The H(+)-K(+)-ATPase alpha(2) (HKalpha(2)) gene plays a central role in potassium homeostasis, yet little is known about its transcriptional control. We recently demonstrated that the proximal promoter confers basal transcriptional activity in mouse inner medullary collecting duct 3 cells. We sought to determine whether the kappaB DNA binding element at -104 to -94 influences basal HKalpha(2) gene transcription in these cells. Recombinant NF-kappaB p50 footprinted the region -116/-94 in vitro. Gel shift and supershift analysis revealed NF-kappaB p50- and p65-containing DNA-protein complexes in nuclear extracts of mouse inner medullary collecting duct 3 cells. A promoter-luciferase construct with a mutated -104/-94 NF-kappaB element exhibited higher activity than the wild-type promoter in transfection assays. Overexpression of NF-kappaB p50, p65, or their combination trans-repressed the HKalpha(2) promoter. The histone deacetylase (HDAC) inhibitor trichostatin A partially reversed NF-kappaB-mediated trans-repression of the HKalpha(2) promoter. HDAC6 overexpression inhibited HKalpha(2) promoter activity, and HDAC6 coimmunoprecipitated with NF-kappaB p50 and p65. These results suggest that HDAC6, recruited to the DNA protein complex, acts with NF-kappaB to suppress HKalpha(2) transcription and identify NF-kappaB p50 and p65 as novel binding partners for HDAC6.