CIITA contains an acidic transcriptional activation domain, four LRRs (leucine-rich repeats) and a GTP binding domain. It is located in the nucleus and acts as a positive regulator of class II major histocompatibility complex gene transcription, and is referred to as the ""master control factor"" for the expression of these genes. CIITA also binds GTP and uses GTP binding to facilitate its own transport into the nucleus. Once in the nucleus it does not bind DNA but rather uses an intrinsic acetyltransferase (AT) activity to act in a coactivator-like fashion. Mutations in this gene have been associated with bare lymphocyte syndrome type II (also known as hereditary MHC class II deficiency or HLA class II-deficient combined immunodeficiency), increased susceptibility to rheumatoid arthritis, multiple sclerosis, and possibly myocardial infarction.