5R1R

RIBONUCLEOTIDE REDUCTASE E441A MUTANT R1 PROTEIN FROM ESCHERICHIA COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A new mechanism-based radical intermediate in a mutant R1 protein affecting the catalytically essential Glu441 in Escherichia coli ribonucleotide reductase.

Persson, A.L.Eriksson, M.Katterle, B.Potsch, S.Sahlin, M.Sjoberg, B.M.

(1997) J.Biol.Chem. 272: 31533-31541

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The invariant active site residue Glu441 in protein R1 of ribonucleotide reductase from Escherichia coli has been engineered to alanine, aspartic acid, and glutamic acid. Each mutant protein was structurally and enzymatically characterized. Glu441 co ...

    The invariant active site residue Glu441 in protein R1 of ribonucleotide reductase from Escherichia coli has been engineered to alanine, aspartic acid, and glutamic acid. Each mutant protein was structurally and enzymatically characterized. Glu441 contributes to substrate binding, and a carboxylate side chain at position 441 is essential for catalysis. The most intriguing results are the suicidal mechanism-based reaction intermediates observed when R1 E441Q is incubated with protein R2 and natural substrates (CDP and GDP). In a consecutive reaction sequence, we observe at least three clearly discernible steps: (i) a rapid decay (k1 >/= 1.2 s-1) of the catalytically essential tyrosyl radical of protein R2 concomitant with formation of an early transient radical intermediate species, (ii) a slower decay (k2 = 0.03 s-1) of the early intermediate concomitant with formation of another intermediate with a triplet EPR signal, and (iii) decay (k3 = 0.004 s-1) of the latter concomitant with formation of a characteristic substrate degradation product. The characteristics of the triplet EPR signal are compatible with a substrate radical intermediate (most likely localized at the 3'-position of the ribose moiety of the substrate nucleotide) postulated to occur in the wild type reaction mechanism as well.


    Related Citations: 
    • Structure of Ribonucleotide Reductase Protein R1
      Uhlin, U.,Eklund, H.
      (1994) Nature 370: 533
    • Binding of Allosteric Effectors to Ribonucleotide Reductase Protein R1: Reduction of Active-Site Cysteines Promotes Substrate Binding
      Eriksson, M.,Uhlin, U.,Ramaswamy, S.,Ekberg, M.,Regnstrom, K.,Sjoberg, B.M.,Eklund, H.
      (1997) Structure 5: 1077


    Organizational Affiliation

    Department of Molecular Biology, Stockholm University, Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
A, B, C
761Escherichia coli (strain K12)Mutation(s): 1 
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
RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
D, E, F, P
20Escherichia 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 223.810α = 90.00
b = 223.810β = 90.00
c = 334.260γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
TNTrefinement
DENZOdata reduction
REFMACrefinement
TNTphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-03-18
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance