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
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.
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.

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

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
36062
15379
26689
27140
18046
PubChem 23925
72
977
1b4uA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1b4uC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1bouA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1bouC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1b4uB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:DHB Unbound Unbound
1b4uD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:DHB Unbound Unbound
1bouB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Unbound Unbound Unbound
1bouD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1b4uC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bouA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bouC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1b4uB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 127;HIS 195 HIS 12;HIS 61;GLU 242(Iron binding)
1b4uD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 127;HIS 195 HIS 12;HIS 61;GLU 242(Iron binding)
1bouB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 127;HIS 195 HIS 12;HIS 61;GLU 242(Iron binding)
1bouD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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