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396  structures 2473  species 3  interactions 3701  sequences 30  architectures

Family: Sod_Fe_N (PF00081)

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

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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

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Domain organisation

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Alignments

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  Seed
(24)
Full
(3701)
Representative proteomes UniProt
(17100)
NCBI
(18133)
Meta
(939)
RP15
(963)
RP35
(2554)
RP55
(4336)
RP75
(6829)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(24)
Full
(3701)
Representative proteomes UniProt
(17100)
NCBI
(18133)
Meta
(939)
RP15
(963)
RP35
(2554)
RP55
(4336)
RP75
(6829)
Alignment:
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  Seed
(24)
Full
(3701)
Representative proteomes UniProt
(17100)
NCBI
(18133)
Meta
(939)
RP15
(963)
RP35
(2554)
RP55
(4336)
RP75
(6829)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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.

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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

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Curation View help on the curation process

Seed source: Overington and HMM_iterative_training
Previous IDs: sodfe;
Type: Domain
Author: Eddy SR, Griffiths-Jones SR
Number in seed: 24
Number in full: 3701
Average length of the domain: 83.30 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 38.00 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 82
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 3 interactions for this family. More...

Sod_Fe_C Sod_Fe_N Sod_Fe_C

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 396 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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