Naphthalene 1,2-dioxygenase

 

The naphthalene dioxygenase (NDO) multicomponent enzyme system catalyses the incorporation of both atoms of molecular oxygen into naphthalene to form cis-naphthalene dihydrodiol. The enzyme comprises an NADH binding reductase, a Rieske feredoxin, and a oxygenase component. All three units contain [2Fe-2S] clusters. NDO is a member of the ring-hydroxylating dioxygenase (RHD) family of bacterial enzymes that play a critical role in the degradation of aromatic compounds.

 

Reference Protein and Structure

Sequences
P0A110 UniProt (1.14.12.12)
P0A112 UniProt IPR015879 (Sequence Homologues) (PDB Homologues)
Biological species
Pseudomonas putida (Bacteria) Uniprot
PDB
1ndo - NAPHTHALENE 1,2-DIOXYGENASE (2.25 Å) PDBe PDBsum 1ndo
Catalytic CATH Domains
2.102.10.10 CATHdb 3.90.380.10 CATHdb (see all for 1ndo)
Cofactors
Iron(3+) (1), Di-mu-sulfido-diiron(2+) (3), Fadh2(2-) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:1.14.12.12)

hydron
CHEBI:15378ChEBI
+
NADH(2-)
CHEBI:57945ChEBI
+
naphthalene
CHEBI:16482ChEBI
+
dioxygen
CHEBI:15379ChEBI
→
(1R,2S)-1,2-dihydronaphthalene-1,2-diol
CHEBI:44343ChEBI
+
NAD(1-)
CHEBI:57540ChEBI
Alternative enzyme names: Naphthalene dioxygenase, Naphthalene oxygenase, NDO,

Enzyme Mechanism

Introduction

NAD initiates a hydride transfer to the FAD cofactor, which then undergoes a rearrangement to transfer a single electron to the final of three iron-sulfur clusters. This electron is then transferred to a dixygen molecule via a three residue relay (His104, Asp205 and His208). The peroxo group formed then attacks the naphthalene substrate in a nucleophilic addition that causes the double bond to attack the peroxo group, cleaving the O-O bond and forming the epoxide intermediate. This intermediate then collapses in a heterolysis resulting in a carbocation and anioinc oxygen bound to the Fe(III) centre. The iron-bound hydroxide group attacks the carbocation in a coordination reaction. The second electron transfer is initiated by the deprotonation of the FAD and occurs in the same manner as the first. In the final step of the reaction the cis-1,2-dihydronaphthalene-1,2-diol product deprotonates a water molecule and de-coordinates from the Fe(II) centre.

Catalytic Residues Roles

UniProt PDB* (1ndo)
His104, Asp205 His104A, Asp205E Forms part of the electron relay chain between the final iron sulfur cluster and the active site iron and dioxygen moleucles. single electron relay, single electron acceptor, single electron donor
His208 His208E Forms part of the catalytic iron binding site and acts as an electron relay from the final iron sulfur cluster to the dioxygen molecule. single electron relay, single electron acceptor, single electron donor, metal ligand
His213, Asp362 His213E, Asp362E Forms part of the catalytic iron binding site. metal ligand
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

aromatic unimolecular elimination by the conjugate base, aromatic bimolecular nucleophilic addition, hydride transfer, overall reactant used, cofactor used, intermediate formation, overall product formed, redox reaction, radical formation, electron relay, electron transfer, proton transfer, bimolecular nucleophilic addition, coordination, native state of cofactor regenerated, coordination to a metal ion, bimolecular nucleophilic substitution, rate-determining step, heterolysis, decoordination from a metal ion, intermediate terminated, native state of enzyme regenerated

References

  1. Karlsson A et al. (2003), Science, 299, 1039-1042. Crystal Structure of Naphthalene Dioxygenase: Side-on Binding of Dioxygen to Iron. DOI:10.1126/science.1078020. PMID:12586937.
  2. Dawson WK et al. (2016), PLoS One, 11, e0162031-. Electron Transport in a Dioxygenase-Ferredoxin Complex: Long Range Charge Coupling between the Rieske and Non-Heme Iron Center. DOI:10.1371/journal.pone.0162031. PMID:27656882.
  3. White MD et al. (2016), Curr Opin Chem Biol, 31, 126-135. Catalytic strategies of the non-heme iron dependent oxygenases and their roles in plant biology. DOI:10.1016/j.cbpa.2016.02.017. PMID:27015291.
  4. Barry SM et al. (2013), ACS Catal, 3,Mechanism and Catalytic Diversity of Rieske Non-Heme Iron-Dependent Oxygenases. DOI:10.1021/cs400087p. PMID:24244885.
  5. Ashikawa Y et al. (2012), BMC Struct Biol, 12, 15-. Structural insight into the substrate- and dioxygen-binding manner in the catalytic cycle of rieske nonheme iron oxygenase system, carbazole 1,9a-dioxygenase. DOI:10.1186/1472-6807-12-15. PMID:22727022.
  6. Bassan A et al. (2004), J Biol Inorg Chem, 9, 439-452. A theoretical study of the cis -dihydroxylation mechanism in naphthalene 1,2-dioxygenase. DOI:10.1007/s00775-004-0537-0. PMID:15042436.
  7. Wolfe MD et al. (2003), J Biol Chem, 278, 829-835. Hydrogen Peroxide-coupled cis-Diol Formation Catalyzed by Naphthalene 1,2-Dioxygenase. DOI:10.1074/jbc.m209604200. PMID:12403773.
  8. Carredano E et al. (2000), J Mol Biol, 296, 701-712. Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding. DOI:10.1006/jmbi.1999.3462. PMID:10669618.
  9. Parales RE et al. (1999), J Bacteriol, 181, 1831-1837. Aspartate 205 in the catalytic domain of naphthalene dioxygenase is essential for activity. PMID:10074076.
  10. Kauppi B et al. (1998), Structure, 6, 571-586. Structure of an aromatic-ring-hydroxylating dioxygenase – naphthalene 1,2-dioxygenase. DOI:10.1016/s0969-2126(98)00059-8. PMID:9634695.

