Summary: 2OG-Fe(II) oxygenase superfamily
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2OG-Fe(II) oxygenase superfamily Provide feedback
This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily . This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:220.127.116.11 catalysing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site . The family also includes lysyl hydrolases, isopenicillin synthases and AlkB.
Aravind L, Koonin EV; , Genome Biol 2001;2:RESEARCH0007.: The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. PUBMED:11276424 EPMC:11276424
Annunen P, Helaakoski T, Myllyharju J, Veijola J, Pihlajaniemi T, Kivirikko KI; , J Biol Chem 1997;272:17342-17348.: Cloning of the human prolyl 4-hydroxylase alpha subunit isoform alpha(II) and characterization of the type II enzyme tetramer. The alpha(I) and alpha(II) subunits do not form a mixed alpha(I)alpha(II)beta2 tetramer. PUBMED:9211872 EPMC:9211872
Helaakoski T, Annunen P, Vuori K, MacNeil IA, Pihlajaniemi T, Kivirikko KI; , Proc Natl Acad Sci U S A 1995;92:4427-4431.: Cloning, baculovirus expression, and characterization of a second mouse prolyl 4-hydroxylase alpha-subunit isoform: formation of an alpha 2 beta 2 tetramer with the protein disulfide-isomerase/beta subunit. PUBMED:7753822 EPMC:7753822
Roach PL, Clifton IJ, Fulop V, Harlos K, Barton GJ, Hajdu J, Andersson I, Schofield CJ, Baldwin JE; , Nature 1995;375:700-704.: Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes. PUBMED:7791906 EPMC:7791906
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR005123
Enzymes with the Fe(2+) and 2-oxoglutarate (2OG)-dependent dioxygenase domain typically catalyse the oxidation of an organic substrate using a dioxygen molecule, mostly by using ferrous iron as the active site cofactor and 2OG as a co-substrate which is decarboxylated to succinate and CO2 [PUBMED:11276424]. Iron 2OG dioxygenase domain proteins are widespread among eukaryotes and bacteria. In metazoans, prolyl hydroxylases containing the domain act as oxygen sensors and catalyse the hydroxylation of conserved prolyl residues in hypoxia-inducible transcription factor (HIF) alpha [PUBMED:16782814, PUBMED:19756382]. In plants, Fe(II) 2OG dioxygenase domain enzymes catalyse the formation of plant hormones, such as ethylene, gibberellins, anthocyanidins and pigments such as flavones. In bacteria and fungi Fe(II) 2OG dioxygenase domain enzymes participate in the biosynthesis of antibiotics such as penicillin and cephalosporin. The eukaryotic and bacterial protein AlkB that also shows this structural domain is involved in DNA-repair [PUBMED:11276424, PUBMED:19786499].
The iron 2OG dioxygenase domain has a conserved beta-barrel structure [PUBMED:16782814], which forms a double-stranded beta-helix core fold that forms the predominant class of the cupin superfamily ('cupa' means a small barrel in Latin) [PUBMED:14697267]. Two histidines and an aspartate residue catalytically bind a metal ion, in general iron but in some cases another metal, directly involved in catalysis. A conserved arginine or lysine residue further near the C-terminal part acts as the basic residue that interacts with the acidic substrate.
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This clan represents the conserved barrel domain of the 'cupin' superfamily  ('cupa' is the Latin term for a small barrel). The cupin fold is found in a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.
The clan contains the following 57 members:2OG-Fe_Oxy_2 2OG-FeII_Oxy 2OG-FeII_Oxy_2 2OG-FeII_Oxy_3 2OG-FeII_Oxy_4 2OG-FeII_Oxy_5 3-HAO AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox Auxin_BP CDO_I CENP-C_C CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_4 Cupin_5 Cupin_6 Cupin_7 Cupin_8 DMSP_lyase dTDP_sugar_isom DUF1255 DUF1479 DUF1498 DUF1637 DUF1971 DUF386 DUF4437 DUF4867 Ectoine_synth EutQ FdtA FTO_NTD GPI HgmA HutD JmjC KduI MannoseP_isomer Ofd1_CTDD Oxygenase-NA PhyH Pirin Pirin_C PMI_typeI Popeye Pox_C4_C10 TauD Tet_JBP Ureidogly_hydro VIT VIT_2
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Key: available, not generated, — not available.
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Curation and family details
|Seed source:||Aravind L|
|Number in seed:||138|
|Number in full:||15040|
|Average length of the domain:||103.60 aa|
|Average identity of full alignment:||30 %|
|Average coverage of the sequence by the domain:||31.00 %|
|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:||16|
|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 2OG-FeII_Oxy domain has been found. There are 69 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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