Modeling the sequence-structure-function relationships of ThDP-dependent enzymes

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While the reaction mechanisms of thiamine diphosphate (ThDP)-dependent enzymes have been investigated for years, a comprehensive model allowing for the prediction of the catalytic activity, specificity, and selectivity of difterent enzymes is not yet available. Their highly diverse substrate specificity and catalytic activity is reflected in the high diversity in sequence and structure of the difterent families of ThDP-dependent enzymes. During the course of evolution, shuftling, rearrangement, and fusion of domains, mutations, and gene duplications have led to an enormous diversity of ThDP-dependent enzymes. However, all ThDP-dependent enzymes contain at least two domains, the pyrophosphate-binding (PP) and the pyrimidine-binding (PYR) domain, which have a similar structure and are essential for binding and activating ThDP. Recently, we established the ThDP-dependent Enzymes Engineering Database (TEED) as a tool for a systematic comparison of ThDP-dependent enzymes. In cooperation with our research partners, this database will be used to create structure models, to model the binding of substrates, to interpret biochemical data, and to re-design selected enzymes for changed specificity, chemo-, regio- and stereoselectivity. Combining a comprehensive sequence and structure comparison analysis with molecular modeling of substrate recognition by the difterent enzymes will lead to a mechanistic understanding of how biochemical properties are encoded in the sequence and structure of ThDP-dependent enzymes.