1HK8

STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DGTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Metal-Binding Site in the Catalytic Subunit of Anaerobic Ribonucleotide Reductase.

Logan, D.T.Mulliez, E.Larsson, K.-M.Bodevin, S.Atta, M.Garnaud, P.E.Sjoberg, B.-M.Fontecave, M.

(2003) Proc.Natl.Acad.Sci.USA 100: 3826

  • DOI: 10.1073/pnas.0736456100

  • PubMed Abstract: 
  • A Zn(Cys)(4) center has been found in the C-terminal region of the crystal structure of the anaerobic class III ribonucleotide reductase (RNR) from bacteriophage T4. The metal center is structurally related to the zinc ribbon motif and to rubredoxin ...

    A Zn(Cys)(4) center has been found in the C-terminal region of the crystal structure of the anaerobic class III ribonucleotide reductase (RNR) from bacteriophage T4. The metal center is structurally related to the zinc ribbon motif and to rubredoxin and rubrerythrin. Mutant enzymes of the homologous RNR from Escherichia coli, in which the coordinating cysteines, conserved in almost all known class III RNR sequences, have been mutated into alanines, are shown to be inactive as the result of their inability to generate the catalytically essential glycyl radical. The possible roles of the metal center are discussed in relationship to the currently proposed reaction mechanism for generation of the glycyl radical in class III RNRs.


    Related Citations: 
    • Structural Basis for Allosteric Substrate Specificty Regulation in Anaerobic Ribonucleotide Reductase
      Larsson, K.-M.,Andersson, J.,Sjoeberg, B.-M.,Nordlund, P.,Logan, D.T.
      (2001) Structure 9: 739


    Organizational Affiliation

    Department of Molecular Biophysics, Lund University, Box 124, 221 00 Lund, Sweden. derek.logan@mbfys.lu.se




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE
A
605Enterobacteria phage T4Gene Names: NRDD (49.1, 55.11/55.13, SUNY)
EC: 1.17.4.2
Find proteins for P07071 (Enterobacteria phage T4)
Go to UniProtKB:  P07071
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
DGT
Query on DGT

Download SDF File 
Download CCD File 
A
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.204 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.163α = 90.00
b = 98.163β = 90.00
c = 246.131γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-17
    Type: Data collection