The tetrameric structure of NF-mu NR provides a mechanism for cooperative binding to the immunoglobulin heavy chain mu enhancer.

We have analyzed the structure and DNA-binding characteristics of the IgH enhancer-binding regulatory protein NF-mu NR. We estimate that there are at least 5000 molecules of NF-mu NR protein/nucleus of non-B cells, based on the yield of active protein following purification. Purified NF-mu NR exists as a tetramer of 40-kDa subunits, even in the absence of its DNA-binding substrate. The protein complex binds to four binding sites flanking the immunoglobulin heavy chain mu enhancer core. Separately, individual sites bind to the tetrameric complex with affinities varying over a 100-fold range. However, when a low affinity site and a high affinity site are present on the same DNA molecule, both are occupied at the same NF-mu NR concentration; thus, there is a strong cooperative interaction between binding sites. The tetrameric structure provides a mechanism for binding cooperativity in which initial binding is mediated through a high affinity site on the DNA molecule followed by the engagement of the low affinity site juxtaposed to adjacent protein subunits. The presence of multiple binding sites flanking the mu enhancer core may reflect the influence of NF-mu NR binding on enhancer three-dimensional structure, transcription factor binding, and/or nuclear matrix interactions for cell type-specific enhancer function.