The modular structure of ThDP-dependent enzymes

Thiamine diphosphate (ThDP)-dependent enzymes form a diverse protein family which was classified into nine superfamilies. The cofactor ThDP is bound at the interface between two catalytic domains, the PYR and the PP domain. The nine superfamilies were assigned to five different structural architectures. Two superfamilies, the sulfopyruvate decarboxylases and α-ketoacid dehydrogenases 2, consist of separate PYR and PP domains. The oxidoreductase superfamily is of the intra-monomer/PYR-PP type with an N-terminal PYR and a subsequent PP domain. The active enzymes form homodimers with the ThDP cofactor bound at the interface between a PYR and a PP domain of the same monomer. Decarboxylases are of the inter-monomer/PYR-PP type with the cofactor bound between domains from different monomers. 1-Deoxy-d-xylulose-5-phosphate synthases are of the intra-monomer/PP-PYR type. The transketolases, α-ketoglutarate dehydrogenases, and α-ketoacid dehydrogenases 1 are of the inter-monomer/PP-PYR type. For the phosphonopyruvate decarboxylases, definitive assessment of the structural architecture is not possible due to lack of structure information. By applying a structure-based domain alignment method, sequences of more than 62,000 PYR and PP domains were identified and aligned. Although the sequence similarity of the catalytic domains is low between different superfamilies, seven positions were identified to be highly conserved, including the cofactor binding GDGX(24,27) N motif, the cofactor-activating glutamic acid, and two structurally equivalent glycines in both the PYR and the PP domain. An evolutionary pathway of ThDP-dependent enzymes is proposed which explains the sequence and structure diversity of this family by three basic evolutionary events: domain recruitment, domain linkage, and structural rearrangement of catalytic domains.