Computational protein design enables a novel one-carbon assimilation pathway

Proc Natl Acad Sci U S A. 2015 Mar 24;112(12):3704-9. doi: 10.1073/pnas.1500545112. Epub 2015 Mar 9.


We describe a computationally designed enzyme, formolase (FLS), which catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon dihydroxyacetone molecule. The existence of FLS enables the design of a new carbon fixation pathway, the formolase pathway, consisting of a small number of thermodynamically favorable chemical transformations that convert formate into a three-carbon sugar in central metabolism. The formolase pathway is predicted to use carbon more efficiently and with less backward flux than any naturally occurring one-carbon assimilation pathway. When supplemented with enzymes carrying out the other steps in the pathway, FLS converts formate into dihydroxyacetone phosphate and other central metabolites in vitro. These results demonstrate how modern protein engineering and design tools can facilitate the construction of a completely new biosynthetic pathway.

Keywords: carbon fixation; computational protein design; pathway engineering.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Biomass
  • Biosynthetic Pathways
  • Carbon / chemistry*
  • Carbon Cycle
  • Catalysis
  • Cloning, Molecular
  • Escherichia coli / enzymology
  • Formaldehyde / chemistry
  • Formates / chemistry
  • Magnetic Resonance Spectroscopy
  • Polymerase Chain Reaction
  • Protein Engineering / methods*
  • Proteins / chemistry*
  • Software
  • Thermodynamics


  • Formates
  • Proteins
  • formic acid
  • Formaldehyde
  • Carbon

Associated data

  • PDB/4QPZ
  • PDB/4QQ8