Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA.
Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia.
Protein Sci. 2022 Dec;31(12):e4483. doi: 10.1002/pro.4483.
Ribonucleotide reductases (RNRs) are used by all free-living organisms and many viruses to catalyze an essential step in the de novo biosynthesis of DNA precursors. RNRs are remarkably diverse by primary sequence and cofactor requirement, while sharing a conserved fold and radical-based mechanism for nucleotide reduction. In this work, we expand on our recent phylogenetic inference of the entire RNR family and describe the evolutionarily relatedness of insertions and extensions around the structurally homologous catalytic barrel. Using evo-velocity and sequence similarity network (SSN) analyses, we show that the N-terminal regulatory motif known as the ATP-cone domain was likely inherited from an ancestral RNR. By combining SSN analysis with AlphaFold2 predictions, we also show that the C-terminal extensions of class II RNRs can contain folded domains that share homology with an Fe-S cluster assembly protein. Finally, using sequence analysis and AlphaFold2, we show that the sequence motif of a catalytically essential insertion known as the finger loop is tightly coupled to the catalytic mechanism. Based on these results, we propose an evolutionary model for the diversification of the RNR family.
核苷酸还原酶（RNRs）被所有自由生活的生物和许多病毒用来催化 DNA 前体从头生物合成中的一个必需步骤。RNRs 在一级序列和辅助因子需求上差异显著，同时共享保守的折叠和基于自由基的核苷酸还原机制。在这项工作中，我们扩展了我们最近对整个 RNR 家族的系统发育推断，并描述了结构同源催化桶周围插入和扩展的进化相关性。使用进化速度和序列相似性网络（SSN）分析，我们表明，称为 ATP 锥域的 N 端调节基序很可能是从祖先 RNR 继承而来的。通过将 SSN 分析与 AlphaFold2 预测相结合，我们还表明，II 类 RNR 的 C 端延伸可以包含与 Fe-S 簇组装蛋白具有同源性的折叠结构域。最后，通过序列分析和 AlphaFold2，我们表明，称为指环的催化必需插入的序列基序与催化机制紧密相关。基于这些结果，我们提出了 RNR 家族多样化的进化模型。
