4ERM

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex at 4 Angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase.

Zimanyi, C.M.Ando, N.Brignole, E.J.Asturias, F.J.Stubbe, J.Drennan, C.L.

(2012) Structure 20: 1374-1383

  • DOI: 10.1016/j.str.2012.05.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ribonucleotide reductases (RNRs) provide the precursors for DNA biosynthesis and repair and are successful targets for anticancer drugs such as clofarabine and gemcitabine. Recently, we reported that dATP inhibits E. coli class Ia RNR by driving form ...

    Ribonucleotide reductases (RNRs) provide the precursors for DNA biosynthesis and repair and are successful targets for anticancer drugs such as clofarabine and gemcitabine. Recently, we reported that dATP inhibits E. coli class Ia RNR by driving formation of RNR subunits into α4β4 rings. Here, we present the first X-ray structure of a gemcitabine-inhibited E. coli RNR and show that the previously described α4β4 rings can interlock to form an unprecedented (α4β4)2 megacomplex. This complex is also seen in a higher-resolution dATP-inhibited RNR structure presented here, which employs a distinct crystal lattice from that observed in the gemcitabine-inhibited case. With few reported examples of protein catenanes, we use data from small-angle X-ray scattering and electron microscopy to both understand the solution conditions that contribute to concatenation in RNRs as well as present a mechanism for the formation of these unusual structures.


    Organizational Affiliation

    Department of Chemistry, 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 4 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
DAT
Query on DAT

Download SDF File 
Download CCD File 
A, B, C, D
2'-DEOXYADENOSINE-5'-DIPHOSPHATE
DADP
C10 H15 N5 O9 P2
DAEAPNUQQAICNR-RRKCRQDMSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FEO
Query on FEO

Download SDF File 
Download CCD File 
E, F, G, H
MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.259 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 280.471α = 90.00
b = 155.744β = 119.07
c = 166.919γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
CNSphasing
HKL-2000data reduction
HKL-2000data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2012-10-24
    Type: Database references