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Life 2015, 5(1), 604-636; doi:10.3390/life5010604

The Origin and Evolution of Ribonucleotide Reduction

1
Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden
2
Department of Biochemistry and Structural Biology, Lund University, Box 124, SE-221 00 Lund, Sweden
Current address: Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
*
Author to whom correspondence should be addressed.
Academic Editor: Niles Lehman
Received: 15 January 2015 / Revised: 4 February 2015 / Accepted: 6 February 2015 / Published: 27 February 2015
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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Abstract

Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA- to DNA-encoded genomes. While it is entirely possible that a different pathway was later replaced with the modern mechanism, here we explore the evolutionary and biochemical limits for an origin of the mechanism in the RNA + protein world and suggest a model for a prototypical ribonucleotide reductase (protoRNR). From the protoRNR evolved the ancestor to modern RNRs, the urRNR, which diversified into the modern three classes. Since the initial radical generation differs between the three modern classes, it is difficult to establish how it was generated in the urRNR. Here we suggest a model that is similar to the B12-dependent mechanism in modern class II RNRs. View Full-Text
Keywords: ribonucleotide reductase (RNR); RNA/RNP world; DNA building blocks; protein evolution; redox chemistry; radical chemistry; deoxyribonucleotides; primordial hydrogen atom abstraction; structural phylogenetics; allosteric regulation ribonucleotide reductase (RNR); RNA/RNP world; DNA building blocks; protein evolution; redox chemistry; radical chemistry; deoxyribonucleotides; primordial hydrogen atom abstraction; structural phylogenetics; allosteric regulation
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Lundin, D.; Berggren, G.; Logan, D.T.; Sjöberg, B.-M. The Origin and Evolution of Ribonucleotide Reduction. Life 2015, 5, 604-636.

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