NAK has been identified as an IkappaB-kinase activating-kinase that plays an important role in NF-kappaB activation in response to several pro-inflammatory cytokines such as TNF-alpha. We describe here the genomic structure of the human NAK gene and analysis of the promoter. The gene spanned 40.5 kb and contained 21 exons with lengths ranging from 39 to 196 bp. Comparison of the phase and position of intron insertions within the human NAK gene with those within IKKalpha, IKKbeta and IKK epsilon indicated that the exon/intron organization of IKK epsilon is more highly conserved than that of IKKalpha or IKKbeta. The transcriptional start site was mapped at a position about 98 bp upstream from the translation start site by means of both an RNase protection assay and a primer extension method. Fluorescence in situ hybridization using full-length human NAK cDNA as a probe showed that the human NAK gene is localized to human chromosome 13q14.2-3, a region in which the loss of heterozygosity is associated with squamous cell carcinoma and leukemia. By using a series of deletion constructs in performing a reporter assay, a minimal 77 bp upstream of the transcriptional initiation site was shown to contribute to the major promoter activity.