The first comprehensive phylogenetic and biochemical analysis of NADH diphosphatases reveals that the enzyme from Tuber melanosporum is highly active towards NAD

• Published in: Scientific reports 2019-11, Vol.9 (1), p.16753-14, Article 16753
• Main Authors: García-Saura, Antonio Ginés, Zapata-Pérez, Rubén, Martínez-Moñino, Ana Belén, Hidalgo, José Francisco, Morte, Asunción, Pérez-Gilabert, Manuela, Sánchez-Ferrer, Álvaro
• Format: Article
• Language: English
• Subjects: 38/77; 631/45/607/1164; 631/61; 82/16; 82/29; 82/80; 82/83; Amino acids; BASIC BIOLOGICAL SCIENCES; Biochemical analysis; Biology; Biotechnology; Computational Biology - methods; Computer Simulation; Databases, Protein; E coli; Ectomycorrhizas; Enzymes; Evolution, Molecular; Fungal Proteins - chemistry; Fungal Proteins - genetics; Fungal Proteins - metabolism; Humanities and Social Sciences; Hydrolases; multidisciplinary; NAD; NADH; Phylogenetics; Phylogeny; Protein Domains; Proteins; Pyrophosphatases - chemistry; Pyrophosphatases - genetics; Pyrophosphatases - metabolism; Saccharomycetales - enzymology; Saccharomycetales - genetics; Science; Science & Technology - Other Topics; Science (multidisciplinary); Substrate Specificity; Tuber melanosporum; Tuberculosis
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-019-53138-w

Nudix (for nu cleoside di phosphatases linked to other moieties, X ) hydrolases are a diverse family of proteins capable of cleaving an enormous variety of substrates, ranging from nucleotide sugars to NAD + -capped RNAs. Although all the members of this superfamily share a common conserved catalytic motif, the Nudix box, their substrate specificity lies in specific sequence traits, which give rise to different subfamilies. Among them, NADH pyrophosphatases or diphosphatases (NADDs) are poorly studied and nothing is known about their distribution. To address this, we designed a Prosite-compatible pattern to identify new NADDs sequences. In silico scanning of the UniProtKB database showed that 3% of Nudix proteins were NADDs and displayed 21 different domain architectures, the canonical architecture (NUDIX-like_zf-NADH-PPase_NUDIX) being the most abundant (53%). Interestingly, NADD fungal sequences were prominent among eukaryotes, and were distributed over several Classes, including Pezizomycetes. Unexpectedly, in this last fungal Class, NADDs were found to be present from the most common recent ancestor to Tuberaceae, following a molecular phylogeny distribution similar to that previously described using two thousand single concatenated genes. Finally, when truffle-forming ectomycorrhizal Tuber melanosporum NADD was biochemically characterized, it showed the highest NAD + /NADH catalytic efficiency ratio ever described.