8PN8

Engineered glycolyl-CoA carboxylase (L100N variant) with bound CoA

Summary for 8PN8

• Entry DOI: 10.2210/pdb8pn8/pdb
• EMDB information: 17778
• Descriptor: Propionyl-CoA carboxylase beta chain, Propionyl-CoA carboxylase alpha subunit, COENZYME A, ... (5 entities in total)
• Functional Keywords: glycolyl-coa carboxylase, ligase
• Biological source: Methylorubrum extorquens AM1; More
• Total number of polymer chains: 12
• Total formula weight: 773842.55

Authors

Zarzycki, J.,Marchal, D.G.,Schulz, L.,Prinz, S.,Erb, T.J. (deposition date: 2023-06-30, release date: 2023-11-29, Last modification date: 2023-12-27)

Primary citation

Marchal, D.G.,Schulz, L.,Schuster, I.,Ivanovska, J.,Paczia, N.,Prinz, S.,Zarzycki, J.,Erb, T.J.
Machine Learning-Supported Enzyme Engineering toward Improved CO 2 -Fixation of Glycolyl-CoA Carboxylase.
Acs Synth Biol, 12:3521-3530, 2023

PubMed Abstract: Glycolyl-CoA carboxylase (GCC) is a new-to-nature enzyme that catalyzes the key reaction in the tartronyl-CoA (TaCo) pathway, a synthetic photorespiration bypass that was recently designed to improve photosynthetic CO fixation. GCC was created from propionyl-CoA carboxylase (PCC) through five mutations. However, despite reaching activities of naturally evolved biotin-dependent carboxylases, the quintuple substitution variant GCC M5 still lags behind 4-fold in catalytic efficiency compared to its template PCC and suffers from futile ATP hydrolysis during CO fixation. To further improve upon GCC M5, we developed a machine learning-supported workflow that reduces screening efforts for identifying improved enzymes. Using this workflow, we present two novel GCC variants with 2-fold increased carboxylation rate and 60% reduced energy demand, respectively, which are able to address kinetic and thermodynamic limitations of the TaCo pathway. Our work highlights the potential of combining machine learning and directed evolution strategies to reduce screening efforts in enzyme engineering.

PubMed: 37983631
DOI: 10.1021/acssynbio.3c00403

Experimental method

ELECTRON MICROSCOPY (2.31 Å)