5DCO

R2-like ligand-binding oxidase with aerobically reconstituted diiron cofactor (short soak)

Summary for 5DCO

• Entry DOI: 10.2210/pdb5dco/pdb
• Related: 4HR0 4HR4 4HR5 4XB9 4XBV 4XBW
• Descriptor: Ribonucleotide reductase small subunit, FE (III) ION, PALMITIC ACID, ... (4 entities in total)
• Functional Keywords: r2-like ligand-binding oxidase, diiron cofactor, ribonucleotide reductase r2 subunit fold, metalloprotein oxidoreductase, oxidoreductase
• Biological source: Geobacillus kaustophilus (strain HTA426)
• Total number of polymer chains: 1
• Total formula weight: 37330.92

Authors

Griese, J.J.,Hogbom, M. (deposition date: 2015-08-24, release date: 2015-09-09, Last modification date: 2024-01-10)

Primary citation

Griese, J.J.,Kositzki, R.,Schrapers, P.,Branca, R.M.,Nordstrom, A.,Lehtio, J.,Haumann, M.,Hogbom, M.
Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/Iron Cofactor.
J.Biol.Chem., 290:25254-25272, 2015

PubMed Abstract: Two recently discovered groups of prokaryotic di-metal carboxylate proteins harbor a heterodinuclear Mn/Fe cofactor. These are the class Ic ribonucleotide reductase R2 proteins and a group of oxidases that are found predominantly in pathogens and extremophiles, called R2-like ligand-binding oxidases (R2lox). We have recently shown that the Mn/Fe cofactor of R2lox self-assembles from Mn(II) and Fe(II) in vitro and catalyzes formation of a tyrosine-valine ether cross-link in the protein scaffold (Griese, J. J., Roos, K., Cox, N., Shafaat, H. S., Branca, R. M., Lehtiö, J., Gräslund, A., Lubitz, W., Siegbahn, P. E., and Högbom, M. (2013) Proc. Natl. Acad. Sci. U.S.A. 110, 17189-17194). Here, we present a detailed structural analysis of R2lox in the nonactivated, reduced, and oxidized resting Mn/Fe- and Fe/Fe-bound states, as well as the nonactivated Mn/Mn-bound state. X-ray crystallography and x-ray absorption spectroscopy demonstrate that the active site ligand configuration of R2lox is essentially the same regardless of cofactor composition. Both the Mn/Fe and the diiron cofactor activate oxygen and catalyze formation of the ether cross-link, whereas the dimanganese cluster does not. The structures delineate likely routes for gated oxygen and substrate access to the active site that are controlled by the redox state of the cofactor. These results suggest that oxygen activation proceeds via similar mechanisms at the Mn/Fe and Fe/Fe center and that R2lox proteins might utilize either cofactor in vivo based on metal availability.

PubMed: 26324712
DOI: 10.1074/jbc.M115.675223

Experimental method

X-RAY DIFFRACTION (2.326 Å)