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MetaCyc Enzyme: protocatechuate 3,4-dioxygenase

Synonyms: P3,4O, 3,4-PCD

Species: Pseudomonas putida

Subunit composition of protocatechuate 3,4-dioxygenase = [PcaH]4[PcaG]4
         protocatechuate 3,4-dioxygenase β subunit = PcaH
         protocatechuate 3,4-dioxygenase α subunit = PcaG

Summary:
protocatechuate:oxygen 3,4-oxidoreductase (3,4-PCD) catalyzes the intradiol addition of both oxygen atoms from molecular oxygen to protocatechuate, cleaving the aromatic ring and producing 3-carboxy-cis,cis-muconate [Bull81].

3,4-PCD has been purified from several different species. Thus far, all of the well-characterized 3,4-PCDs are composed of equimolar amounts of two different subunits, α and β, which appear to be present in varying amounts, ranging from 3 to 12 [Harwood96, Frazee93]. 3,4-PCD purified from Pseudomonas putida appears to be composed of four α subunits, four β subunits, and four ferric irons, which suggests a tetrameric composition of (αβFe3+)4 [Bull81]. The crystal structure of a 3,4-PCD purified from a different Pseudomonas putida strain (formerly classified as Pseudomonas aeruginosa) indicated that that enzyme possessed an (αβFe3+)12 quaternary structure [Ohlendorf94, Frazee93].

The active site and ferric iron are located at the interface between the α and β subunits (as reported in [Harwood96]. The active site has many basic amino acid residues, which may promote binding of the acidic substrate [Ohlendorf94]. Acetate, chloride, iodide, and fluoride inhibited 3,4-PCD by competing with protocatechuate [Bull81].

3,4-PCD is induced by protocatechuate (as reported in [Harwood96]).

Molecular Weight: 200 kD (experimental) [Bull81 ]

Gene-Reaction Schematic: ?


Enzymatic reaction of: gallate:oxygen 3,4-oxidoreductase (protocatechuate 3,4-dioxygenase)

EC Number: 1.13.11.-

gallate + oxygen <=> 2-pyrone-4,6-dicarboxylate + H2O + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

In Pathways: gallate degradation II

Summary:
Protocatechuate 3,4-dioxygenase can use gallate as a substrate. Gallate was a competitive inhibitor of protocatechuate oxidation [Sparnins75]. Separate gallate dioxygenases have also been identified in Pseudomonas putida [Sparnins75, Kersten82, Nogales05].


Enzymatic reaction of: protocatechuate:oxygen 3,4-oxidoreductase (protocatechuate 3,4-dioxygenase)

EC Number: 1.13.11.3

protocatechuate + oxygen <=> 3-carboxy-cis,cis-muconate + 2 H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

In Pathways: superpathway of aromatic compound degradation via 3-oxoadipate , aromatic compounds degradation via β-ketoadipate , protocatechuate degradation II (ortho-cleavage pathway)

Cofactors or Prosthetic Groups: Fe3+ [Bull81]

Inhibitors (Competitive): fluoride [Bull81] , iodide [Bull81] , acetate [Bull81] , chloride [Bull81]


Subunit of protocatechuate 3,4-dioxygenase: protocatechuate 3,4-dioxygenase β subunit

Synonyms: PcaH

Gene: pcaH Accession Number: G-2285 (MetaCyc)

Sequence Length: 239 AAs

Molecular Weight: 26.662 kD (from nucleotide sequence)

Molecular Weight: 26.5 kD (experimental) [Bull81]

Unification Links: ModBase:P00437 , Protein Model Portal:P00437 , SMR:P00437 , Swiss-Model:P00437 , UniProt:P00437

Relationship Links: InterPro:IN-FAMILY:IPR000627 , InterPro:IN-FAMILY:IPR012785 , InterPro:IN-FAMILY:IPR015889 , InterPro:IN-FAMILY:IPR024756 , PDB:Structure:1YKK , PDB:Structure:1YKL , PDB:Structure:1YKM , PDB:Structure:1YKN , PDB:Structure:1YKO , PDB:Structure:1YKP , PDB:Structure:2PCD , PDB:Structure:3LKT , PDB:Structure:3LMX , PDB:Structure:3LXV , PDB:Structure:3MFL , PDB:Structure:3MI1 , PDB:Structure:3MI5 , PDB:Structure:3MV4 , PDB:Structure:3MV6 , PDB:Structure:3PCA , PDB:Structure:3PCB , PDB:Structure:3PCC , PDB:Structure:3PCD , PDB:Structure:3PCE , PDB:Structure:3PCF , PDB:Structure:3PCG , PDB:Structure:3PCH , PDB:Structure:3PCI , PDB:Structure:3PCJ , PDB:Structure:3PCK , PDB:Structure:3PCL , PDB:Structure:3PCM , PDB:Structure:3PCN , PDB:Structure:3T63 , PDB:Structure:3T67 , Pfam:IN-FAMILY:PF00775 , Pfam:IN-FAMILY:PF12391 , Prosite:IN-FAMILY:PS00083


