337-B

Revision History  

• Version 1.0: 2023-09-27
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Database references
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary