6EBQ

Crystal Structure of the Flavoprotein NrdI from Aerococcus urinae in Oxidized Form

Summary for 6EBQ

• Entry DOI: 10.2210/pdb6ebq/pdb
• Descriptor: Protein NrdI, FLAVIN MONONUCLEOTIDE (3 entities in total)
• Functional Keywords: ribonucleotide reductase, nrdi, flavoprotein, rnr, fmn, class ie
• Biological source: Aerococcus urinae
• Total number of polymer chains: 2
• Total formula weight: 36576.47

Authors

Palowitch, G.M.,Alapati, R.B.,Boal, A.K. (deposition date: 2018-08-06, release date: 2018-09-19, Last modification date: 2023-10-11)

Primary citation

Blaesi, E.J.,Palowitch, G.M.,Hu, K.,Kim, A.J.,Rose, H.R.,Alapati, R.,Lougee, M.G.,Kim, H.J.,Taguchi, A.T.,Tan, K.O.,Laremore, T.N.,Griffin, R.G.,Krebs, C.,Matthews, M.L.,Silakov, A.,Bollinger Jr., J.M.,Allen, B.D.,Boal, A.K.
Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical.
Proc. Natl. Acad. Sci. U.S.A., 115:10022-10027, 2018

PubMed Abstract: All cells obtain 2'-deoxyribonucleotides for DNA synthesis through the activity of a ribonucleotide reductase (RNR). The class I RNRs found in humans and pathogenic bacteria differ in () use of Fe(II), Mn(II), or both for activation of the dinuclear-metallocofactor subunit, β; () reaction of the reduced dimetal center with dioxygen or superoxide for this activation; () requirement (or lack thereof) for a flavoprotein activase, NrdI, to provide the superoxide from O; and () use of either a stable tyrosyl radical or a high-valent dimetal cluster to initiate each turnover by oxidizing a cysteine residue in the α subunit to a radical (Cys•). The use of manganese by bacterial class I, subclass b-d RNRs, which contrasts with the exclusive use of iron by the eukaryotic Ia enzymes, appears to be a countermeasure of certain pathogens against iron deprivation imposed by their hosts. Here, we report a metal-free type of class I RNR (subclass e) from two human pathogens. The Cys• in its α subunit is generated by a stable, tyrosine-derived dihydroxyphenylalanine radical (DOPA•) in β. The three-electron oxidation producing DOPA• occurs in only if the β is coexpressed with the NrdI activase encoded adjacently in the pathogen genome. The independence of this new RNR from transition metals, or the requirement for a single metal ion only transiently for activation, may afford the pathogens an even more potent countermeasure against transition metal-directed innate immunity.

PubMed: 30224458
DOI: 10.1073/pnas.1811993115

Experimental method

X-RAY DIFFRACTION (1.95 Å)