1AV8

RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT FROM E. COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Characterization of Y122F R2 of Escherichia coli ribonucleotide reductase by time-resolved physical biochemical methods and X-ray crystallography.

Tong, W.Burdi, D.Riggs-Gelasco, P.Chen, S.Edmondson, D.Huynh, B.H.Stubbe, J.Han, S.Arvai, A.Tainer, J.A.

(1998) Biochemistry 37: 5840-5848

  • DOI: 10.1021/bi9728811
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ribonucleotide reductase (RNR) from Escherichia coli catalyzes the conversion of ribonucleotides to deoxyribonucleotides. It is composed of two homodimeric subunits, R1 and R2. R2 contains the diferric-tyrosyl radical cofactor essential for the nucle ...

    Ribonucleotide reductase (RNR) from Escherichia coli catalyzes the conversion of ribonucleotides to deoxyribonucleotides. It is composed of two homodimeric subunits, R1 and R2. R2 contains the diferric-tyrosyl radical cofactor essential for the nucleotide reduction process. The in vitro mechanism of assembly of this cluster starting with apo R2 or with a diferrous form of R2 has been examined by time-resolved physical biochemical methods. An intermediate, Fe3+/Fe4+ cluster (intermediate X), has been identified that is thought to be directly involved in the oxidation of Y122 to the tyrosyl radical (*Y122). An R2 mutant in which phenylalanine has replaced Y122 has been used to accumulate intermediate X at sufficient levels that it can be studied using a variety of spectroscopic methods. The details of the reconstitution of the apo and diferrous forms of Y122F R2 have been examined by stopped-flow UV/vis spectroscopy and by rapid freeze quench electron paramagnetic resonance, and Mössbauer spectroscopies. In addition the structure of this mutant, crystallized at pH 7.6 in the absence of mercury, at 2.46 A resolution has been determined. These studies suggest that Y122F R2 is an appropriate model for the examination of intermediate X in the assembly process. Studies with two mutants, Y356F and double mutant Y356F and Y122F R2, are interpreted in terms of the possible role of Y356 in the putative electron transfer reaction between the R1 and R2 subunits of this RNR.


    Related Citations: 
    • Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2
      Nordlund, P.,Eklund, H.
      (1993) J.Mol.Biol. 232: 123


    Organizational Affiliation

    Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEOTIDE REDUCTASE R2
A, B
340Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nrdB (ftsB)
EC: 1.17.4.1
Find proteins for P69924 (Escherichia coli (strain K12))
Go to UniProtKB:  P69924
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FEO
Query on FEO

Download SDF File 
Download CCD File 
A, B
MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.139 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 139.700α = 90.00
b = 139.700β = 90.00
c = 110.600γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORphasing
X-PLORrefinement
DENZOdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-28
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-06-27
    Type: Advisory, Data collection, Derived calculations, Other