title: Structure of the human NF-kappaB p52 homodimer-DNA complex at 2.1 A resolution.
abstract: The crystal structure of human NF-kappaB p52 in its specific complex with the natural kappaB DNA binding site MHC H-2 has been solved at 2.1 A resolution. Whereas the overall structure resembles that of the NF-kappaB p50-DNA complex, pronounced differences are observed within the 'insert region'. This sequence segment differs in length between different Rel proteins. Compared with NF-kappaB p50, the compact alpha-helical insert region element is rotated away from the core of the N-terminal domain, opening up a mainly polar cleft. The insert region presents potential interaction surfaces to other proteins. The high resolution of the structure reveals many water molecules which mediate interactions in the protein-DNA interface. Additional complexity in Rel protein-DNA interaction comes from an extended interfacial water cavity that connects residues at the edge of the dimer interface to the central DNA bases. The observed water network might acount for differences in binding specificity between NF-kappaB p52 and NF-kappaB p50 homodimers.
authors.affiliation: European Molecular Biology Laboratory (EMBL), Grenoble Outstation, c/o ILL, BP 156, 38042 Grenoble Cedex 9, France.
authors.forename: P
authors.initials: P
authors.lastname: Cramer
authors.forename: C J
authors.initials: CJ
authors.lastname: Larson
authors.forename: G L
authors.initials: GL
authors.lastname: Verdine
authors.forename: C W
authors.initials: CW
authors.lastname: Müller
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D019281:Dimerization; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016328:NF-kappa B / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D011485:Protein Binding / Q000187:drug effects; D011487:Protein Conformation; D011518:Proto-Oncogene Proteins / Q000737:chemistry; D020569:Proto-Oncogene Proteins c-rel; D017386:Sequence Homology, Amino Acid; D014867:Water / Q000494:pharmacology
chemical_list: D016328:NF-kappa B; D011518:Proto-Oncogene Proteins; D020569:Proto-Oncogene Proteins c-rel; D014867:Water; D004247:DNA