Ribonucleotide Reductase Protein R1E from Salmonella typhimurium

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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This is version 1.3 of the entry. See complete history


Structure of the large subunit of class Ib ribonucleotide reductase from Salmonella typhimurium and its complexes with allosteric effectors.

Uppsten, M.Farnegardh, M.Jordan, A.Eliasson, R.Eklund, H.Uhlin, U.

(2003) J Mol Biol 330: 87-97

  • DOI: https://doi.org/10.1016/s0022-2836(03)00538-2
  • Primary Citation of Related Structures:  
    1PEM, 1PEO, 1PEQ, 1PEU

  • PubMed Abstract: 

    The three-dimensional structure of the large subunit of the first member of a class Ib ribonucleotide reductase, R1E of Salmonella typhimurium, has been determined in its native form and together with three allosteric effectors. The enzyme contains the characteristic ten-stranded alpha/beta-barrel with catalytic residues at a finger loop in its center and with redox-active cysteine residues at two adjacent barrel strands. Structures where the redox-active cysteine residues are in reduced thiol form and in oxidized disulfide form have been determined revealing local structural changes. The R1E enzyme differs from the class Ia enzyme, Escherichia coli R1, by not having an overall allosteric regulation. This is explained from the structure by differences in the N-terminal domain, which is about 50 residues shorter and lacks the overall allosteric binding site. R1E has an allosteric substrate specificity regulation site and the binding site for the nucleotide effectors is located at the dimer interface similarly as for the class Ia enzymes. We have determined the structures of R1E in the absence of effectors and with dTTP, dATP and dCTP bound. The low affinity for ATP at the specificity site is explained by a tyrosine, which hinders nucleotides containing a 2'-OH group to bind.

  • Organizational Affiliation

    Department of Molecular Biosciences section of Structure Biology, Uppsala Biomedical Center, Swedish University of Agricultural Sciences, Box 590, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase 2 alpha chain714Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: NRDE OR STM2807
Find proteins for Q08698 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q08698 
Go to UniProtKB:  Q08698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08698
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TTP

Download Ideal Coordinates CCD File 
C10 H17 N2 O14 P3
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.144α = 90
b = 99.144β = 90
c = 289.544γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description