1JPR | pdb_00001jpr

Mn substituted Ribonucleotide reductase R2 from E. coli oxidized by nitric oxide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 
    0.213 (Depositor), 0.159 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1JPR

This is version 1.4 of the entry. See complete history

Literature

Crystal structures of oxidized dinuclear manganese centres in Mn-substituted class I ribonucleotide reductase from Escherichia coli: carboxylate shifts with implications for O2 activation and radical generation.

Hogbom, M.Andersson, M.E.Nordlund, P.

(2001) J Biol Inorg Chem 6: 315-323

  • DOI: https://doi.org/10.1007/s007750000205
  • Primary Citation Related Structures: 
    1JPR, 1JQC

  • PubMed Abstract: 

    The di-iron carboxylate proteins constitute a diverse class of non-heme iron enzymes performing a multitude of redox reactions. These reactions usually involve high-valent Fe-oxo species and are thought to be controlled by carboxylate shifts. Owing to their short lifetime, the intermediate structures have so far escaped structural characterization by X-ray crystallography. In an attempt to map the carboxylate conformations available to the protein during different redox states and different ligand environments, we have studied metal-substituted forms of the R2 protein of ribonucleotide reductase from Escherichia coli. In the present work we have solved the crystal structures of Mn-substituted R2 oxidized in two different ways. Oxidation was performed using either nitric oxide or a combination of hydrogen peroxide and hydroxylamine. The two structures are virtually identical, indicating that the oxidation states are the same, most likely a mixed-valent MnII-MnIII centre. One of the carboxylate ligands (D84) adopts a new, so far unseen, conformation, which could participate in the mechanism for radical generation in R2. E238 adopts a bridging-chelating conformation proposed to be important for proper O2 activation but not previously observed in the wild-type enzyme. Probable catalase activity was also observed during the oxidation with H2O2, indicating mechanistic similarities to the di-Mn catalases.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 89.88 kDa 
  • Atom Count: 6,317 
  • Modeled Residue Count: 681 
  • Deposited Residue Count: 750 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein R2 of Ribonucleotide reductase
A, B
375Escherichia coliMutation(s): 0 
EC: 1.17.4.1
UniProt
Find proteins for P69924 (Escherichia coli (strain K12))
Explore P69924 
Go to UniProtKB:  P69924
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69924
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HG

Query on HG



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
I [auth B],
J [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free:  0.213 (Depositor), 0.159 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.826α = 90
b = 84.683β = 90
c = 114.333γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description