DB code: D00063

CATH domain 1.10.700.10 : Protocatechuate 4,5-dioxygenase; Chain A
3.40.830.10 : Protocatechuate 4,5-dioxygenase; Chain B Catalytic domain
E.C. 1.13.11.8
CSA 1bou
M-CSA 1bou
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P22635 Protocatechuate 4,5-dioxygenase alpha chain
EC 1.13.11.8
4,5-PCD
PF07746 (LigA)
[Graphical View]
P22636 Protocatechuate 4,5-dioxygenase beta chain
EC 1.13.11.8
4,5-PCD
PF02900 (LigB)
[Graphical View]

KEGG enzyme name
protocatechuate 4,5-dioxygenase
protocatechuate 4,5-oxygenase
protocatechuic 4,5-dioxygenase
protocatechuic 4,5-oxygenase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P22635 PCYA_PSEPA Protocatechuate + O(2) = 4-carboxy-2- hydroxymuconate semialdehyde. Composed of two subunits (alpha and beta) in a 1:1 ratio. Fe(2+) ion.
P22636 PCYB_PSEPA Protocatechuate + O(2) = 4-carboxy-2- hydroxymuconate semialdehyde. Composed of two subunits (alpha and beta) in a 1:1 ratio. Fe(2+) ion.

KEGG Pathways
Map code Pathways E.C.
MAP00362 Benzoate degradation via hydroxylation
MAP00623 2,4-Dichlorobenzoate degradation

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00023 C00230 C00007 C04484
E.C.
Compound Iron Protocatechuate O2 4-Carboxy-2-hydroxymuconate semialdehyde
Type heavy metal aromatic ring (only carbon atom),carboxyl group others carbohydrate,carboxyl group
ChEBI 18248
 82664
 18248
 82664
 		36062
 36062
 		15379
 26689
 27140
 15379
 26689
 27140
 		18046
 18046
PubChem 23925
 23925
 		72
 72
 		977
 977
1b4uA Unbound Unbound Unbound Unbound
1b4uC Unbound Unbound Unbound Unbound
1bouA Unbound Unbound Unbound Unbound
1bouC Unbound Unbound Unbound Unbound
1b4uB Bound:_FE Bound:DHB Unbound Unbound
1b4uD Bound:_FE Bound:DHB Unbound Unbound
1bouB Bound:_FE Unbound Unbound Unbound
1bouD Bound:_FE Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [5]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1b4uA
1b4uC
1bouA
1bouC
1b4uB HIS 127;HIS 195 HIS 12;HIS 61;GLU 242(Iron binding)
1b4uD HIS 127;HIS 195 HIS 12;HIS 61;GLU 242(Iron binding)
1bouB HIS 127;HIS 195 HIS 12;HIS 61;GLU 242(Iron binding)
1bouD HIS 127;HIS 195 HIS 12;HIS 61;GLU 242(Iron binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.14989
[3]
Scheme 2, p.2177
[5]
p.962-965

References
[1]
Resource
Comments
Medline ID
PubMed ID 6317682
Journal J Biol Chem
Year 1983
Volume 258
Pages 14981-91
Authors Arciero DM, Lipscomb JD, Huynh BH, Kent TA, Munck E
Title EPR and Mossbauer studies of protocatechuate 4,5-dioxygenase. Characterization of a new Fe2+ environment.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2997190
Journal J Biol Chem
Year 1985
Volume 260
Pages 14035-44
Authors Arciero DM, Orville AM, Lipscomb JD
Title 17O]Water and nitric oxide binding by protocatechuate 4,5-dioxygenase and catechol 2,3-dioxygenase. Evidence for binding of exogenous ligands to the active site Fe2+ of extradiol dioxygenases.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 3003098
Journal J Biol Chem
Year 1986
Volume 261
Pages 2170-8
Authors Arciero DM, Lipscomb JD
Title Binding of 17O-labeled substrate and inhibitors to protocatechuate 4,5-dioxygenase-nitrosyl complex. Evidence for direct substrate binding to the active site Fe2+ of extradiol dioxygenases.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 2280721
Journal Methods Enzymol
Year 1990
Volume 188
Pages 89-95
Authors Arciero DM, Orville AM, Lipscomb JD
Title Protocatechuate 4,5-dioxygenase from Pseudomonas testosteroni.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10467151
Journal Structure Fold Des
Year 1999
Volume 7
Pages 953-65
Authors Sugimoto K, Senda T, Aoshima H, Masai E, Fukuda M, Mitsui Y
Title Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions.
Related PDB 1b4u 1bou
Related UniProtKB

Comments
The catalytic mechanism might be similar to Biphenyl-2,3-diol 1,2-dioxygenase (EC 1.13.11.39, D00448 in EzCatDB), although the structure of this enzyme is not similar to that.
Physical and catalytic properties of the R. leguminosarum protocatechuate 4,5-dioxygenase were different from the characteristics of isofunctional enzymes from Pseudomonas paucimobilis and Comamonas testosteroni (Archives of Microbiology 161:191-195).

Created Updated
2004-05-12 2009-02-26