A global view of structure–function relationships in the tautomerase superfamily

• Published in: The Journal of biological chemistry Vol. 293; no. 7; pp. 2342 - 2357
• Main Authors: Davidson, Rebecca, Baas, Bert-Jan, Akiva, Eyal, Holliday, Gemma L., Polacco, Benjamin J., LeVieux, Jake A., Pullara, Collin R., Zhang, Yan Jessie, Whitman, Christian P., Babbitt, Patricia C.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 16.02.2018; American Society for Biochemistry and Molecular Biology
• Subjects: Amino Acid Sequence; Animals; Binding Sites; Biochemistry & Molecular Biology; Computational Biology; Crystallography, X-Ray; enzyme structure; enzyme superfamily; Enzymes - chemistry; Enzymes - genetics; Enzymes - metabolism; Eukaryota - chemistry; Eukaryota - classification; Eukaryota - enzymology; Eukaryota - genetics; evolution; Evolution, Molecular; Humans; Kinetics; Molecular Sequence Data; Multigene Family; Phylogeny; Plants - chemistry; Plants - enzymology; Plants - genetics; protein evolution; protein sequence; protein structure; Sequence Alignment; structure-function; structure–function relationships; tautomerase superfamily; protein structure; enzyme superfamily; protein evolution; structure-function; structure–function relationships; evolution; tautomerase superfamily; enzyme structure; protein sequence
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M117.815340

The tautomerase superfamily (TSF) consists of more than 11,000 nonredundant sequences present throughout the biosphere. Characterized members have attracted much attention because of the unusual and key catalytic role of an N-terminal proline. These few characterized members catalyze a diverse range of chemical reactions, but the full scale of their chemical capabilities and biological functions remains unknown. To gain new insight into TSF structure–function relationships, we performed a global analysis of similarities across the entire superfamily and computed a sequence similarity network to guide classification into distinct subgroups. Our results indicate that TSF members are found in all domains of life, with most being present in bacteria. The eukaryotic members of the cis-3-chloroacrylic acid dehalogenase subgroup are limited to fungal species, whereas the macrophage migration inhibitory factor subgroup has wide eukaryotic representation (including mammals). Unexpectedly, we found that 346 TSF sequences lack Pro-1, of which 85% are present in the malonate semialdehyde decarboxylase subgroup. The computed network also enabled the identification of similarity paths, namely sequences that link functionally diverse subgroups and exhibit transitional structural features that may help explain reaction divergence. A structure-guided comparison of these linker proteins identified conserved transitions between them, and kinetic analysis paralleled these observations. Phylogenetic reconstruction of the linker set was consistent with these findings. Our results also suggest that contemporary TSF members may have evolved from a short 4-oxalocrotonate tautomerase–like ancestor followed by gene duplication and fusion. Our new linker-guided strategy can be used to enrich the discovery of sequence/structure/function transitions in other enzyme superfamilies.