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495  structures 7162  species 0  interactions 11353  sequences 78  architectures

Family: Sod_Fe_N (PF00081)

Summary: Iron/manganese superoxide dismutases, alpha-hairpin domain

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This is the Wikipedia entry entitled "Superoxide dismutase". More...

Superoxide dismutase Edit Wikipedia article

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Iron/manganese superoxide dismutases, alpha-hairpin domain Provide feedback

superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. N-terminal domain is a long alpha antiparallel hairpin. A small fragment of YTRE_LEPBI matches well - sequencing error?

Literature references

  1. Knapp S, Kardinahl S, Hellgren N, Tibbelin G, Schafer G, Ladenstein R; , J Mol Biol 1999;285:689-702.: Refined crystal structure of a superoxide dismutase from the hyperthermophilic archaeon Sulfolobus acidocaldarius at 2.2 A resolution. PUBMED:9878438 EPMC:9878438


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019831

Superoxide dismutases (SODs) ( EC ) catalyse the conversion of superoxide radicals to molecular oxygen. Their function is to destroy the radicals that are normally produced within cells and are toxic to biological systems. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one [ PUBMED:3315461 , PUBMED:3345848 , PUBMED:1556751 ]. This family includes both single metal-binding SODs and cambialistic SOD, which can bind either Mn or Fe. Fe/MnSODs are ubiquitous enzymes that are responsible for the majority of SOD activity in prokaryotes, fungi, blue-green algae and mitochondria. Fe/MnSODs are found as homodimers or homotetramers.

The structure of Fe/MnSODs can be divided into two domains, an alpha N-terminal domain and an alpha/beta C-terminal domain, connected by a loop. The structure of the N-terminal domain consists of a two helices in an antiparallel hairpin, with a left-handed twist [ PUBMED:9537987 ]. The structure of the C-terminal domain is of the alpha/beta type, and consists of a three-stranded antiparallel beta-sheet in the order 213, along with four helices in the arrangement alpha/beta(2)/alpha/beta/alpha(2) [ PUBMED:9931259 ].

This entry represents the N-terminal domain of Manganese/iron superoxide dismutase.

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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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...

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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
(20)
Full
(11353)
Representative proteomes UniProt
(48103)
RP15
(1634)
RP35
(5410)
RP55
(10782)
RP75
(18161)
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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
(20)
Full
(11353)
Representative proteomes UniProt
(48103)
RP15
(1634)
RP35
(5410)
RP55
(10782)
RP75
(18161)
Alignment:
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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
(20)
Full
(11353)
Representative proteomes UniProt
(48103)
RP15
(1634)
RP35
(5410)
RP55
(10782)
RP75
(18161)
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.

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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: Overington and HMM_iterative_training
Previous IDs: sodfe;
Type: Domain
Sequence Ontology: SO:0000417
Author: Eddy SR , Griffiths-Jones SR
Number in seed: 20
Number in full: 11353
Average length of the domain: 83.30 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 37.90 %

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 21.1 21.1
Trusted cut-off 21.1 21.2
Noise cut-off 21.0 21.0
Model length: 82
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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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 Sod_Fe_N domain has been found. There are 495 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
A0A0R0EIY1 View 3D Structure Click here
A0A1D6FNG1 View 3D Structure Click here
A0A1D6GUM7 View 3D Structure Click here
A0A1D6J4T2 View 3D Structure Click here
A0A1D6L5R0 View 3D Structure Click here
A0A1D6LKU6 View 3D Structure Click here
A0A1D6NVP8 View 3D Structure Click here
A0A1D8PQH5 View 3D Structure Click here
A4HTI0 View 3D Structure Click here
A4I5V5 View 3D Structure Click here
A4I7Z7 View 3D Structure Click here
A4I7Z8 View 3D Structure Click here
A4I884 View 3D Structure Click here
A5JVZ7 View 3D Structure Click here
B4F925 View 3D Structure Click here
C0HH91 View 3D Structure Click here
C6KT71 View 3D Structure Click here
I1JYA9 View 3D Structure Click here
I1LCI3 View 3D Structure Click here
K7K772 View 3D Structure Click here
K7LIT3 View 3D Structure Click here
O42919 View 3D Structure Click here
O81235 View 3D Structure Click here
P00447 View 3D Structure Click here
P00448 View 3D Structure Click here
P04179 View 3D Structure Click here
P07895 View 3D Structure Click here
P09233 View 3D Structure Click here
P09671 View 3D Structure Click here
P0A0J3 View 3D Structure Click here
P0AGD3 View 3D Structure Click here
P21276 View 3D Structure Click here
P28759 View 3D Structure Click here
P31161 View 3D Structure Click here
P41977 View 3D Structure Click here
P41978 View 3D Structure Click here
P41979 View 3D Structure Click here
P41980 View 3D Structure Click here
P9WGE7 View 3D Structure Click here
Q00637 View 3D Structure Click here
Q2G261 View 3D Structure Click here
Q43008 View 3D Structure Click here
Q4CRE3 View 3D Structure Click here
Q4D4J5 View 3D Structure Click here
Q4D5A6 View 3D Structure Click here
Q4D9I5 View 3D Structure Click here
Q4DCQ3 View 3D Structure Click here
Q4DI29 View 3D Structure Click here
Q4DMR9 View 3D Structure Click here
Q55BJ9 View 3D Structure Click here
Q5A8Z4 View 3D Structure Click here
Q5VRL3 View 3D Structure Click here
Q5VSB7 View 3D Structure Click here
Q6P980 View 3D Structure Click here
Q8IAY6 View 3D Structure Click here
Q9FMX0 View 3D Structure Click here
Q9LU64 View 3D Structure Click here
Q9LYK8 View 3D Structure Click here
Q9UQX0 View 3D Structure Click here