5CNV

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to GDP and TTP at 3.20 Angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli.

Zimanyi, C.M.Chen, P.Y.Kang, G.Funk, M.A.Drennan, C.L.

(2016) Elife 5: e07141-e07141

  • DOI: 10.7554/eLife.07141
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ribonucleotide reductase (RNR) converts ribonucleotides to deoxyribonucleotides, a reaction that is essential for DNA biosynthesis and repair. This enzyme is responsible for reducing all four ribonucleotide substrates, with specificity regulated by t ...

    Ribonucleotide reductase (RNR) converts ribonucleotides to deoxyribonucleotides, a reaction that is essential for DNA biosynthesis and repair. This enzyme is responsible for reducing all four ribonucleotide substrates, with specificity regulated by the binding of an effector to a distal allosteric site. In all characterized RNRs, the binding of effector dATP alters the active site to select for pyrimidines over purines, whereas effectors dGTP and TTP select for substrates ADP and GDP, respectively. Here, we have determined structures of Escherichia coli class Ia RNR with all four substrate/specificity effector-pairs bound (CDP/dATP, UDP/dATP, ADP/dGTP, GDP/TTP) that reveal the conformational rearrangements responsible for this remarkable allostery. These structures delineate how RNR 'reads' the base of each effector and communicates substrate preference to the active site by forming differential hydrogen bonds, thereby maintaining the proper balance of deoxynucleotides in the cell.


    Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States.




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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B, C, D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-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
TTP
Query on TTP

Download SDF File 
Download CCD File 
A, B, C, D
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-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: 3.2 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.190 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/240 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 274.776α = 90.00
b = 157.753β = 119.49
c = 165.768γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction
Cootmodel building
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health SciencesUnited StatesP30-ES002109
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32GM08334
National Science Foundation (United States)United States0645960

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-05-11
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Data collection, Derived calculations
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence