3UUS

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.65 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase.

Ando, N.Brignole, E.J.Zimanyi, C.M.Funk, M.A.Yokoyama, K.Asturias, F.J.Stubbe, J.Drennan, C.L.

(2011) Proc.Natl.Acad.Sci.USA 108: 21046-21051

  • DOI: 10.1073/pnas.1112715108

  • PubMed Abstract: 
  • Essential for DNA biosynthesis and repair, ribonucleotide reductases (RNRs) convert ribonucleotides to deoxyribonucleotides via radical-based chemistry. Although long known that allosteric regulation of RNR activity is vital for cell health, the mole ...

    Essential for DNA biosynthesis and repair, ribonucleotide reductases (RNRs) convert ribonucleotides to deoxyribonucleotides via radical-based chemistry. Although long known that allosteric regulation of RNR activity is vital for cell health, the molecular basis of this regulation has been enigmatic, largely due to a lack of structural information about how the catalytic subunit (α(2)) and the radical-generation subunit (β(2)) interact. Here we present the first structure of a complex between α(2) and β(2) subunits for the prototypic RNR from Escherichia coli. Using four techniques (small-angle X-ray scattering, X-ray crystallography, electron microscopy, and analytical ultracentrifugation), we describe an unprecedented α(4)β(4) ring-like structure in the presence of the negative activity effector dATP and provide structural support for an active α(2)β(2) configuration. We demonstrate that, under physiological conditions, E. coli RNR exists as a mixture of transient α(2)β(2) and α(4)β(4) species whose distributions are modulated by allosteric effectors. We further show that this interconversion between α(2)β(2) and α(4)β(4) entails dramatic subunit rearrangements, providing a stunning molecular explanation for the allosteric regulation of RNR activity in E. coli.


    Organizational Affiliation

    Department of Chemistry, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonucleoside-diphosphate reductase 1 subunit alpha
A, B, C, D
761Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nrdA (dnaF)
EC: 1.17.4.1
Find proteins for P00452 (Escherichia coli (strain K12))
Go to UniProtKB:  P00452
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribonucleoside-diphosphate reductase 1 subunit beta
E, F, G, H
375Escherichia 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download SDF File 
Download CCD File 
A, B, C, D
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
E, F, G, H
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.65 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.257 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 287.358α = 90.00
b = 153.457β = 119.91
c = 169.416γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
PHASERphasing
HKL-2000data scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2012-01-11
    Type: Database references