Structural Analysis of Phosphonopyruvate Decarboxylase RhiEF: First Insights into an Ancestral Heterooligomeric Thiamine Pyrophosphate-Dependent Decarboxylase

The RhiE and RhiF proteins work together as RhiEF and function as a thiamine pyrophosphate (TPP)-dependent phosphonopyruvate decarboxylase to produce phosphonoacetaldehyde in the rhizocticin biosynthesis pathway. In this study, we determined the crystal structure of the RhiEF complexed with TPP and Mg²⁺. RhiEF forms a dimer of heterodimers, and the cofactor TPP is bound at the heterotetrameric subunit interface. Structural analysis of RhiEF revealed that the RhiE and RhiF moieties correspond to the pyrimidine-binding (PYR) and pyrophosphate-binding (PP) domains commonly found in TPP-dependent enzymes, respectively, as predicted by amino acid sequence alignment analysis. In contrast to other TPP-dependent enzymes with known structures, RhiEF has no domains other than the PYR and PP domains. Furthermore, structure-based evolutionary and sequence-based phylogenetic analyses have suggested that heteromultimeric enzymes such as RhiEF are ancestral types. These results indicate that RhiEF is one of the smallest and most ancient TPP-dependent decarboxylases. Based on the structural comparisons of RhiEF with other TPP-dependent decarboxylases, we identified the amino acid residues responsible for the catalytic mechanism of TPP-dependent decarboxylation in RhiEF.