7URG

cryo-EM structure of ribonucleotide reductase from Synechococcus phage S-CBP4 bound with TTP

Summary for 7URG

• Entry DOI: 10.2210/pdb7urg/pdb
• EMDB information: 26712
• Descriptor: Ribonucleotide reductase, THYMIDINE-5'-TRIPHOSPHATE (2 entities in total)
• Functional Keywords: ribonucleotide reductase, synechoccus phage, ttp, oxidoreductase
• Biological source: Synechococcus phage S-CBP4
• Total number of polymer chains: 2
• Total formula weight: 103807.68

Authors

Xu, D.,Burnim, A.A.,Ando, N. (deposition date: 2022-04-21, release date: 2022-09-07, Last modification date: 2024-11-13)

Primary citation

Burnim, A.A.,Spence, M.A.,Xu, D.,Jackson, C.J.,Ando, N.
Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade.
Elife, 11:-, 2022

PubMed Abstract: 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. Here, we structurally aligned the diverse RNR family by the conserved catalytic barrel to reconstruct the first large-scale phylogeny consisting of 6779 sequences that unites all extant classes of the RNR family and performed evo-velocity analysis to independently validate our evolutionary model. With a robust phylogeny in-hand, we uncovered a novel, phylogenetically distinct clade that is placed as ancestral to the classes I and II RNRs, which we have termed clade Ø. We employed small-angle X-ray scattering (SAXS), cryogenic-electron microscopy (cryo-EM), and AlphaFold2 to investigate a member of this clade from phage S-CBP4 and report the most minimal RNR architecture to-date. Based on our analyses, we propose an evolutionary model of diversification in the RNR family and delineate how our phylogeny can be used as a roadmap for targeted future study.

PubMed: 36047668
DOI: 10.7554/eLife.79790

Experimental method

ELECTRON MICROSCOPY (3.46 Å)