6TQX

Crystal structure of apo (metal-free) ribonucleotide reductase NrdF L61G variant from Bacillus anthracis

Summary for 6TQX

• Entry DOI: 10.2210/pdb6tqx/pdb
• Related: 6TQV 6TQW
• Descriptor: Ribonucleoside-diphosphate reductase subunit beta, SULFATE ION (3 entities in total)
• Functional Keywords: metal binding; oxidation reduction process; 2'-deoxyribonucleotide metabolism; dna replication, oxidoreductase
• Biological source: Bacillus anthracis
• Total number of polymer chains: 2
• Total formula weight: 74576.14

Authors

Grave, K.,Hogbom, M. (deposition date: 2019-12-17, release date: 2020-04-15, Last modification date: 2024-01-24)

Primary citation

Grave, K.,Griese, J.J.,Berggren, G.,Bennett, M.D.,Hogbom, M.
The Bacillus anthracis class Ib ribonucleotide reductase subunit NrdF intrinsically selects manganese over iron.
J.Biol.Inorg.Chem., 25:571-582, 2020

PubMed Abstract: Correct protein metallation in the complex mixture of the cell is a prerequisite for metalloprotein function. While some metals, such as Cu, are commonly chaperoned, specificity towards metals earlier in the Irving-Williams series is achieved through other means, the determinants of which are poorly understood. The dimetal carboxylate family of proteins provides an intriguing example, as different proteins, while sharing a common fold and the same 4-carboxylate 2-histidine coordination sphere, are known to require either a Fe/Fe, Mn/Fe or Mn/Mn cofactor for function. We previously showed that the R2lox proteins from this family spontaneously assemble the heterodinuclear Mn/Fe cofactor. Here we show that the class Ib ribonucleotide reductase R2 protein from Bacillus anthracis spontaneously assembles a Mn/Mn cofactor in vitro, under both aerobic and anoxic conditions, when the metal-free protein is subjected to incubation with Mn and Fe in equal concentrations. This observation provides an example of a protein scaffold intrinsically predisposed to defy the Irving-Williams series and supports the assumption that the Mn/Mn cofactor is the biologically relevant cofactor in vivo. Substitution of a second coordination sphere residue changes the spontaneous metallation of the protein to predominantly form a heterodinuclear Mn/Fe cofactor under aerobic conditions and a Mn/Mn metal center under anoxic conditions. Together, the results describe the intrinsic metal specificity of class Ib RNR and provide insight into control mechanisms for protein metallation.

PubMed: 32296998
DOI: 10.1007/s00775-020-01782-3

Experimental method

X-RAY DIFFRACTION (2.05001760485 Å)