6ZJK

Ribonucleotide reductase R2 subunit from Clostridium botulinum

Summary for 6ZJK

• Entry DOI: 10.2210/pdb6zjk/pdb
• Descriptor: Ribonucleoside-diphosphate reductase subunit beta, GLYCEROL, FE (III) ION, ... (4 entities in total)
• Functional Keywords: ribonucleotide, reductase, nucleotide, r2, metal binding protein
• Biological source: Clostridium botulinum (strain Loch Maree / Type A3)
• Total number of polymer chains: 4
• Total formula weight: 173801.40

Authors

Martinez-Carranza, M.,Stenmark, P. (deposition date: 2020-06-29, release date: 2020-09-30, Last modification date: 2024-01-31)

Primary citation

Martinez-Carranza, M.,Jonna, V.R.,Lundin, D.,Sahlin, M.,Carlson, L.A.,Jemal, N.,Hogbom, M.,Sjoberg, B.M.,Stenmark, P.,Hofer, A.
A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site.
J.Biol.Chem., 295:15576-15587, 2020

PubMed Abstract: Ribonucleotide reductase (RNR) is a central enzyme for the synthesis of DNA building blocks. Most aerobic organisms, including nearly all eukaryotes, have class I RNRs consisting of R1 and R2 subunits. The catalytic R1 subunit contains an overall activity site that can allosterically turn the enzyme on or off by the binding of ATP or dATP, respectively. The mechanism behind the ability to turn the enzyme off via the R1 subunit involves the formation of different types of R1 oligomers in most studied species and R1-R2 octamers in To better understand the distribution of different oligomerization mechanisms, we characterized the enzyme from , which belongs to a subclass of class I RNRs not studied before. The recombinantly expressed enzyme was analyzed by size-exclusion chromatography, gas-phase electrophoretic mobility macromolecular analysis, EM, X-ray crystallography, and enzyme assays. Interestingly, it shares the ability of the RNR to form inhibited R1-R2 octamers in the presence of dATP but, unlike the enzyme, cannot be turned off by combinations of ATP and dGTP/dTTP. A phylogenetic analysis of class I RNRs suggests that activity regulation is not ancestral but was gained after the first subclasses diverged and that RNR subclasses with inhibition mechanisms involving R1 oligomerization belong to a clade separated from the two subclasses forming R1-R2 octamers. These results give further insight into activity regulation in class I RNRs as an evolutionarily dynamic process.

PubMed: 32883811
DOI: 10.1074/jbc.RA120.014895

Experimental method

X-RAY DIFFRACTION (2 Å)