8OE2

Structure of hyperstable haloalkane dehalogenase variant DhaA223

Summary for 8OE2

• Entry DOI: 10.2210/pdb8oe2/pdb
• Descriptor: Haloalkane dehalogenase, CHLORIDE ION, SULFATE ION, ... (7 entities in total)
• Functional Keywords: engineered haloalkane dehalogenase, hydrolase
• Biological source: synthetic construct
• Total number of polymer chains: 6
• Total formula weight: 210550.16

Authors

Marek, M. (deposition date: 2023-03-10, release date: 2024-01-17)

Primary citation

Kunka, A.,Marques, S.M.,Havlasek, M.,Vasina, M.,Velatova, N.,Cengelova, L.,Kovar, D.,Damborsky, J.,Marek, M.,Bednar, D.,Prokop, Z.
Advancing Enzyme's Stability and Catalytic Efficiency through Synergy of Force-Field Calculations, Evolutionary Analysis, and Machine Learning.
Acs Catalysis, 13:12506-12518, 2023

PubMed Abstract: Thermostability is an essential requirement for the use of enzymes in the bioindustry. Here, we compare different protein stabilization strategies using a challenging target, a stable haloalkane dehalogenase DhaA115. We observe better performance of automated stabilization platforms FireProt and PROSS in designing multiple-point mutations over the introduction of disulfide bonds and strengthening the intra- and the inter-domain contacts by saturation mutagenesis. We reveal that the performance of automated stabilization platforms was still compromised due to the introduction of some destabilizing mutations. Notably, we show that their prediction accuracy can be improved by applying manual curation or machine learning for the removal of potentially destabilizing mutations, yielding highly stable haloalkane dehalogenases with enhanced catalytic properties. A comparison of crystallographic structures revealed that current stabilization rounds were not accompanied by large backbone re-arrangements previously observed during the engineering stability of DhaA115. Stabilization was achieved by improving local contacts including protein-water interactions. Our study provides guidance for further improvement of automated structure-based computational tools for protein stabilization.

PubMed: 37822856
DOI: 10.1021/acscatal.3c02575

Experimental method

X-RAY DIFFRACTION (1.51 Å)