MODELING OF NUCLEOTIDE-BINDING DOMAINS OF ABC TRANSPORTER PROTEINS BASED ON A F-1-ATPASE RECA TOPOLOGY - STRUCTURAL MODEL OF THE NUCLEOTIDE-BINDING DOMAINS OF THE CYSTIC-FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR (CFTR)/

Members of the ABC transporter superfamily contain two nucleotide bind ing domains. To date, the three dimensional structure of no member of this super-family has been elucidated. To gain structural insight, the known structures of several other nucleotides binding proteins can be used as a framework for modeling these domains. We have modeled both nucleotide binding domains of the protein CFTR (Cystic Fibrosis Transm embrane Conductance Regulator) using the two similar domains of mitoch ondrial F-1-ATPase. The models obtained, provide useful insights into the putative functions of these domains and their possible interaction as well as a rationale for the basis of Cystic Fibrosis causing mutat ions. First, the two nucleotide binding domains (folds) of CFTR are ea ch predicted to span a 240-250 amino acid sequence rather than the 150 -160 amino acid sequence originally proposed. Second, the first nucleo tide binding fold, is predicted to catalyze significant rates of ATP h ydrolysis as a catalytic base (E504) resides near the gamma phosphate of ATP. This prediction has been verified experimentally [Ko, Y.H., an d Pedersen, P.L. (1995) J, Biol. Chem. 268, 24330-24338], providing su pport for the model. In contrast, the second nucleotide binding fold i s predicted at best to be a weak ATPase as the glutamic acid residue i s replaced with a glutamine. Third, F508, which when deleted causes si milar to 70% of all cases of cystic fibrosis, is predicted to lie in a cleft near the nucleotide binding pocket. All other disease causing m utations within the two nucleotide binding domains of CFTR either resi de near the Walker A and Walker B consensus motifs in the heart of the nucleotide binding pocket, or in the C motif which lies outside but n ear the nucleotide binding pocket. Finally, the two nucleotide binding domains of CFTR are predicted to interact, and in one of the two pred icted orientations, F508 resides near the interface. This is the first report where both nucleotide binding domains of an ABC transporter an d their putative domain-domain interactions have been modeled in three dimensions. The methods and the template used in this work can be use d to analyze the structures and function of the nucleotide binding dom ains of all other members of the ABC transporter super-family.