Larsson K M, Andersson J, Sjöberg B M, Nordlund P, Logan D T
Department of Biochemistry and Biophysics, Stockholm University, S-106 91, Stockholm, Sweden.
Structure. 2001 Aug;9(8):739-50. doi: 10.1016/s0969-2126(01)00627-x.
The specificity of ribonucleotide reductases (RNRs) toward their four substrates is governed by the binding of deoxyribonucleoside triphosphates (dNTPs) to the allosteric specificity site. Similar patterns in the kinetics of allosteric regulation have been a strong argument for a common evolutionary origin of the three otherwise widely divergent RNR classes. Recent structural information settled the case for divergent evolution; however, the structural basis for transmission of the allosteric signal is currently poorly understood. A comparative study of the conformational effects of the binding of different effectors has not yet been possible; in addition, only one RNR class has been studied.
Our presentation of the structures of a class III anaerobic RNR in complex with four dNTPs allows a full comparison of the protein conformations. Discrimination among the effectors is achieved by two side chains, Gln-114 and Glu-181, from separate monomers. Large conformational changes in the active site (loop 2), in particular Phe-194, are induced by effector binding. The conformational differences observed in the protein when the purine effectors are compared with the pyrimidine effectors are large, while the differences observed within the purine group itself are more subtle.
The subtle differences in base size and hydrogen bonding pattern at the effector site are communicated to major conformational changes in the active site. We propose that the altered overlap of Phe-194 with the substrate base governs hydrogen bonding patterns with main and side chain hydrogen bonding groups in the active site. The relevance for evolution is discussed.
核糖核苷酸还原酶（RNRs）对其四种底物的特异性由脱氧核糖核苷三磷酸（dNTPs）与变构特异性位点的结合所决定。变构调节动力学中的相似模式有力地支持了三种原本差异很大的RNR类别具有共同进化起源的观点。最近的结构信息确定了其趋异进化的情况；然而，目前对变构信号传递的结构基础了解甚少。尚未能够对不同效应物结合的构象效应进行比较研究；此外，仅研究了一种RNR类别。
我们展示了与四种dNTPs结合的III类厌氧RNR的结构，从而能够对蛋白质构象进行全面比较。来自不同单体的两个侧链Gln-114和Glu-181实现了对效应物的区分。效应物结合会诱导活性位点（环2）发生大的构象变化，特别是Phe-194。当将嘌呤效应物与嘧啶效应物进行比较时，在蛋白质中观察到的构象差异很大，而在嘌呤组自身内部观察到的差异则更为细微。
效应物位点处碱基大小和氢键模式的细微差异会传递至活性位点的主要构象变化。我们提出，Phe-194与底物碱基重叠的改变决定了活性位点中主链和侧链氢键基团的氢键模式。并讨论了其与进化的相关性。
