Ribonucleotide reductase R2 subunit from Clostridium botulinum

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site.

Martinez-Carranza, M.Jonna, V.R.Lundin, D.Sahlin, M.Carlson, L.A.Jemal, N.Hogbom, M.Sjoberg, B.M.Stenmark, P.Hofer, A.

(2020) J Biol Chem 295: 15576-15587

  • DOI: https://doi.org/10.1074/jbc.RA120.014895
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Ribonucleotide reductase (RNR) is a central enzyme for the synthesis of DNA building blocks. Most aerobic organisms, including nearly all eukaryotes, have class I RNRs consisting of R1 and R2 subunits. The catalytic R1 subunit contains an overall activity site that can allosterically turn the enzyme on or off by the binding of ATP or dATP, respectively. The mechanism behind the ability to turn the enzyme off via the R1 subunit involves the formation of different types of R1 oligomers in most studied species and R1-R2 octamers in Escherichia coli To better understand the distribution of different oligomerization mechanisms, we characterized the enzyme from Clostridium botulinum , which belongs to a subclass of class I RNRs not studied before. The recombinantly expressed enzyme was analyzed by size-exclusion chromatography, gas-phase electrophoretic mobility macromolecular analysis, EM, X-ray crystallography, and enzyme assays. Interestingly, it shares the ability of the E. coli RNR to form inhibited R1-R2 octamers in the presence of dATP but, unlike the E. coli enzyme, cannot be turned off by combinations of ATP and dGTP/dTTP. A phylogenetic analysis of class I RNRs suggests that activity regulation is not ancestral but was gained after the first subclasses diverged and that RNR subclasses with inhibition mechanisms involving R1 oligomerization belong to a clade separated from the two subclasses forming R1-R2 octamers. These results give further insight into activity regulation in class I RNRs as an evolutionarily dynamic process.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase subunit betaA [auth C],
B [auth A],
C [auth D],
D [auth B]
364Clostridium botulinum A3 str. Loch MareeMutation(s): 0 
Gene Names: nrdBCLK_2200
Find proteins for B1KYY8 (Clostridium botulinum (strain Loch Maree / Type A3))
Explore B1KYY8 
Go to UniProtKB:  B1KYY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1KYY8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
E [auth C],
F [auth C],
I [auth A],
N [auth B]
C3 H8 O3
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
G [auth C]
H [auth C]
J [auth A]
K [auth A]
L [auth D]
G [auth C],
H [auth C],
J [auth A],
K [auth A],
L [auth D],
M [auth D],
O [auth B],
P [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.827α = 90
b = 61.854β = 127.46
c = 154.342γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
xia2data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description