Catalyzes the transfer of a gamma-phosphoryl group from a nucleoside triphosphate, mainly ATP, to a nucleoside diphosphate via a ping-pong mechanism involving a phosphohistidine intermediate, therefore contributing to the nucleoside triphosphate homeostasis (PubMed:11277919, PubMed:30587587, PubMed:39337255). In vitro, can also use other phosphate donors such as UTP and GTP (PubMed:30587587, PubMed:39337255). Independently of its nucleoside diphosphate kinase activity, involved in mitochondrial membrane tethering, a prerequisite for fusion through direct membrane-binding and hexamerization (PubMed:30587587, PubMed:37584589). Involved in DNA repair of both single- and double-stranded breaks by associating with the ribonucleotide reductase (RNR) complex via interaction with the histone acetyltransferase KAT5, facilitating recruitment to DNA damage sites independently of its kinase activity (PubMed:26945015). Inhibits granulocyte differentiation (PubMed:7638209). May be required for ciliary function during renal development (By similarity). {ECO:0000250|UniProtKB:Q9PTF3, ECO:0000269|PubMed:11277919, ECO:0000269|PubMed:26945015, ECO:0000269|PubMed:30587587, ECO:0000269|PubMed:37584589, ECO:0000269|PubMed:39337255, ECO:0000269|PubMed:7638209}. This is the function of NME3 (NME/NM23 nucleoside diphosphate kinase 3, Ensembl gene identifier ENSG00000103024).