PROSITE documentation PDOC00695

Nudix hydrolase domain signatures and profile

The Nudix superfamily is widespread among eucaryotes, bacteria, archaea and viruses and consists mainly of pyrophosphohydrolases that act upon substrates of general structure NUcleoside DIphosphate linked to another moiety, X (NDP-X) to yield NMP plus P-X. Such substrates include (d)NTPs (both canonical and oxidised derivatives), nucleotide sugars and alcohols, dinucleoside polyphosphates (NpnN), dinucleotide coenzymes and capped RNAs. However, phosphohydrolase activity, including activity towards NDPs themselves, and non-nucleotide substrates such as diphosphoinositol polyphosphates (DIPs), 5-phosphoribosyl 1-pyrophosphate (PRPP), thiamine pyrophosphate (TPP) and dihydroneopterin triphosphate (DHNTP) have also been described. Some superfamily members, such as Escherichia coli mutT, have the ability to degrade potentially mutagenic, oxidised nucleotides while others control the levels of metabolic intermediates and signalling compounds. In procaryotes and simple eucaryotes, the number of Nudix genes varies from 0 to over 30, reflecting the metabolic complexity and adaptability of the organism. Nudix hydrolases are typically small proteins, larger ones having additional domains with interactive or other catalytic functions [1].

The Nudix domain formed by two β-sheets packed between α-helices (see <PDB:1G0S; A>) [2,3]. It can accomodate sequences of different lengths in the connecting loops and in the amtiparallel β-sheet. Catalysis depends on the conserved 23-amino acid Nudix motif (Nudix box), G-x(5)-E-x(5)-[UA]-x-R-E-x(2)-E-E-x-G-U, where U is an aliphatic, hydrophobic residue. This sequence is located in a loop-helix-loop structural motif and the Glu residues in the core of the motif, R-E-x(2)-E-E, play an important role in binding essential divalent cations [1]. The substrate specificity is determined by other residues outside the Nudix box. For example, CoA pyrophosphatases share the NuCoA motif L-L-T-x-R-[SA]-x(3)-R-x(3)-G-x(3)-F-P-G-G that is located N-terminal of the Nudix box and is involved in CoA recognition [4].

Some proteins known to contain a Nudix domain are listed below:

• Bacterial mutator mutT protein (7,8-dihydro-8-oxoguanine-triphosphatase) (8-oxo-dGTPase) (3.6.1.-) (dGTP pyrophosphohydrolase).
• Streptomyces pneumoniae mutX.
• Escherichia coli nudB (ntpA) dihydroneopterin triphosphate pyrophosphatase (EC 3.6.1.-) (dATP pyrophosphohydrolase).
• Escherichia coli (yjaD) and Haemophilus influenzae (HI0432) nudC NADH pyrophosphatase (EC 3.6.1.22).
• Escherichia coli nudE (yrfE) ADP compounds hydrolase (EC 3.6.1.-).
• Bacterial nudH (rppH) RNA pyrophosphohydrolase (EC 3.6.1.-) ((Di)nucleoside polyphosphate hydrolase).
• Escherichia coli nudI (yfaO) nucleoside triphosphatase (EC 3.6.1.-).
• Escherichia coli uncharacterized Nudix hydrolase nudL (EC 3.6.1.-).
• Streptomyces ambofaciens MutT-like protein from plasmid pSAM2.
• Bacillus subtilis hypothetical protein yqkG.
• Bacillus subtilis hypothetical protein yzgD.
• Mammalian NUDT1 and NUDT15 7,8-dihydro-8-oxoguanine triphosphatase (EC 3.1.6.-).
• Mammalian NUDT2 diadenosine 5',5'''-P1,P4-tetraphosphate asymmetrical hydrolase (Ap4Aase) (EC 3.6.1.17) [5], which cleaves A-5'-PPPP-5'A to yield AMP and ATP.
• Higher vertebrates NUDT6 nucleoside diphosphate-linked moiety X motif 6, a protein encoded on the antisense RNA of the basic fibroblast growth factor gene.
• Yeast ADP-ribose pyrophosphatase (EC 3.6.1.13) (YSA1).
• Yeast NADH pyrophosphatase (EC 3.6.1.22) (NPY1) (YGL067W).
• Yeast peroxisomal coenzyme A diphosphatase 1, peroxisomal (EC 3.6.1.-) (PCD1).
• African swine fever viruses protein D250.
• Poxviruses proteins D9 and D10.

We developed two patterns for the Nudix domain. The first one covers the Nudix box and the second the NuCoA motif. We also developed a profile which covers the entire Nudix domain.