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

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Structural Basis for Superoxide Activation of Flavobacterium johnsoniae Class I Ribonucleotide Reductase and for Radical Initiation by Its Dimanganese Cofactor.

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.

(2018) Biochemistry 57: 2679-2693

  • DOI: https://doi.org/10.1021/acs.biochem.8b00247
  • Primary Citation of Related Structures:  
    6CWO, 6CWP, 6CWQ

  • 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 2 - ) for activation, but it does not require the O 2 - -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 2 - to the Mn 2 II/II 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.

  • Organizational Affiliation

    Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleotide reductase
A, B
308Flavobacterium johnsoniae UW101Mutation(s): 0 
Gene Names: Fjoh_4066
Find proteins for A5FCJ5 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101))
Explore A5FCJ5 
Go to UniProtKB:  A5FCJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5FCJ5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.356α = 106.15
b = 50.816β = 105.03
c = 79.285γ = 95.75
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Derived calculations