Step 1. NAD initiates a hydride transfer to the FAD cofactor.

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Catalytic Residues Roles

Residue Roles
Asp362E metal ligand
His208E metal ligand
His213E metal ligand

Chemical Components

ingold: aromatic unimolecular elimination by the conjugate base, ingold: aromatic bimolecular nucleophilic addition, hydride transfer, overall reactant used, cofactor used, intermediate formation, overall product formed

Step 2. FAD undergoes a double bond rearrangement that results in the transfer of a single electron from the FAD to one of the iron-sulfur clusters. This then initiates an electron relay through a second iron-sulfur cluster to a third.

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Catalytic Residues Roles

Residue Roles
Asp362E metal ligand
His208E metal ligand
His213E metal ligand

Chemical Components

redox reaction, radical formation, cofactor used, intermediate formation, electron relay

Step 3. The electron is transferred from the final iron-sulfur cluster to a dioxygen molecule, which also accepts a second electron from another Fe(II) centre, and deprotonates a water molecule.

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Catalytic Residues Roles

Residue Roles
Asp205E single electron donor
Asp362E metal ligand
His208E metal ligand
His213E metal ligand
His104A single electron relay
Asp205E single electron relay
His208E single electron relay, single electron acceptor, single electron donor
His104A single electron donor, single electron acceptor
Asp205E single electron acceptor

Chemical Components

electron transfer, proton transfer, ingold: bimolecular nucleophilic addition, coordination, overall reactant used, native state of cofactor regenerated, coordination to a metal ion, intermediate formation, electron relay

Step 4. The peroxo group attacks the naphthalene substrate in a nucleophilic addition that causes the double bond to attack the peroxo group, cleaving the O-O bond and forming the epoxide intermediate.

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Catalytic Residues Roles

Residue Roles
Asp362E metal ligand
His208E metal ligand
His213E metal ligand

Chemical Components

ingold: bimolecular nucleophilic addition, ingold: bimolecular nucleophilic substitution, overall reactant used, intermediate formation, rate-determining step

Step 5. The epoxide intermediate collapses in a heterolysis resulting in a carbocation and anioinc oxygen bound to the Fe(III) centre.

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Catalytic Residues Roles

Residue Roles
Asp362E metal ligand
His208E metal ligand
His213E metal ligand

Chemical Components

heterolysis, intermediate formation

Step 6. The iron-bound hydroxide group attacks the carbocation in a coordination reaction.

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Catalytic Residues Roles

Residue Roles
Asp362E metal ligand
His208E metal ligand
His213E metal ligand

Chemical Components

coordination, intermediate formation

Step 7. An unidentified base deprotonates the FAD, initiating a single electron transfer to the one of the iron-sulfur clusters. This then initiates an electron relay through a second iron-sulfur cluster to a third.

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Catalytic Residues Roles

Residue Roles
Asp362E metal ligand
His208E metal ligand
His213E metal ligand

Chemical Components

proton transfer, electron transfer, native state of cofactor regenerated, cofactor used, intermediate formation, electron relay

Step 8. The electron is transferred from the final iron-sulfur cluster to the Fe(III) centre

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Catalytic Residues Roles

Residue Roles
Asp362E metal ligand
His208E metal ligand
His213E metal ligand

Chemical Components

electron transfer, native state of cofactor regenerated, electron relay, intermediate formation

Step 9. The cis-1,2-dihydronaphthalene-1,2-diol product deprotonates a water molecule and de-coordinates from the Fe(II) centre.

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Catalytic Residues Roles

Residue Roles
Asp362E metal ligand
His208E metal ligand
His213E metal ligand

Chemical Components

proton transfer, heterolysis, decoordination from a metal ion, intermediate terminated, native state of cofactor regenerated, overall product formed, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. NAD initiates a hydride transfer to the FAD cofactor.

Step 2. FAD undergoes a double bond rearrangement that results in the transfer of a single electron from the FAD to one of the iron-sulfur clusters. This then initiates an electron relay through a second iron-sulfur cluster to a third.

Step 3. The electron is transferred from the final iron-sulfur cluster to a dioxygen molecule, which also accepts a second electron from another Fe(II) centre, and deprotonates a water molecule.

Step 4. The peroxo group attacks the naphthalene substrate in a nucleophilic addition that causes the double bond to attack the peroxo group, cleaving the O-O bond and forming the epoxide intermediate.

Step 5. The epoxide intermediate collapses in a heterolysis resulting in a carbocation and anioinc oxygen bound to the Fe(III) centre.

Step 6. The iron-bound hydroxide group attacks the carbocation in a coordination reaction.

Step 7. An unidentified base deprotonates the FAD, initiating a single electron transfer to the one of the iron-sulfur clusters. This then initiates an electron relay through a second iron-sulfur cluster to a third.

Step 8. The electron is transferred from the final iron-sulfur cluster to the Fe(III) centre

Step 9. The cis-1,2-dihydronaphthalene-1,2-diol product deprotonates a water molecule and de-coordinates from the Fe(II) centre.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Alex Gutteridge, Craig Porter