PDBsum entry 1o7h

Oxidoreductase

PDB id: 1o7h

Contents

Protein chains

448 a.a. *

193 a.a. *

Ligands

EDO ×4

SO4 ×4

FES

Metals

_FE

Waters ×358

* Residue conservation analysis

PDB id:

1o7h

Name:

Oxidoreductase

Title:

Naphthalene 1,2-dioxygenase with oxidized rieske iron sulphur center site.

Structure:

Naphthalene 1,2-dioxygenase alpha subunit. Chain: a. Synonym: naphthalene 1,2-dioxygenase isp alpha, ndob, nahac. Engineered: yes. Naphthalene 1,2-dioxygenase beta subunit. Chain: b. Synonym: naphthalene 1,2-dioxygenase isp beta, ndoc, nahad. Engineered: yes

Source:

Pseudomonas putida. Organism_taxid: 303. Strain: ncib 9816-4. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.20Å R-factor: 0.208 R-free: 0.242

Authors:

A.Karlsson,J.V.Parales,R.E.Parales,D.T.Gibson,H.Eklund,S.Ramaswamy

Key ref:

A.Karlsson et al. (2003). Crystal structure of naphthalene dioxygenase: side-on binding of dioxygen to iron. Science, 299, 1039-1042. PubMed id: 12586937 DOI: 10.1126/science.1078020

Date:

05-Nov-02 Release date: 20-Feb-03

Protein chain

P0A110  (NDOB_PSEPU) -  Naphthalene 1,2-dioxygenase system, large oxygenase component from Pseudomonas putida

Seq: 449 a.a.

Struc: 448 a.a.

Protein chain

P0A112  (NDOC_PSEPU) -  Naphthalene 1,2-dioxygenase system, small oxygenase component from Pseudomonas putida

Seq: 194 a.a.

Struc: 193 a.a.

Enzyme reactions

• Enzyme class: Chain A: E.C.1.14.12.12 - naphthalene 1,2-dioxygenase.
• Pathway: Aromatic 1,2-Dioxygenases
• Reaction: naphthalene + NADH + O2 + H⁺ = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD⁺
• Cofactor: Fe cation

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1126/science.1078020

Science 299:1039-1042 (2003)

PubMed id: 12586937

Crystal structure of naphthalene dioxygenase: side-on binding of dioxygen to iron.

A.Karlsson, J.V.Parales, R.E.Parales, D.T.Gibson, H.Eklund, S.Ramaswamy.

ABSTRACT

Binding of oxygen to iron is exploited in several biological and chemical processes. Although computational and spectroscopic results have suggested side-on binding, only end-on binding of oxygen to iron has been observed in crystal structures. We have determined structures of naphthalene dioxygenase that show a molecular oxygen species bound to the mononuclear iron in a side-on fashion. In a complex with substrate and dioxygen, the dioxygen molecule is lined up for an attack on the double bond of the aromatic substrate. The structures reported here provide the basis for a reaction mechanism and for the high stereospecificity of the reaction catalyzed by naphthalene dioxygenase.

Selected figure(s)

Figure 1.
Fig. 1. (All panels are stereopairs.) (A) Binding of naphthalene at the active site of NDO. The gray 2F[obs] - F[calc] map is contoured at 1.0 . (B) Binding of dioxygen to the mononuclear iron in the absence of substrate. The gray 2F[obs] - F[calc] map is contoured at 1.15 and the green F[obs] - F[calc] map (computed before the dioxygen molecule was modeled) at 3.8 × RMS (root mean square). (C) Binding of oxygen to the mononuclear iron in the presence of indole. The gray 2F[obs] - F[calc] map is contoured at 1.0 and the green F[obs] - F[calc] map (computed before the dioxygen molecule was modeled) at 4.0 × RMS. (D) Naphthalene cis-dihydrodiol bound to the active site of NDO. The gray 2F[obs] - F[calc] map is contoured at 1.0 . Superposition of the product complex and the substrate complex shows that the positions of the rings in the product and the substrate are similar. The product cannot move any closer to the iron, as it would bring the O from the product into van der Waals short contact with the His ligand of the Fe. The current distance between the O and the N of His is 2.9 Å. Color code: yellow, carbon; blue, nitrogen; red, oxygen; purple, iron.

Figure 2.
Fig. 2. (A) Scheme showing how the different structures in Fig. 1 can be arranged to follow the dihydroxylation reaction catalyzed by NDO. Naphthalene and indole are both substrates for the enzyme, and we have used them interchangeably in different studies of the enzyme (23). For simplicity we show only naphthalene here. The structures are as follows: 1, the resting enzyme with oxidized Rieske center and ferrous active site [Protein Data Bank (PDB) code 1O7H]; 2, the reduced enzyme (PDB code 1O7W); 3, binary dioxgen complex (PDB code 1O7M); 4, binary substrate complex, structures with both indole and naphthalene [PDB codes 1EG9 (indole) and 1O7G (naphthalene)]; 5, ternary substrate dioxygen species, structure with indole (PDB code 1O7N); and 6, product naphthalene cis-1,2-dihydrodiol (PDB code 1O7P). [2Fe-2S] refers to the nearest Rieske iron-sulfur cluster. (B) Chemical steps in the dioxygenation reaction carried out by Rieske dioxygenases.

The above figures are reprinted by permission from the AAAs: Science (2003, 299, 1039-1042) copyright 2003.

Author's comment

Figure 2: It is has been shown spectroscopically by the John Lipscomb group, during the catalytic cycle, the substrate binds before dioxygen to the active site of the enzyme.
S. Ramaswamy.