7AYG

oxalyl-CoA decarboxylase from Methylorubrum extorquens with bound TPP and ADP

Summary for 7AYG

• Entry DOI: 10.2210/pdb7ayg/pdb
• Descriptor: Putative oxalyl-CoA decarboxylase (Oxc, yfdU), THIAMINE DIPHOSPHATE, ADENOSINE-5'-DIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: lyase, decarboxylase, carboxylase, ligase, formyl-coa, oxalyl-coa, mandelyl-coa
• Biological source: Methylorubrum extorquens AM1
• Total number of polymer chains: 8
• Total formula weight: 501165.72

Authors

Pfister, P.,Burgener, S.,Nattermann, M.,Zarzycki, J.,Erb, T.J. (deposition date: 2020-11-12, release date: 2021-04-28, Last modification date: 2024-01-31)

Primary citation

Nattermann, M.,Burgener, S.,Pfister, P.,Chou, A.,Schulz, L.,Lee, S.H.,Paczia, N.,Zarzycki, J.,Gonzalez, R.,Erb, T.J.
Engineering a Highly Efficient Carboligase for Synthetic One-Carbon Metabolism.
Acs Catalysis, 11:5396-5404, 2021

PubMed Abstract: One of the biggest challenges to realize a circular carbon economy is the synthesis of complex carbon compounds from one-carbon (C1) building blocks. Since the natural solution space of C1-C1 condensations is limited to highly complex enzymes, the development of more simple and robust biocatalysts may facilitate the engineering of C1 assimilation routes. Thiamine diphosphate-dependent enzymes harbor great potential for this task, due to their ability to create C-C bonds. Here, we employed structure-guided iterative saturation mutagenesis to convert oxalyl-CoA decarboxylase (OXC) from into a glycolyl-CoA synthase (GCS) that allows for the direct condensation of the two C1 units formyl-CoA and formaldehyde. A quadruple variant MeOXC4 showed a 100 000-fold switch between OXC and GCS activities, a 200-fold increase in the GCS activity compared to the wild type, and formaldehyde affinity that is comparable to natural formaldehyde-converting enzymes. Notably, MeOCX4 outcompetes all other natural and engineered enzymes for C1-C1 condensations by more than 40-fold in catalytic efficiency and is highly soluble in . In addition to the increased GCS activity, MeOXC4 showed up to 300-fold higher activity than the wild type toward a broad range of carbonyl acceptor substrates. When applied in vivo, MeOXC4 enables the production of glycolate from formaldehyde, overcoming the current bottleneck of C1-C1 condensation in whole-cell bioconversions and paving the way toward synthetic C1 assimilation routes in vivo.

PubMed: 34484855
DOI: 10.1021/acscatal.1c01237

Experimental method

X-RAY DIFFRACTION (1.9 Å)