6I90

R2-like ligand-binding oxidase G68F mutant with aerobically reconstituted Mn/Fe cofactor

Summary for 6I90

• Entry DOI: 10.2210/pdb6i90/pdb
• Related: 4HR0 4HR4 4HR5 4XB9 4XBV 4XBW 5DCO 5DCR 5DCS 5EKB 5OMJ 5OMK 6F65 6F6B 6F6C 6F6E 6F6F 6F6G 6F6H 6F6K 6F6L 6F6M 6I92 6I93 6I94 6I95
• Descriptor: Ribonucleotide reductase small subunit, PALMITIC ACID, MANGANESE (III) ION, ... (6 entities in total)
• Functional Keywords: r2-like ligand-binding oxidase, mn/fe cofactor, ribonucleotide reductase r2 subunit fold, metalloprotein oxidoreductase, oxidoreductase
• Biological source: Geobacillus kaustophilus (strain HTA426)
• Total number of polymer chains: 1
• Total formula weight: 37475.08

Authors

Griese, J.J.,Hogbom, M. (deposition date: 2018-11-22, release date: 2019-10-16, Last modification date: 2024-01-24)

Primary citation

Kutin, Y.,Kositzki, R.,Branca, R.M.M.,Srinivas, V.,Lundin, D.,Haumann, M.,Hogbom, M.,Cox, N.,Griese, J.J.
Chemical flexibility of heterobimetallic Mn/Fe cofactors: R2lox and R2c proteins.
J.Biol.Chem., 294:18372-18386, 2019

PubMed Abstract: A heterobimetallic Mn/Fe cofactor is present in the R2 subunit of class Ic ribonucleotide reductases (R2c) and in R2-like ligand-binding oxidases (R2lox). Although the protein-derived metal ligands are the same in both groups of proteins, the connectivity of the two metal ions and the chemistry each cofactor performs are different: in R2c, a one-electron oxidant, the Mn/Fe dimer is linked by two oxygen bridges (μ-oxo/μ-hydroxo), whereas in R2lox, a two-electron oxidant, it is linked by a single oxygen bridge (μ-hydroxo) and a fatty acid ligand. Here, we identified a second coordination sphere residue that directs the divergent reactivity of the protein scaffold. We found that the residue that directly precedes the N-terminal carboxylate metal ligand is conserved as a glycine within the R2lox group but not in R2c. Substitution of the glycine with leucine converted the resting-state R2lox cofactor to an R2c-like cofactor, a μ-oxo/μ-hydroxo-bridged Mn/Fe dimer. This species has recently been observed as an intermediate of the oxygen activation reaction in WT R2lox, indicating that it is physiologically relevant. Cofactor maturation in R2c and R2lox therefore follows the same pathway, with structural and functional divergence of the two cofactor forms following oxygen activation. We also show that the leucine-substituted variant no longer functions as a two-electron oxidant. Our results reveal that the residue preceding the N-terminal metal ligand directs the cofactor's reactivity toward one- or two-electron redox chemistry, presumably by setting the protonation state of the bridging oxygens and thereby perturbing the redox potential of the Mn ion.

PubMed: 31591267
DOI: 10.1074/jbc.RA119.010570

Experimental method

X-RAY DIFFRACTION (1.803 Å)