Thiamin-Diphosphate Enzymes Are an Ancient Family of Repeat Proteins

A repeating sequence and structure pattern that is highly similar to the canonical cofactor binding motif has been identified in the thiamin-diphosphate dependent (ThDP) enzyme family. We have identified more than a thousand of these repeats in a non-redundant set (N = 58) of ThDP enzyme structures. The repeating element has a helix-turn-strand secondary structure which typically begins with an [G/A]{X(1,2)}[G/A] sequence motif with a typical length of 29 residues. The catalytically important diphosphate and aminopyrimidine interacting domains are comprised of a set of six of these repeats in a conserved architecture with a flavodoxin-like 213465 strand order. The canonical ThDP binding motif is the fourth repeat in the ThDP binding domain, while the conserved aminopyrimidine interacting glutamate is part of the second repeat in its domain. The third and fourth repeats form a contact between the functional domains, while the fifth repeat in the N-terminal domain forms an inter-chain contact. The conservation of these functional properties highlights the role of these repeats in the function and structure of this well-studied enzyme family and agrees with the principle of modular assembly in protein ancestry.