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 

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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 U S A 108: 21046-21051

  • DOI: 10.1073/pnas.1112715108
  • Primary Citation of Related Structures:  
    3UUS

  • 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 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase 1 subunit alphaA, B, C, D761Escherichia coli K-12Mutation(s): 0 
Gene Names: b2234dnaFJW2228nrdA
EC: 1.17.4.1
UniProt
Find proteins for P00452 (Escherichia coli (strain K12))
Explore P00452 
Go to UniProtKB:  P00452
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00452
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase 1 subunit betaE, F, G, H375Escherichia coli K-12Mutation(s): 0 
Gene Names: b2235ftsBJW2229nrdB
EC: 1.17.4.1
UniProt
Find proteins for P69924 (Escherichia coli (strain K12))
Explore P69924 
Go to UniProtKB:  P69924
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69924
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth C],
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth C],
N [auth C],
O [auth D],
P [auth D]
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
Q [auth E],
R [auth E],
S [auth F],
T [auth F],
U [auth G],
Q [auth E],
R [auth E],
S [auth F],
T [auth F],
U [auth G],
V [auth G],
W [auth H],
X [auth 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
b = 153.457β = 119.91
c = 169.416γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data 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: 2011-12-21
    Type: Initial release
  • Version 1.1: 2012-01-11
    Changes: Database references