Mitochondrial NMNAT isoform. Catalyzes the formation of NAD+ from nicotinamide mononucleotide (NMN) and ATP. Can also use the deamidated form of nicotinic acid mononucleotide (NAMN) as substrate with the same efficiency. Can use tiazofurin monophosphate as substrate. Can also use GTP and ITP as nucleotide donors. Also catalyzes the reverse reaction, i. e. the pyrophosphorolytic cleavage of NAD+. For the pyrophosphorolytic activity, mitochondrial NMNAT isoform can use NAD(+), NADH, NAAD, nicotinic acid adenine dinucleotide phosphate (NHD), nicotinamide guanine dinucleotide (NGD) as substrates. Fails to cleave phosphorylated dinucleotides NADP+, NADPH and NAADP+. Protects against axonal degeneration following injury.