1eg9

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spinqualitylabelsall models 1eg9, resolution 1.60Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

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

Overview

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.

About this Structure

1EG9 is a Protein complex structure of sequences from Pseudomonas putida with SO4, FE, FES and IND as ligands. Active as Naphthalene 1,2-dioxygenase, with EC number 1.14.12.12 Full crystallographic information is available from OCA.

Reference

Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding., Carredano E, Karlsson A, Kauppi B, Choudhury D, Parales RE, Parales JV, Lee K, Gibson DT, Eklund H, Ramaswamy S, J Mol Biol. 2000 Feb 18;296(2):701-12. PMID:10669618

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