PROSITE documentation PDOC00409

Nucleoside diphosphate kinase (NDPK) active site signature and NDPK-like domain profile

The Nme (Non-metastatic) protein family, previously known as Non-metastatic 23 (Nm23) or nucleoside diphosphate kinase (NDPK), consists of evolutionarily conserved proteins present in all three domains of life (bacteria, archaea and eukaryotes) and in some viruses. Some members of the family, but not all, exhibit a Nucleoside Diphosphate Kinase (NDPK) activity (EC 2.7.4.6). NDPKs catalyze the transfer of the terminal phosphoryl group of a donor nucleoside triphosphate (NTP) to an acceptor nucleoside diphosphate (NDP) in the presence of divalent cations, preferably Mg(2+), by a ping-pong mechanism involving the formation of a phosphohistidine intermediate. They have broad substrate specificity, can use both ribo- and deoxyribonucleotides of purines or pyrimidines, and are not known to be allosterically regulated. In all organisms, NDPKs are considered as housekeeping enzymes involved in energy metabolism and homeostasis of intracellular NTP pools. NDPKs are therefore major players in the synthesis of macromolecules since they provide the neosynthetized triphosphates used for cell anabolic processes. They supply NTPs for nucleic acid synthesis, CTP for lipid synthesis, UTP for polysaccharide synthesis, and GTP for protein elongation, signal transduction, and microtubule polymerization. Beside this basic function, the Nme proteins have several other biochemical roles. They function as transcription regulators, protein kinases and DNases [1,2,3,4,5,6].

Unicellular organisms possess one Nme ortholog, whilst vertebrates possess several. In vertebrates, the Nme family of proteins is composed of 10 isoforms, designated Nme1-10, which are diverse in their enzymatic activities and patterns of subcellular localization. They display a large range of physiological and pathological functions at the cellular and organ levels, including bioenergetics, cytoskeleton and membrane dynamics, cell signaling, DNA repair, metastasis, maintenance of vascular and cardiac function, and development in general. Many Nme proteins are multifunctional, i.e., they present more than one and often unrelated molecular activities. Each contains a conserved domain of ~150 amino acids associated with a NDPK function, although not all are catalytically active. Basically, the 10 Nme isoforms can be subdivided into two groups. The quite conserved and ubiquitously expressed members Nme1-4 (group I) form hexamers, possess the NDPK active site motif (NXXHG/ASD) and are catalytically active with similar kinetic parameters. The more divergent members Nme5-10 (group II) probably lack both hexameric structure and NDPK activity. Some contain NDPK domain duplications and further domains with mostly unknown function. Only Nme6 is ubiquitously expressed, most others were reported in association with ciliary and flagellar structures. Several of the Nme isoforms (Nme1, Nme5, Nme7, and Nme8) also exhibit a 3'-5' exonuclease activity, suggesting roles in DNA proofreading and repair. Nme1 and Nme2 have been identified as potential canonical transcription factors that regulate gene transcription through their DNA-binding activities [7,8,9,10].

The sequence of the NDPK-like domain has been highly conserved through evolution. There is a single histidine residue involved in the catalytic mechanism, conserved in all known active NDPK enzymes. The NDPK-like domain folds into a compact α/β domain built around an antiparallel β sheet with topology β4β1β3β2 (see <PDB:1NUE>). The active site is located in a cleft formed by two helices. Active NDPK-like domain possess nine residues that are most essential for catalysis and stability of a prototypical NDPK [10,11,12].

Our signature pattern contains the histidine residue involved in the catalytic mechanism. We also developed a profile that covers the whole NDPK-like domain.