3MZB

X-ray structure of NikA in complex with the doubly hydroxylated iron complex, 1-O2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallographic snapshots of the reaction of aromatic C-H with O(2) catalysed by a protein-bound iron complex

Cavazza, C.Bochot, C.Rousselot-Pailley, P.Carpentier, P.Cherrier, M.V.Martin, L.Marchi-Delapierre, C.Fontecilla-Camps, J.C.Menage, S.

(2010) NAT.CHEM. 2: 1069-1076

  • DOI: 10.1038/nchem.841
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chemical reactions inside single crystals are quite rare because crystallinity is difficult to retain owing to atomic rearrangements. Protein crystals in general have a high solvent content. This allows for some molecular flexibility, which makes it ...

    Chemical reactions inside single crystals are quite rare because crystallinity is difficult to retain owing to atomic rearrangements. Protein crystals in general have a high solvent content. This allows for some molecular flexibility, which makes it possible to trap reaction intermediates of enzymatic reactions without disrupting the crystal lattice. A similar approach has not yet been fully implemented in the field of inorganic chemistry. Here, we have combined model chemistry and protein X-ray crystallography to study the intramolecular aromatic dihydroxylation by an arene-containing protein-bound iron complex. The bound complex was able to activate dioxygen in the presence of a reductant, leading to the formation of catechol as the sole product. The structure determination of four of the catalytic cycle intermediates and the end product showed that the hydroxylation reaction implicates an iron peroxo, generated by reductive O(2) activation, an intermediate already observed in iron monooxygenases. This strategy also provided unexpected mechanistic details such as the rearrangement of the iron coordination sphere on metal reduction.


    Organizational Affiliation

    Laboratoire de Cristallographie et de Cristallogenèse des Protéines, Institut de Biologie Structurale J.P. Ebel, UMR 5075 CEA, CNRS, Université Joseph Fourier, 41 rue Horowitz, 38027 Grenoble Cedex 1, France. christine.cavazza@ibs.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nickel-binding periplasmic protein
A, B
501Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nikA
Find proteins for P33590 (Escherichia coli (strain K12))
Go to UniProtKB:  P33590
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BHR
Query on BHR

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A, B
2-[2-[carboxymethyl-[(2-hydroxyphenyl)methyl]amino]ethyl-[(2,3-dihydroxyphenyl)methyl]amino]ethanoic acid
C20 H24 N2 O7
PIRBWSIWJQHRSO-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
DTD
Query on DTD

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A, B
DITHIANE DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-IMJSIDKUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.040α = 90.00
b = 93.873β = 90.00
c = 124.726γ = 90.00
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
XDSdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance