1EG9

NAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding.

Carredano, E.Karlsson, A.Kauppi, B.Choudhury, D.Parales, R.E.Parales, J.V.Lee, K.Gibson, D.T.Eklund, H.Ramaswamy, S.

(2000) J Mol Biol 296: 701-712

  • DOI: 10.1006/jmbi.1999.3462
  • Primary Citation of Related Structures:  
    1EG9

  • PubMed Abstract: 
  • The three-dimensional structure of the aromatic hydroxylating enzyme naphthalene dioxygenase (NDO) from Pseudomonas sp. NCIB 9816-4 was recently determined. The refinement of the structure together with cyclic averaging showed that in the active site of the enzyme there is electron density for a flat aromatic compound ...

    The three-dimensional structure of the aromatic hydroxylating enzyme naphthalene dioxygenase (NDO) from Pseudomonas sp. NCIB 9816-4 was recently determined. The refinement of the structure together with cyclic averaging showed that in the active site of the enzyme there is electron density for a flat aromatic compound. This compound appears to be an indole adduct, which in Escherichia coli is derived from tryptophan present in the rich culture medium. An indole-dioxygen adduct has been built which fits the electron density convincingly. Support for this interpretation was obtained from crystals of the enzyme purified from cells grown in the absence of tryptophan which had an empty substrate pocket. These types of crystals were soaked in indole solutions and the position of indole in this complex was similar to the corresponding part in the modelled indole-oxygen adduct. This suggests that a peroxide bound to iron end-on attacks the substrate and forms this intermediate. The substrate position has implications for the substrate specificity of the enzyme. Docking studies with indole, naphthalene and biphenyl inside the substrate pocket of NDO suggest the presence of subpockets where the one close to the active site iron is reserved for the binding of the aromatic ring which is hydroxylated upon catalysis. The plausible location for the binding of dioxygen is between this pocket and the catalytic iron. This is in accordance with the enantiospecificity of the products.


    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, S-751 24, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT)A449Pseudomonas putidaMutation(s): 0 
Gene Names: ndoBnahA3nahACndoC2
EC: 1.14.12.12
UniProt
Find proteins for P0A110 (Pseudomonas putida)
Explore P0A110 
Go to UniProtKB:  P0A110
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT)B194Pseudomonas putidaMutation(s): 0 
Gene Names: ndoCnahAD
EC: 1.14.12.12
UniProt
Find proteins for P0A112 (Pseudomonas putida)
Explore P0A112 
Go to UniProtKB:  P0A112
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download Ideal Coordinates CCD File 
E [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
IND
Query on IND

Download Ideal Coordinates CCD File 
F [auth A]INDOLE
C8 H7 N
SIKJAQJRHWYJAI-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], G [auth B], H [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
D [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.169α = 90
b = 140.169β = 90
c = 209.248γ = 120
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance