Navigating within thiamine diphosphate‐dependent decarboxylases: Sequences, structures, functional positions, and binding sites

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2019-09, Vol.87 (9), p.774-785
• Main Authors: Buchholz, Patrick C. F., Ferrario, Valerio, Pohl, Martina, Gardossi, Lucia, Pleiss, Jürgen
• Format: Article
• Language: English
• Subjects: Amino acid sequence; Binding Sites; biocatalysis; BioGPS; Carboxy-Lyases - chemistry; Carboxy-Lyases - metabolism; Catalytic Domain; Crystal structure; enzyme function; Enzymes; Homology; Identification methods; molecular descriptor; Principal components analysis; principal coordinate analysis; principle component analysis; protein family; Protein structure; Proteins; sequence‐structure‐function relationship; Thiamine; Thiamine diphosphate; Thiamine Pyrophosphate - chemistry
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.25706

Thiamine diphosphate‐dependent decarboxylases catalyze both cleavage and formation of CC bonds in various reactions, which have been assigned to different homologous sequence families. This work compares 53 ThDP‐dependent decarboxylases with known crystal structures. Both sequence and structural information were analyzed synergistically and data were analyzed for global and local properties by means of statistical approaches (principle component analysis and principal coordinate analysis) enabling complexity reduction. The different results obtained both locally and globally, that is, individual positions compared with the overall protein sequence or structure, revealed challenges in the assignment of separated homologous families. The methods applied herein support the comparison of enzyme families and the identification of functionally relevant positions. The findings for the family of ThDP‐dependent decarboxylases underline that global sequence identity alone is not sufficient to distinguish enzyme function. Instead, local sequence similarity, defined by comparisons of structurally equivalent positions, allows for a better navigation within several groups of homologous enzymes. The differentiation between homologous sequences is further enhanced by taking structural information into account, such as BioGPS analysis of the active site properties or pairwise structural superimpositions. The methods applied herein are expected to be transferrable to other enzyme families, to facilitate family assignments for homologous protein sequences.