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


Ligand Structure Quality Assessment 


This is version 1.5 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 U S A 100: 3826

  • DOI: https://doi.org/10.1073/pnas.0736456100
  • Primary Citation of Related Structures:  
    1HK8

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE605Tequatrovirus T4Mutation(s): 1 
EC: 1.17.4.2
UniProt
Find proteins for P07071 (Enterobacteria phage T4)
Explore P07071 
Go to UniProtKB:  P07071
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07071
Sequence Annotations
Expand
  • Reference Sequence
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
b = 98.163β = 90
c = 246.131γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description