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The origin and evolution of ribonucleotide reduction.

Lundin D, Berggren G, Logan DT, Sjöberg BM - Life (Basel) (2015)

Bottom Line: 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).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).

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden. daniel.lundin@scilifelab.se.

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.

No MeSH data available.


General reaction mechanism for class I and II RNRs, with important side chains in the active site indicated. The radical cysteine (top of the active site) is also present in class III RNR, while the electron donating cysteine pair (bottom of the active site) is replaced in the majority of class III RNRs with a single cysteine. Additionally, in most class III RNRs no residue corresponding to the proton shuttling glutamate has been found, and instead formate has been proposed to fill this function. Figure adapted from reference [55].
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life-05-00604-f005: General reaction mechanism for class I and II RNRs, with important side chains in the active site indicated. The radical cysteine (top of the active site) is also present in class III RNR, while the electron donating cysteine pair (bottom of the active site) is replaced in the majority of class III RNRs with a single cysteine. Additionally, in most class III RNRs no residue corresponding to the proton shuttling glutamate has been found, and instead formate has been proposed to fill this function. Figure adapted from reference [55].

Mentions: Even before structures provided conclusive evidence of the homology of all RNRs, it was still widely believed that the classes were evolutionarily related, since the reaction mechanism is highly similar between all studied RNRs (Figure 5) [48]. A cysteinyl radical activates the substrate by abstracting the 3' H-atom from the ribose on the substrate, resulting in the formation of a 3' carbon radical. In structures of class I, II and III RNRs this cysteine is positioned on a finger loop protruding through the center of the barrel, within van der Waals distance of the substrate’s 3' carbon. After activation and rearrangements, the 2' OH-group leaves as a water molecule, with the proton donated by a second conserved cysteine. A third cysteine, conserved in class I and II RNRs and present in some class III RNRs [46], forms a disulfide bridge with the second cysteine. This cysteine pair acts as an electron relay, providing the reducing equivalents required for the reaction. Finally there is also a number of H-bonding interactions between the protein and the nucleotide, firmly anchoring the phosphate moiety in the active site. The binding to the phosphate groups is likely to have evolved early, as it provides an efficient handle for binding all four substrates in the active site. Crystallographic studies in class I and II RNRs have revealed well-defined interactions between the substrate and a glutamate carboxylate group that is perfectly positioned to act as a base during deprotonation of the 3' OH-group and is involved in proton shuttling during the reaction [49,50,51,52,53]. The ancestry of the glutamate is questionable. It is conserved in both class I and II RNR, but rarely found in class III. For class III, it has been suggested that the electron donating formate also serves as a base during the reaction [54]. Thus the issue whether the protein backbone or a small molecule provided the required base in the urRNR is an open question.


The origin and evolution of ribonucleotide reduction.

Lundin D, Berggren G, Logan DT, Sjöberg BM - Life (Basel) (2015)

General reaction mechanism for class I and II RNRs, with important side chains in the active site indicated. The radical cysteine (top of the active site) is also present in class III RNR, while the electron donating cysteine pair (bottom of the active site) is replaced in the majority of class III RNRs with a single cysteine. Additionally, in most class III RNRs no residue corresponding to the proton shuttling glutamate has been found, and instead formate has been proposed to fill this function. Figure adapted from reference [55].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390871&req=5

life-05-00604-f005: General reaction mechanism for class I and II RNRs, with important side chains in the active site indicated. The radical cysteine (top of the active site) is also present in class III RNR, while the electron donating cysteine pair (bottom of the active site) is replaced in the majority of class III RNRs with a single cysteine. Additionally, in most class III RNRs no residue corresponding to the proton shuttling glutamate has been found, and instead formate has been proposed to fill this function. Figure adapted from reference [55].
Mentions: Even before structures provided conclusive evidence of the homology of all RNRs, it was still widely believed that the classes were evolutionarily related, since the reaction mechanism is highly similar between all studied RNRs (Figure 5) [48]. A cysteinyl radical activates the substrate by abstracting the 3' H-atom from the ribose on the substrate, resulting in the formation of a 3' carbon radical. In structures of class I, II and III RNRs this cysteine is positioned on a finger loop protruding through the center of the barrel, within van der Waals distance of the substrate’s 3' carbon. After activation and rearrangements, the 2' OH-group leaves as a water molecule, with the proton donated by a second conserved cysteine. A third cysteine, conserved in class I and II RNRs and present in some class III RNRs [46], forms a disulfide bridge with the second cysteine. This cysteine pair acts as an electron relay, providing the reducing equivalents required for the reaction. Finally there is also a number of H-bonding interactions between the protein and the nucleotide, firmly anchoring the phosphate moiety in the active site. The binding to the phosphate groups is likely to have evolved early, as it provides an efficient handle for binding all four substrates in the active site. Crystallographic studies in class I and II RNRs have revealed well-defined interactions between the substrate and a glutamate carboxylate group that is perfectly positioned to act as a base during deprotonation of the 3' OH-group and is involved in proton shuttling during the reaction [49,50,51,52,53]. The ancestry of the glutamate is questionable. It is conserved in both class I and II RNR, but rarely found in class III. For class III, it has been suggested that the electron donating formate also serves as a base during the reaction [54]. Thus the issue whether the protein backbone or a small molecule provided the required base in the urRNR is an open question.

Bottom Line: 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).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).

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden. daniel.lundin@scilifelab.se.

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.

No MeSH data available.