Kornev Alexandr P, Taylor Susan S, Ten Eyck Lynn F
San Diego Supercomputer Center, University of California San Diego, La Jolla, California, United States of America.
PLoS Comput Biol. 2008 Apr 11;4(4):e1000056. doi: 10.1371/journal.pcbi.1000056.
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 beta(2,3) 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 beta(2,3) 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 the N3A-motif, and its long range allosteric interactions are substantially different from the cis-regulated CNB domains.
环核苷酸（cAMP和cGMP）调节多种细胞内过程，因此分子生物学家和结构生物学家对其普遍极为关注。为了研究不同环核苷酸结合（CNB）结构域的变构机制，我们使用一种新的生物信息学方法：局部空间模式比对，比较了结合cAMP和未结合cAMP的结构（蛋白激酶A、交换蛋白直接激活剂（Epac）和两种离子通道）。我们的分析突出了四个主要的保守结构基序：1）磷酸结合盒（PBC），它结合cAMP的核糖 - 磷酸；2）“铰链”，一个灵活的螺旋，与PBC接触；3）β(2,3)环，它为PBC中一个不变的精氨酸提供精确定位；4）一个由N端螺旋、一个八残基环和A螺旋组成的保守结构元件（N3A基序）。PBC和铰链包含在先前报道的变构模型中，而将β(2,3)环和N3A基序定义为保守元件是新的。N3A基序存在于所有顺式调节的CNB结构域中，我们提出了这些结构域中变构机制的模型。分解代谢基因激活蛋白（CAP）代表一个反式调节的CNB结构域家族：它不包含N3A基序，其长程变构相互作用与顺式调节的CNB结构域有很大不同。
