Ribonucleotide Reductase NrdF from Escherichia coli Soaked with Ferrous Ions

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

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Structural basis for activation of class Ib ribonucleotide reductase.

Boal, A.K.Cotruvo, J.A.Stubbe, J.Rosenzweig, A.C.

(2010) Science 329: 1526-1530

  • DOI: https://doi.org/10.1126/science.1190187
  • Primary Citation of Related Structures:  
    3N37, 3N38, 3N39, 3N3A, 3N3B

  • PubMed Abstract: 

    The class Ib ribonucleotide reductase of Escherichia coli can initiate reduction of nucleotides to deoxynucleotides with either a Mn(III)2-tyrosyl radical (Y•) or a Fe(III)2-Y• cofactor in the NrdF subunit. Whereas Fe(III)2-Y• can self-assemble from Fe(II)2-NrdF and O2, activation of Mn(II)2-NrdF requires a reduced flavoprotein, NrdI, proposed to form the oxidant for cofactor assembly by reduction of O2. The crystal structures reported here of E. coli Mn(II)2-NrdF and Fe(II)2-NrdF reveal different coordination environments, suggesting distinct initial binding sites for the oxidants during cofactor activation. In the structures of Mn(II)2-NrdF in complex with reduced and oxidized NrdI, a continuous channel connects the NrdI flavin cofactor to the NrdF Mn(II)2 active site. Crystallographic detection of a putative peroxide in this channel supports the proposed mechanism of Mn(III)2-Y• cofactor assembly.

  • Organizational Affiliation

    Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase 2 subunit beta319Escherichia coli K-12Mutation(s): 0 
Gene Names: b2676JW2651nrdFygaD
Find proteins for P37146 (Escherichia coli (strain K12))
Explore P37146 
Go to UniProtKB:  P37146
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37146
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.137α = 90
b = 79.137β = 90
c = 267.981γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description