Summary: Ring hydroxylating beta subunit
Ring hydroxylating beta subunit Provide feedback
This subunit has a similar structure to NTF-2 and scytalone dehydratase.
Kauppi B, Lee K, Carredano E, Parales RE, Gibson DT, Eklund H, Ramaswamy S; , Structure 1998;6:571-586.: Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1, 2-dioxygenase. PUBMED:9634695 EPMC:9634695
Internal database links
|Similarity to PfamA using HHSearch:||SnoaL_4|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000391The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the substrate by nonhaem iron-containing dioxygenases. These enzymes consist of two or three soluble proteins that interact to form an electron-transport chain that transfers electrons from reduced nucleotides (NADH) via flavin and [2Fe-2S] redox centres to a terminal dioxygenase [PUBMED:1444257]. Aromatic-ring-hydroxylating dioxygenases oxidise aromatic hydrocarbons and related compounds to cis-arene diols. These enzymes utilise a mononuclear non-haem iron centre to catalyse the addition of dioxygen to their respective substrates.
Naphthalene 1,2-dioxygenase (NDO) from Pseudomonas sp. NCIB9816-4 has a domain structure and iron coordination of the Rieske domain is very similar to that of the cytochrome bc1 domain. The active-site iron centre of one of the alpha subunits is directly connected by hydrogen bonds through a single amino acid, Asp205, to the Rieske [2Fe-2S] centre in a neighbouring alpha subunit. This may be the main route for electron transfer [PUBMED:9634695].
|Molecular function||catalytic activity (GO:0003824)|
|Biological process||cellular aromatic compound metabolic process (GO:0006725)|
|oxidation-reduction process (GO:0055114)|
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This superfamily contains a variety of enzymes such as Scytalone dehydratase, Delta-5-3-ketosteroid isomerase, Limonene-1,2-epoxide hydrolase among others. The family also includes presumed non-enzymatic homologues such as NTF2.
The clan contains the following 24 members:CaMKII_AD DUF1348 DUF2358 DUF3225 DUF3804 DUF4440 DUF4467 LEH Lumazine_bd Lumazine_bd_2 MBA1 MecA_N Mtr2 NTF2 PHZA_PHZB Ring_hydroxyl_B Scytalone_dh SnoaL SnoaL_2 SnoaL_3 SnoaL_4 Tim44 VirB8 WI12
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||Pfam-B_771 (release 3.0)|
|Number in seed:||44|
|Number in full:||1346|
|Average length of the domain:||141.90 aa|
|Average identity of full alignment:||28 %|
|Average coverage of the sequence by the domain:||83.48 %|
|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:||13|
|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 Ring_hydroxyl_B domain has been found. There are 109 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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