9DWS | pdb_00009dws

X-ray crystal structure of Francisella hispaniensis apo ribonucleotide reductase beta subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.209 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A Structurally Divergent Class Ia Ribonucleotide Reductase from a Tick-Borne Pathogen.

Peduzzi, O.M.Palowitch, G.M.Gajewski, J.P.Hu, K.Wheeler, A.Laremore, T.N.Silletti, S.Komives, E.A.Allen, B.D.Silakov, A.Krebs, C.Bollinger Jr., J.M.Lin, C.Y.Boal, A.K.

(2025) Biochemistry 64: 3935-3955

  • DOI: https://doi.org/10.1021/acs.biochem.5c00316
  • Primary Citation of Related Structures:  
    9DWS

  • PubMed Abstract: 

    Ribonucleotide reductases (RNRs) generate 2'-deoxynucleotides for DNA biosynthesis, a reaction essential to all life. Class I RNRs have two subunits, α and β. α binds and reduces the substrate, whereas β oxidizes one of the cysteines in α to a C3'-H-bond-cleaving thiyl radical to begin the reaction. The α-Cys oxidant in β is variously a tyrosyl radical (Y ) generated by a diiron or dimanganese cluster, a high-valent dimetal cluster [Mn(IV)/Fe(III) or Mn 2 (IV/III)], or a dihydroxylphenylalanine (DOPA) radical that operates without need of a transition metal. The metal (in)dependence of the Cys oxidant in β correlates loosely with sequence-similarity groupings. We show here that Francisella hispaniensis ( Fh ) β, which lies within an uncharacterized sequence cluster that contains orthologs from multiple human pathogens, harbors a Fe 2 (III/III)/Y cofactor, as in class Ia RNRs from eukaryotes and Escherichia coli . Fh β has several unusual structural features that may reflect adaptation to the bacterium's environment(s). In its apo form, an unwound helix everts a metal ligand toward solvent, and the radical-harboring Y points away from the diiron cluster. An additional aromatic residue (W194), conserved within the sequence cluster, is found close to the universally conserved W37, which is thought to mediate α-Cys oxidation in all class I enzymes. The Y in resting β is remarkably resistant to reduction by hydroxyurea but becomes 8000 times more sensitive when β is engaged in turnover with α. These structural and functional distinctions could be counter measures against host redox defenses that would target the pathogen's RNR and its cofactor.


  • Organizational Affiliation
    • Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ribonucleoside-diphosphate reductase
A, B
328Francisella hispaniensisMutation(s): 0 
Gene Names: FN3523_1088
EC: 1.17.4.1
UniProt
Find proteins for F4BFZ7 (Francisella hispaniensis)
Explore F4BFZ7 
Go to UniProtKB:  F4BFZ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4BFZ7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.209 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.67α = 90
b = 98.03β = 90
c = 100.5γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
iMOSFLMdata reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references