Pathways & interactions
Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B (IPR004183)
Short name: Xdiol_dOase_suB
Overlapping homologous superfamilies
- Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B (IPR004183)
- Gallate dioxygenase, N-terminal (IPR034939)
Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [PMID: 10730195, PMID: 15264822]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33 kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar.
Class III enzymes usually have two subunits, designated A and B. Enzymes that belong to the extradiol class III family include Protocatechuate 4,5-dioxygenase (4,5-PCD; LigAB) (EC:184.108.40.206) [PMID: 10467151]; and 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase (CarBaBb) [PMID: 12728990].
The crystal structure of dioxygenase LigAB revealed that the molecule is an alpha2beta2 tetramer. The active site contains a non-heme iron coordinated by His12, His61, Glu242, and a water molecule located in a deep cleft of the beta subunit, which is covered by the alpha subunit [PMID: 10467151].
This entry represents the structural domain of subunit B.
- PF02900 (LigB)