6CWP

X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) ribonucleotide reductase beta subunit (anaerobic)

Summary for 6CWP

• Entry DOI: 10.2210/pdb6cwp/pdb
• Descriptor: Ribonucleotide reductase, VAL-GLU-TYR-THR-LYS-HIS, MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: ribonucleotide reductase, four-helix bundle, dimanganese cluster, oxidoretuctase, oxidoreductase
• Biological source: Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / UW101) (Cytophaga johnsonae); More
• Total number of polymer chains: 3
• Total formula weight: 72518.73

Authors

Maggiolo, A.O.,Rose, H.R.,Boal, A.K. (deposition date: 2018-03-30, release date: 2018-04-18, Last modification date: 2024-03-13)

Primary citation

Rose, H.R.,Ghosh, M.K.,Maggiolo, A.O.,Pollock, C.J.,Blaesi, E.J.,Hajj, V.,Wei, Y.,Rajakovich, L.J.,Chang, W.C.,Han, Y.,Hajj, M.,Krebs, C.,Silakov, A.,Pandelia, M.E.,Bollinger, J.M.,Boal, A.K.
Structural Basis for Superoxide Activation of Flavobacterium johnsoniae Class I Ribonucleotide Reductase and for Radical Initiation by Its Dimanganese Cofactor.
Biochemistry, 57:2679-2693, 2018

PubMed Abstract: A ribonucleotide reductase (RNR) from Flavobacterium johnsoniae ( Fj) differs fundamentally from known (subclass a-c) class I RNRs, warranting its assignment to a new subclass, Id. Its β subunit shares with Ib counterparts the requirements for manganese(II) and superoxide (O) for activation, but it does not require the O-supplying flavoprotein (NrdI) needed in Ib systems, instead scavenging the oxidant from solution. Although Fj β has tyrosine at the appropriate sequence position (Tyr 104), this residue is not oxidized to a radical upon activation, as occurs in the Ia/b proteins. Rather, Fj β directly deploys an oxidized dimanganese cofactor for radical initiation. In treatment with one-electron reductants, the cofactor can undergo cooperative three-electron reduction to the II/II state, in contrast to the quantitative univalent reduction to inactive "met" (III/III) forms seen with I(a-c) βs. This tendency makes Fj β unusually robust, as the II/II form can readily be reactivated. The structure of the protein rationalizes its distinctive traits. A distortion in a core helix of the ferritin-like architecture renders the active site unusually open, introduces a cavity near the cofactor, and positions a subclass-d-specific Lys residue to shepherd O to the Mn cluster. Relative to the positions of the radical tyrosines in the Ia/b proteins, the unreactive Tyr 104 of Fj β is held away from the cofactor by a hydrogen bond with a subclass-d-specific Thr residue. Structural comparisons, considered with its uniquely simple mode of activation, suggest that the Id protein might most closely resemble the primordial RNR-β.

PubMed: 29609464
DOI: 10.1021/acs.biochem.8b00247

Experimental method

X-RAY DIFFRACTION (1.92 Å)