Ribonucleotide Reductase class Ie R2 from Mesoplasma florum, DOPA-active form

Experimental Data Snapshot

  • Resolution: 1.48 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.154 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens.

Srinivas, V.Lebrette, H.Lundin, D.Kutin, Y.Sahlin, M.Lerche, M.Eirich, J.Branca, R.M.M.Cox, N.Sjoberg, B.M.Hogbom, M.

(2018) Nature 563: 416-420

  • DOI: https://doi.org/10.1038/s41586-018-0653-6
  • Primary Citation of Related Structures:  
    6GP2, 6GP3

  • PubMed Abstract: 

    Ribonucleotide reductase (RNR) catalyses the only known de novo pathway for the production of all four deoxyribonucleotides that are required for DNA synthesis 1,2 . It is essential for all organisms that use DNA as their genetic material and is a current drug target 3,4 . Since the discovery that iron is required for function in the aerobic, class I RNR found in all eukaryotes and many bacteria, a dinuclear metal site has been viewed as necessary to generate and stabilize the catalytic radical that is essential for RNR activity 5-7 . Here we describe a group of RNR proteins in Mollicutes-including Mycoplasma pathogens-that possess a metal-independent stable radical residing on a modified tyrosyl residue. Structural, biochemical and spectroscopic characterization reveal a stable 3,4-dihydroxyphenylalanine (DOPA) radical species that directly supports ribonucleotide reduction in vitro and in vivo. This observation overturns the presumed requirement for a dinuclear metal site in aerobic ribonucleotide reductase. The metal-independent radical requires new mechanisms for radical generation and stabilization, processes that are targeted by RNR inhibitors. It is possible that this RNR variant provides an advantage under metal starvation induced by the immune system. Organisms that encode this type of RNR-some of which are developing resistance to antibiotics-are involved in diseases of the respiratory, urinary and genital tracts. Further characterization of this RNR family and its mechanism of cofactor generation will provide insight into new enzymatic chemistry and be of value in devising strategies to combat the pathogens that utilize it. We propose that this RNR subclass is denoted class Ie.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden. hogbom@dbb.su.se.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase beta chain
A, B
345Mesoplasma florum L1Mutation(s): 0 
Gene Names: Mfl530
Find proteins for Q6F0T5 (Mesoplasma florum (strain ATCC 33453 / NBRC 100688 / NCTC 11704 / L1))
Explore Q6F0T5 
Go to UniProtKB:  Q6F0T5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6F0T5
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on DAH
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 1.48 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.154 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.162α = 90
b = 53.744β = 108.58
c = 79.284γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2017-04018
European Research CouncilSwedenHIGH-GEAR 724394
Knut and Alice Wallenberg FoundationSweden2012.0233
Knut and Alice Wallenberg FoundationSweden2017.0275

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-21
    Changes: Data collection, Database references
  • Version 1.3: 2018-11-28
    Changes: Data collection, Database references