a generalized allosteric mechanism for cis-regulated cyclic nucleotide binding domains广义变构机制cis-regulated环核苷酸结合域.pdfVIP

A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains 1 2,3 1,2 Alexandr P. Kornev , Susan S. Taylor *, Lynn F. Ten Eyck 1 San Diego Supercomputer Center, University of California San Diego, La Jolla, California, United States of America, 2 Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America, 3 Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America Abstract Cyclic nucleotides (cAMP and cGMP) regulate multiple intracellular processes and are thus of a great general interest for molecular and structural biologists. To study the allosteric mechanism of different cyclic nucleotide binding (CNB) domains, we compared cAMP-bound and cAMP-free structures (PKA, Epac, and two ionic channels) using a new bioinformatics method: local spatial pattern alignment. Our analysis highlights four major conserved structural motifs: 1) the phosphate binding cassette (PBC), which binds the cAMP ribose-phosphate, 2) the ‘‘hinge,’’ a flexible helix, which contacts the PBC, 3) the b2,3 loop, which provides precise positioning of an invariant arginine from the PBC, and 4) a conserved structural element consisting of an N- terminal helix, an eight residue loop and the A-helix (N3A-motif). The PBC and the hinge were included in the previously reported allosteric model, whereas the definition of the b2,3 loop and the N3A-motif as conserved elements is novel. The N3A- motif is found in all cis-regulated CNB domains, and we present a model for an allosteric mechanism in these domains. Catabolite gene activator protein (CAP) represents a trans-regulated CNB domain family: it does not contain t