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96  structures 3855  species 0  interactions 16815  sequences 288  architectures

Family: 2OG-FeII_Oxy_3 (PF13640)

Summary: 2OG-Fe(II) oxygenase superfamily

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

2OG-Fe(II) oxygenase superfamily Provide feedback

This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1].

Literature references

  1. 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


Internal 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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(308)
Full
(16815)
Representative proteomes UniProt
(55462)
RP15
(3312)
RP35
(7972)
RP55
(15010)
RP75
(22299)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(308)
Full
(16815)
Representative proteomes UniProt
(55462)
RP15
(3312)
RP35
(7972)
RP55
(15010)
RP75
(22299)
Alignment:
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Sequence:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(308)
Full
(16815)
Representative proteomes UniProt
(55462)
RP15
(3312)
RP35
(7972)
RP55
(15010)
RP75
(22299)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Jackhmmer:B8H030
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 308
Number in full: 16815
Average length of the domain: 103.10 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 27.97 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 96
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

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_3 domain has been found. There are 96 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2JZ28 View 3D Structure Click here
A0A0P0VTI7 View 3D Structure Click here
A0A0P0VTI8 View 3D Structure Click here
A0A0R0FPQ8 View 3D Structure Click here
A0A0R0L133 View 3D Structure Click here
A0A0R4I9E8 View 3D Structure Click here
A0A0R4IJJ1 View 3D Structure Click here
A0A0R4IU86 View 3D Structure Click here
A0A1D6EDJ6 View 3D Structure Click here
A0A1D6GFB9 View 3D Structure Click here
A0A1D6JLF6 View 3D Structure Click here
A0A1D6KRT5 View 3D Structure Click here
A0A1D6KVC3 View 3D Structure Click here
A0A1D6L5N5 View 3D Structure Click here
A0A1D6M707 View 3D Structure Click here
A0A1D6NWD3 View 3D Structure Click here
A0A1D6PF75 View 3D Structure Click here
A0A1D8PGA7 View 3D Structure Click here
A0A286Y8C8 View 3D Structure Click here
A0A2R8Q3J3 View 3D Structure Click here
A0A2R8QH86 View 3D Structure Click here
A0A2R8QKC5 View 3D Structure Click here
A0A2R8QV03 View 3D Structure Click here
A0A2R8RIQ1 View 3D Structure Click here
A0A2R8RN68 View 3D Structure Click here
A4HWQ3 View 3D Structure Click here
A4I6C0 View 3D Structure Click here
A8DYR4 View 3D Structure Click here
B1V8J1 View 3D Structure Click here
B1V8J4 View 3D Structure Click here
B4FGT5 View 3D Structure Click here
B5DFB0 View 3D Structure Click here
B6TD48 View 3D Structure Click here
C6TJY4 View 3D Structure Click here
D3ZGT6 View 3D Structure Click here
D3ZJG3 View 3D Structure Click here
E7F8S1 View 3D Structure Click here
E7FEB4 View 3D Structure Click here
F1Q9H1 View 3D Structure Click here
F1QB32 View 3D Structure Click here
F4ILF8 View 3D Structure Click here
F4J0A8 View 3D Structure Click here
F4JNU8 View 3D Structure Click here
F4JZ24 View 3D Structure Click here
F6P6J7 View 3D Structure Click here
F8W5S7 View 3D Structure Click here
G4XT43 View 3D Structure Click here
G5EBV0 View 3D Structure Click here
I1J8H0 View 3D Structure Click here
I1J9C5 View 3D Structure Click here
I1JCD3 View 3D Structure Click here
I1JSZ3 View 3D Structure Click here
I1K2C7 View 3D Structure Click here
I1K7G3 View 3D Structure Click here
I1KN53 View 3D Structure Click here
I1KRR4 View 3D Structure Click here
I1LEG4 View 3D Structure Click here
I1LFK7 View 3D Structure Click here
I1LI50 View 3D Structure Click here
I1LWH3 View 3D Structure Click here
I1M192 View 3D Structure Click here
I1MF99 View 3D Structure Click here
I1MVP6 View 3D Structure Click here
I1N610 View 3D Structure Click here
K7LDR0 View 3D Structure Click here
K7LN47 View 3D Structure Click here
K7MI44 View 3D Structure Click here
K7N386 View 3D Structure Click here
K7N5J4 View 3D Structure Click here
O15460 View 3D Structure Click here
P13674 View 3D Structure Click here
P54001 View 3D Structure Click here
P59722 View 3D Structure Click here
P75779 View 3D Structure Click here
Q0D7Z6 View 3D Structure Click here
Q0KHY7 View 3D Structure Click here
Q109P7 View 3D Structure Click here
Q10PC9 View 3D Structure Click here
Q24JN5 View 3D Structure Click here
Q32P28 View 3D Structure Click here
Q337H1 View 3D Structure Click here
Q3V1T4 View 3D Structure Click here
Q4CWZ0 View 3D Structure Click here
Q4DA24 View 3D Structure Click here
Q4KLM6 View 3D Structure Click here
Q54CK1 View 3D Structure Click here
Q54K28 View 3D Structure Click here
Q54N51 View 3D Structure Click here
Q54PP0 View 3D Structure Click here
Q54TF2 View 3D Structure Click here
Q553P3 View 3D Structure Click here
Q5M843 View 3D Structure Click here
Q5PP31 View 3D Structure Click here
Q60716 View 3D Structure Click here
Q6AVM9 View 3D Structure Click here
Q6AYU4 View 3D Structure Click here
Q6PK18 View 3D Structure Click here
Q6W3E9 View 3D Structure Click here
Q6W3F0 View 3D Structure Click here
Q7XNS6 View 3D Structure Click here
Q7Z4N8 View 3D Structure Click here
Q84T04 View 3D Structure Click here
Q86A19 View 3D Structure Click here
Q86KR9 View 3D Structure Click here
Q8BG58 View 3D Structure Click here
Q8CG70 View 3D Structure Click here
Q8CG71 View 3D Structure Click here
Q8IMI2 View 3D Structure Click here
Q8IQS7 View 3D Structure Click here
Q8IVL5 View 3D Structure Click here
Q8IVL6 View 3D Structure Click here
Q8L970 View 3D Structure Click here
Q8LAN3 View 3D Structure Click here
Q8MSK0 View 3D Structure Click here
Q8SX21 View 3D Structure Click here
Q8T294 View 3D Structure Click here
Q8T5S8 View 3D Structure Click here
Q91UZ4 View 3D Structure Click here
Q91YE2 View 3D Structure Click here
Q91YE3 View 3D Structure Click here
Q94H92 View 3D Structure Click here
Q961I8 View 3D Structure Click here
Q96KS0 View 3D Structure Click here
Q9D136 View 3D Structure Click here
Q9GZT9 View 3D Structure Click here
Q9H6Z9 View 3D Structure Click here
Q9I7H5 View 3D Structure Click here
Q9LN20 View 3D Structure Click here
Q9NXG6 View 3D Structure Click here
Q9SZT0 View 3D Structure Click here
Q9VA50 View 3D Structure Click here
Q9VA52 View 3D Structure Click here
Q9VA61 View 3D Structure Click here
Q9VA63 View 3D Structure Click here
Q9VA69 View 3D Structure Click here
Q9VHU7 View 3D Structure Click here
Q9VVQ5 View 3D Structure Click here
Q9VVQ6 View 3D Structure Click here
Q9VVQ9 View 3D Structure Click here
Q9XUP0 View 3D Structure Click here
X1WG80 View 3D Structure Click here
Z4YHZ5 View 3D Structure Click here