Summary: Catalytic LigB subunit of aromatic ring-opening dioxygenase
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Catalytic LigB subunit of aromatic ring-opening dioxygenase Provide feedback
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Sugimoto K, Senda T, Aoshima H, Masai E, Fukuda M, Mitsui Y; , Structure Fold Des 1999;7:953-965.: Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions. PUBMED:10467151 EPMC:10467151
Internal database links
|SCOOP:||DltD_M TrfA DUF1869 TAXi_C|
|Similarity to PfamA using HHSearch:||Memo|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR004183
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 (INTERPRO) 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) [PUBMED:10730195, PUBMED: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 (INTERPRO) 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) [PUBMED:10467151]; and 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase (CarBaBb) [PUBMED: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 [PUBMED:10467151].
This entry represents the structural domain of subunit B.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||oxidoreductase activity (GO:0016491)|
|ferrous iron binding (GO:0008198)|
|Biological process||cellular aromatic compound metabolic process (GO:0006725)|
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|Seed source:||Structural domain|
|Number in seed:||14|
|Number in full:||12676|
|Average length of the domain:||264.30 aa|
|Average identity of full alignment:||26 %|
|Average coverage of the sequence by the domain:||92.88 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the LigB domain has been found. There are 39 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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