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TitleMachine Learning-Supported Enzyme Engineering toward Improved CO-Fixation of Glycolyl-CoA Carboxylase.
Journal, issue, pagesACS Synth Biol, Vol. 12, Issue 12, Page 3521-3530, Year 2023
Publish dateDec 15, 2023
AuthorsDaniel G Marchal / Luca Schulz / Ingmar Schuster / Jelena Ivanovska / Nicole Paczia / Simone Prinz / Jan Zarzycki / Tobias J Erb /
PubMed AbstractGlycolyl-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 ...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.
External linksACS Synth Biol / PubMed:37983631 / PubMed Central
MethodsEM (single particle)
Resolution2.03 - 2.31 Å
Structure data

17777

8pn7

EMDB-17777, PDB-8pn7:
Engineered glycolyl-CoA carboxylase (G20R variant) with bound CoA
Method: EM (single particle) / Resolution: 2.03 Å

17778

8pn8

EMDB-17778: Engineered glycolyl-CoA carboxylase (G20R variant) with bound CoA
PDB-8pn8: Engineered glycolyl-CoA carboxylase (L100N variant) with bound CoA
Method: EM (single particle) / Resolution: 2.31 Å

Chemicals

ChemComp-COA:
COENZYME A / Coenzyme A

ChemComp-BTI:
5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

ChemComp-HOH:
WATER / Water

Source
  • methylorubrum extorquens am1 (bacteria)
KeywordsLIGASE / glycolyl-CoA carboxylase

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