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Overview for MACiE Entry M0034

Version history

General Information

EC Number: 1.13.11.2 (A member of the Oxidoreductases, Acting on single donors with O2 as oxidant and incorporation of oxygen into the substrate (oxygenases). The oxygen incorporated need not be derived from O2, With incorporation of two atoms of oxygen)

Enzyme Name: catechol 2,3-dioxygenase

Biological Species: Pseudomonas putida (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

Representative PDB Code: 1mpy - STRUCTURE OF CATECHOL 2,3-DIOXYGENASE (METAPYROCATECHASE)FROM PSEUDOMONAS PUTIDA MT-2 (Resolution = 2.80 Å).

Catalytic CATH Codes:

  • 3.10.180.10 - 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

"Other" CATH Codes:

  • 3.10.180.10 - 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

Display structure information

Overall Reaction:

Image of oxygen

Image of catechol

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Image of 2-hydroxymuconate semialdehyde

oxygen
C00007
CHEBI:15379
catechol
C00090
CHEBI:18135
2-hydroxymuconate semialdehyde
C00682
CHEBI:17236

Overall Comment: Circular dichroism, magnetic circular dichroism and X-ray absorption spectroscopy on the resting enzyme all support the presence of a five-coordinated Fe(II) site with square-pyramidal geometry. In the active site of catechol 2,3-dioxygenase only the Glu265, Tyr255 and the water molecules - of which there are two bound to the active site Fe(II) - can take an anionic form. This suggests that one of the water ligands is bound as a hydroxide ion to maintain a charge neutral active site [2]. The role of His246 and Tyr255 is tentatively assigned only. Both residues may play a role in the correct orientation of the oxygen molecule to allow it to bind to the vacant 6th site on the iron (II) ion [2].


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Stepwise Description of the Reaction

Step 1The leaving hydroxide ion deprotonates the catechol, which binds to the Fe(II) centre in a substitution reaction.
Step 2Iron donates an electron to the oxygen substrate, which becomes a ligand of the iron in a redox reaction.
Step 3His199 deprotonates the remaining hydroxyl group of the bound catechol, initiating double bond rearrangement that results in a single electron transfer from the catechol to the iron centre
Step 4The dioxygen iron ligand initiates a nucleophilic attack on the carbon adjacent to the radical formed in the previous step in an addition reaction. The oxygen of the catechol bound to the iron donates one electron to the radical iron-bound oxygen, and another to the carbon radical, forming a carbonyl bond. Double bond rearrangement from the addition results in deprotonation of His199.
Step 5His199 deprotonates the hydroxide, initiating double bond rearrangement which results in extension of the ring by one atom and cleavage of the peroxo bond in a substitution reaction.
Step 6The oxo iron-ligand initiated a nucleophilic attack on the carbonyl carbon in a substitution reaction, cleaving the rind and initiating double bond rearrangement that results in the deprotonation of His199.
Step 7The product deprotonates a water molecule and is displaced from the iron centre by the hydroxide and water in an inferred return step.

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Catalytic Residues Involved

Type Number Chain Location of Function
His 199 A Side Chain
His 246 A Side Chain
Tyr 255 A Side Chain

Metal Cofactors for M0034

Type Het group Number Chain
iron FE2 308 A Overview

References

  1. R. N. Armstrong et al. (2000), Biochemistry, 39, 13625-13632. Mechanistic diversity in a metalloenzyme superfamily.
    Medline: 11076500
  2. A. Kita et al. (1999), Structure, 7, 25-34. An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Ppseudomonas putida mt-2.
    Medline: 10368270

Homologue information for M0034 (1mpy)

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
M0032 lactoylglutathione lyase
4.4.1.5
1qin 3.10.180.10
0.19750.0114Compare
M0033 methylmalonyl-CoA epimerase
5.1.99.1
1jc5 3.10.180.10
0.10180.0164Compare

View a comparison of the other reactions in MACiE with the CATH domain 3.10.180.10


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 Link to SFLD

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catalytic activity (molecular function)
cellular aromatic compound metabolic process (biological process)
ferrous iron binding (molecular function)
oxidoreductase activity (molecular function)
oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (molecular function)
catechol 2,3-dioxygenase activity (molecular function)
aromatic compound catabolic process (biological process)
metal ion binding (molecular function)
oxidation-reduction process (biological process)
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