Summary: Aromatic-ring-opening dioxygenase LigAB, LigA subunit
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Aromatic-ring-opening dioxygenase LigAB, LigA subunit Provide feedback
This is a family of aromatic ring opening dioxygenases which catalyse the ring-opening reaction of protocatechuate and related compounds .
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
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This tab holds annotation information from the InterPro database.
InterPro entry IPR011986
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 (INTERPRO) and B (INTERPRO).
LigAB is a protocatechuate 4,5-dioxygenase (EC) that belongs to the extradiol class III enzyme family. The LigA subunit of this enzyme is multi-helical, containing a compact array of 6 short helices [PUBMED:10467151].
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Curation and family details
|Seed source:||Pfam-B_18522 (release 14.0)|
|Author:||Bateman A, Finn RD|
|Number in seed:||40|
|Number in full:||275|
|Average length of the domain:||83.40 aa|
|Average identity of full alignment:||30 %|
|Average coverage of the sequence by the domain:||44.05 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||6|
|Download:||download the raw HMM for this family|
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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 LigA domain has been found. There are 4 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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