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Overview for MACiE Entry M0130

Version history

General Information

EC Number: 1.14.12.12 (A member of the Oxidoreductases, Acting on paired donors, with O2 as oxidant and incorporation or reduction of oxygen. The oxygen incorporated need not be derived from O2, With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor)

Enzyme Name: naphthalene 1,2-dioxygenase

Biological Species: Pseudomonas putida (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • P0A110 - Naphthalene 1,2-dioxygenase subunit alpha

Representative PDB Code: 1ndo - NAPTHALENE 1,2-DIOXYGENASE (Resolution = 2.25 Å).

Catalytic CATH Codes:

  • 2.102.10.10 - 'Rieske'-like iron-sulphur domains
  • 3.90.380.10 - Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1

"Other" CATH Codes:

  • 3.90.380.10 - Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
  • 3.10.450.50 - Nuclear Transport Factor 2; Chain: A,

Display structure information

Overall Reaction:

Image of naphthalene

Image of oxygen

Image of proton

Image of NADH

right arrow

Image of NAD

Image of cis-1,2-dihydronaphthalene-1,2-diol

naphthalene
C00829
CHEBI:16482
oxygen
C00007
CHEBI:15379
proton
C00080
CHEBI:24636
NADH
C00004
CHEBI:16908
NAD
C00003
CHEBI:15846
cis-1,2-dihydronaphthalene-1,2-diol
C04314
CHEBI:15561

Overall Comment: This is a multicomponent enzyme comprising a NADH binding reductase a Rieske feredoxin and a oxygenase component. All three units contain [Fe2-S2] clusters.

The enzyme does not return to a state in which it can catalyse another reaction


View similar reactions


Stepwise Description of the Reaction

Step 1NAD initiates a hydride transfer to the FAD cofactor.
Step 2FAD 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 3The 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 4The 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 5The epoxide intermediate collapses in a heterolysis resulting in a carbocation and anioinc oxygen bound to the Fe(III) centre.
Step 6The iron-bound hydroxide group attacks the carbocation in a coordination reaction.
Step 7An 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 8The electron is transferred from the final iron-sulfur cluster to the Fe(III) centre
Step 9The cis-1,2-dihydronaphthalene-1,2-diol product deprotonates a water molecule and de-coordinates from the Fe(II) centre.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
His 104 A Side Chain
Asp 205 E Side Chain
His 208 E Side Chain

Organic Cofactors for M0130

Type Identity Chain
FAD FAD 0 Overview

Metal Cofactors for M0130

Type Het group Number Chain
iron FES 451 A Overview
iron FE 452 A Overview
iron FE(not in PDB) 1 x Overview
iron FE(not in PDB) 2 x Overview

References

  1. M. D. Wolfe et al. (2003), J. Biol. Chem., 278, 829-835. Hydrogen peroxide-coupled cis-diol formation catalyzed by naphthalene 1,2-dioxygenase.
    Medline: 12403773
  2. A. Karlsson et al. (2003), Science, 299, 1039-1042. Crystal structure of naphthalene dioxygenase: side-on binding of dioxygen to iron.
    Medline: 12586937
  3. A. Bassan et al. (2004), J. Biol. Inorg. Chem., 9, 439-452. A theoretical study of the cis-dihydroxylation mechanism in naphthalene 1,2-dioxygenase.
    Medline: 15042436
  4. B. Kauppi et al. (1998), Structure, 6, 571-586. Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase.
    Medline: 9634695

Homologue information for M0130 (1ndo)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0208 ubiquinol-cytochrome-c reductase
1.10.2.2
1ezv 2.102.10.10
0.19350.5625Compare
M0144 arsenite oxidase
1.20.98.1
1g8k 2.102.10.10
0.09370.2399Compare

View a comparison of the other reactions in MACiE with the CATH domain 2.102.10.10


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ
Link to EzCatDB

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catalytic activity (molecular function)
iron ion binding (molecular function)
protein binding (molecular function)
cellular aromatic compound metabolic process (biological process)
oxidoreductase activity (molecular function)
oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (molecular function)
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (molecular function)
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor (molecular function)
naphthalene 1,2-dioxygenase activity (molecular function)
aromatic compound catabolic process (biological process)
metal ion binding (molecular function)
iron-sulfur cluster binding (molecular function)
2 iron, 2 sulfur cluster binding (molecular function)
oxidation-reduction process (biological process)
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