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The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer

Abstract

Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides, an essential step in DNA biosynthesis and repair. Here we present the crystal structure of class II (coenzyme B12-dependent) ribonucleoside triphosphate reductase (RTPR) from Lactobacillus leichmannii in the apo enzyme form and in complex with the B12 analog adeninylpentylcobalamin at 1.75 and 2.0 Å resolution, respectively. This monomeric, allosterically regulated class II RNR retains all the key structural features associated with the catalytic and regulatory machinery of oligomeric RNRs. Surprisingly, the dimer interface responsible for effector binding in class I RNR is preserved through a single 130-residue insertion in the class II structure. Thus, L. leichmannii RNR is a paradigm for the simplest structural entity capable of ribonucleotide reduction, a reaction linking the RNA and DNA worlds.

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Figure 1: General reaction catalyzed by ribonucleotide reductases.
Figure 2: Global fold conservation: the RNR structural family.
Figure 3: Active site conservation between class I and II RNRs.
Figure 4: B12 bound to RNR.
Figure 5: RTPR conformational changes, domain architecture and thiyl radical formation.
Figure 6: Allosteric regulation of specificity in dimeric versus monomeric RNRs.

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Acknowledgements

We thank T. Earnest (ALS), G. McDermott (ALS), R. Sweet (NSLS) and M. Becker (NSLS) for help with data collection, and C.C. Lawrence for help with protein purification. Support has been provided by the Surdna and Searle foundations (C.L.D.) and an NIH Grant (J.S.). The data collection facilities at ALS and NSLS are funded by the U.S. Department of Energy, Office of Basic Energy Sciences.

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Correspondence to Catherine L. Drennan.

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Sintchak, M., Arjara, G., Kellogg, B. et al. The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer. Nat Struct Mol Biol 9, 293–300 (2002). https://doi.org/10.1038/nsb774

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