Catechol 2,3-dioxygenase

 

The catecholic dioxygenases catalyse the addition of molecular oxygen and subsequent ring cleavage into catecholic ring structures. Extradiol catecholic dioxygenases add oxygen into bonds other than the intradiol 4,5 bond.

 

Reference Protein and Structure

Sequence
P06622 UniProt (1.13.11.2) IPR017624 (Sequence Homologues) (PDB Homologues)
Biological species
Pseudomonas putida (Bacteria) Uniprot
PDB
1mpy - STRUCTURE OF CATECHOL 2,3-DIOXYGENASE (METAPYROCATECHASE) FROM PSEUDOMONAS PUTIDA MT-2 (2.8 Å) PDBe PDBsum 1mpy
Catalytic CATH Domains
3.10.180.10 CATHdb (see all for 1mpy)
Cofactors
Iron(2+) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:1.13.11.2)

dioxygen
CHEBI:15379ChEBI
+
catechol
CHEBI:18135ChEBI
→
2-hydroxy-6-oxohexa-2,4-dienoic acid
CHEBI:17236ChEBI
Alternative enzyme names: 2,3-pyrocatechase, Catechol 2,3-oxygenase, Catechol oxygenase, Metapyrocatechase, Pyrocatechol 2,3-dioxygenase, Cato2ase, XylE (gene name),

Enzyme Mechanism

Introduction

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. Fe is co-ordinated by histidines 153 and 214, and glutamate 265 as well as a water and a hydroxyl. 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 [PMID:10368270].

Catechol enters the active site and replaces the water and hydroxyl group around the Fe. The leaving hydroxyl abstracts a proton from one of the catecholic hydroxyl. Oxygen enters the active site and is orientated as a sixth Fe ligand and also parallel to the catechol bond to be broken. Histidine 199 acts as a base and abstracts the proton from the other catecholic hydroxyl. This allows the oxygen to attack the aromatic ring and cleaves it. Addition of water releases the oxygenated product and replaces the Fe ligands.

Catalytic Residues Roles

UniProt PDB* (1mpy)
His199 His199A Acts as a general acid/base. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
His246, Tyr255 His246A, Tyr255A Help direct the steric outcome of the reaction. steric role, polar/non-polar interaction
His153, His214, Glu265 His153A, His214A, Glu265A Bind the Fe(II) ion. 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

proton transfer, bimolecular nucleophilic substitution, overall reactant used, decoordination from a metal ion, coordination to a metal ion, intermediate formation, redox reaction, radical formation, bimolecular homolytic addition, bimolecular nucleophilic addition, radical termination, electron transfer, intramolecular nucleophilic substitution, decyclisation, intermediate terminated, native state of enzyme regenerated, overall product formed, inferred reaction step

References

  1. Vaillancourt FH et al. (2002), J Am Chem Soc, 124, 2485-2496. Definitive Evidence for Monoanionic Binding of 2,3-Dihydroxybiphenyl to 2,3-Dihydroxybiphenyl 1,2-Dioxygenase from UV Resonance Raman Spectroscopy, UV/Vis Absorption Spectroscopy, and Crystallography. DOI:10.1021/ja0174682.
  2. Viggiani A et al. (2004), J Biol Chem, 279, 48630-48639. The Role of the Conserved Residues His-246, His-199, and Tyr-255 in the Catalysis of Catechol 2,3-Dioxygenase from Pseudomonas stutzeri OX1. DOI:10.1074/jbc.m406243200. PMID:15347689.
  3. Bugg TDH et al. (2001), Chem Commun (Camb), 941-952. Solving the riddle of the intradiol and extradiol catechol dioxygenases: how do enzymes control hydroperoxide rearrangements? DOI:10.1039/b100484k.
  4. Armstrong RN (2000), Biochemistry, 39, 13625-13632. Mechanistic Diversity in a Metalloenzyme Superfamily†. DOI:10.1021/bi001814v. PMID:11076500.
  5. Kita A et al. (1999), Structure, 7, 25-34. An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Pseudomonas putida mt-2. DOI:10.1016/s0969-2126(99)80006-9. PMID:10368270.

Step 1. The leaving hydroxide ion deprotonates the catechol, which binds to the Fe(II) centre in a substitution reaction.

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Catalytic Residues Roles

Residue Roles
His199A hydrogen bond acceptor
His153A metal ligand
His214A metal ligand
Glu265A metal ligand

Chemical Components

proton transfer, ingold: bimolecular nucleophilic substitution, overall reactant used, decoordination from a metal ion, coordination to a metal ion, intermediate formation

Step 2. Iron donates an electron to the oxygen substrate, which becomes a ligand of the iron in a redox reaction.

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Catalytic Residues Roles

Residue Roles
His246A steric role, polar/non-polar interaction
Tyr255A steric role, polar/non-polar interaction
His199A hydrogen bond acceptor
Glu265A metal ligand
His153A metal ligand
His214A metal ligand

Chemical Components

redox reaction, radical formation, ingold: bimolecular homolytic addition, overall reactant used, coordination to a metal ion, intermediate formation

Step 3. His199 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

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Catalytic Residues Roles

Residue Roles
Tyr255A steric role, polar/non-polar interaction
His199A hydrogen bond acceptor
His246A steric role, polar/non-polar interaction
His153A metal ligand
His214A metal ligand
Glu265A metal ligand
His199A proton acceptor

Chemical Components

radical formation, proton transfer, redox reaction, intermediate formation

Step 4. The 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.

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Catalytic Residues Roles

Residue Roles
His246A steric role, polar/non-polar interaction
Tyr255A steric role, polar/non-polar interaction
His199A hydrogen bond donor
His153A metal ligand
Glu265A metal ligand
His214A metal ligand
His199A proton donor

Chemical Components

ingold: bimolecular nucleophilic addition, proton transfer, radical termination, electron transfer, intermediate formation

Step 5. His199 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.

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Catalytic Residues Roles

Residue Roles
His246A polar/non-polar interaction
Tyr255A polar/non-polar interaction
His199A hydrogen bond acceptor
Glu265A metal ligand
His214A metal ligand
His153A metal ligand
His199A proton acceptor

Chemical Components

proton transfer, ingold: intramolecular nucleophilic substitution, intermediate formation

Step 6. The 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.

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Catalytic Residues Roles

Residue Roles
His199A hydrogen bond donor
His153A metal ligand
His214A metal ligand
Glu265A metal ligand
His199A proton donor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic substitution, decyclisation, intermediate formation

Step 7. The product deprotonates a water molecule and is displaced from the iron centre by the hydroxide and water in an inferred return step.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His199A hydrogen bond donor
His153A metal ligand
His214A metal ligand
Glu265A metal ligand

Chemical Components

proton transfer, ingold: bimolecular nucleophilic substitution, decoordination from a metal ion, intermediate terminated, coordination to a metal ion, native state of enzyme regenerated, overall product formed, inferred reaction step
Download: Image, Marvin File

Step 1. The leaving hydroxide ion deprotonates the catechol, which binds to the Fe(II) centre in a substitution reaction.

Step 2. Iron donates an electron to the oxygen substrate, which becomes a ligand of the iron in a redox reaction.

Step 3. His199 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 4. The 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 5. His199 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 6. The 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 7. The product deprotonates a water molecule and is displaced from the iron centre by the hydroxide and water in an inferred return step.

Products.

Contributors

Gemma L. Holliday, Gail J. Bartlett, Daniel E. Almonacid, Sophie T. Williams, Alex Gutteridge, Craig Porter