Subunit of protocatechuate 3,4-dioxygenase: protocatechuate 3,4-dioxygenase α subunit

Synonyms: PcaG

Gene: pcaG Accession Number: G-2286 (MetaCyc)

Sequence Length: 201 AAs

Molecular Weight: 22.256 kD (from nucleotide sequence)

Molecular Weight: 23 kD (experimental) [Bull81]

Unification Links: ModBase:P00436 , Protein Model Portal:P00436 , SMR:P00436 , Swiss-Model:P00436 , UniProt:P00436

Relationship Links: InterPro:IN-FAMILY:IPR000627 , InterPro:IN-FAMILY:IPR012786 , InterPro:IN-FAMILY:IPR015889 , PDB:Structure:1YKK , PDB:Structure:1YKL , PDB:Structure:1YKM , PDB:Structure:1YKN , PDB:Structure:1YKO , PDB:Structure:1YKP , PDB:Structure:2PCD , PDB:Structure:3LKT , PDB:Structure:3LMX , PDB:Structure:3LXV , PDB:Structure:3MFL , PDB:Structure:3MI1 , PDB:Structure:3MI5 , PDB:Structure:3MV4 , PDB:Structure:3MV6 , PDB:Structure:3PCA , PDB:Structure:3PCB , PDB:Structure:3PCC , PDB:Structure:3PCD , PDB:Structure:3PCE , PDB:Structure:3PCF , PDB:Structure:3PCG , PDB:Structure:3PCH , PDB:Structure:3PCI , PDB:Structure:3PCJ , PDB:Structure:3PCK , PDB:Structure:3PCL , PDB:Structure:3PCM , PDB:Structure:3PCN , PDB:Structure:3T63 , PDB:Structure:3T67 , Pfam:IN-FAMILY:PF00775 , Prosite:IN-FAMILY:PS00083


References

Bull81: Bull C, Ballou DP (1981). "Purification and properties of protocatechuate 3,4-dioxygenase from Pseudomonas putida. A new iron to subunit stoichiometry." J Biol Chem 256(24);12673-80. PMID: 6273403

Frazee93: Frazee RW, Livingston DM, LaPorte DC, Lipscomb JD (1993). "Cloning, sequencing, and expression of the Pseudomonas putida protocatechuate 3,4-dioxygenase genes." J Bacteriol 175(19);6194-202. PMID: 8407791

Harwood96: Harwood CS, Parales RE (1996). "The beta-ketoadipate pathway and the biology of self-identity." Annu Rev Microbiol 50;553-90. PMID: 8905091

Kersten82: Kersten PJ, Dagley S, Whittaker JW, Arciero DM, Lipscomb JD (1982). "2-pyrone-4,6-dicarboxylic acid, a catabolite of gallic acids in Pseudomonas species." J Bacteriol 1982;152(3);1154-62. PMID: 7142106

Nogales05: Nogales J, Canales A, Jimenez-Barbero J, Garcia JL, Diaz E (2005). "Molecular characterization of the gallate dioxygenase from Pseudomonas putida KT2440: The prototype of a new subgroup of extradiol dioxygenases." J Biol Chem 280(42):35382-90. PMID: 16030014

Ohlendorf94: Ohlendorf DH, Orville AM, Lipscomb JD (1994). "Structure of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa at 2.15 A resolution." J Mol Biol 244(5);586-608. PMID: 7990141

Sparnins75: Sparnins VL, Dagley S (1975). "Alternative routes of aromatic catabolism in Pseudomonas acidovorans and Pseudomonas putida: gallic acid as a substrate and inhibitor of dioxygenases." J Bacteriol 124(3);1374-81. PMID: 1194238


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Thu Nov 27, 2014, BIOCYC14B.