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20  structures 898  species 0  interactions 1598  sequences 30  architectures

Family: AOX (PF01786)

Summary: Alternative oxidase

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This is the Wikipedia entry entitled "Alternative oxidase". More...

Alternative oxidase Edit Wikipedia article

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Alternative oxidase Provide feedback

The alternative oxidase is used as a second terminal oxidase in the mitochondria, electrons are transfered directly from reduced ubiquinol to oxygen forming water [2]. This is not coupled to ATP synthesis and is not inhibited by cyanide, this pathway is a single step process [1]. In rice the transcript levels of the alternative oxidase are increased by low temperature [1].

Literature references

  1. Ito Y, Saisho D, Nakazono M, Tsutsumi N, Hirai A; , Gene 1997;203:121-129.: Transcript levels of tandem-arranged alternative oxidase genes in rice are increased by low temperature. PUBMED:9426242 EPMC:9426242

  2. Li Q, Ritzel RG, McLean LL, McIntosh L, Ko T, Bertrand H, Nargang FE; , Genetics 1996;142:129-140.: Cloning and analysis of the alternative oxidase gene of Neurospora crassa. PUBMED:8770590 EPMC:8770590


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002680

The alternative oxidase (AOX) is an enzyme that forms part of the electron transport chain in mitochondria of different organisms [PUBMED:15370881, PUBMED:9698817]. Proteins homologous to the mitochondrial oxidase have also been identified in bacterial genomes [PUBMED:15082931, PUBMED:15087133]. The oxidase provides an alternative route for electrons passing through the electron transport chain to reduce oxygen. However, as several proton-pumping steps are bypassed in this alternative pathway, activation of the oxidase reduces ATP generation. This enzyme was first identified as a distinct oxidase pathway from cytochrome c oxidase as the alternative oxidase is resistant to inhibition by the poison cyanide [PUBMED:1883834].

The alternative oxidase (also known as ubiquinol oxidase) is used as a second terminal oxidase in the mitochondria, electrons are transferred directly from reduced ubiquinol to oxygen forming water [PUBMED:8770590]. This is not coupled to ATP synthesis and is not inhibited by cyanide, this pathway is a single step process [PUBMED:9426242]. In Oryza sativa (rice) the transcript levels of the alternative oxidase are increased by low temperature [PUBMED:9426242]. It has been predicted to contain a coupled diiron centre on the basis of a conserved sequence motif consisting of the proposed iron ligands, four Glu and two His residues [PUBMED:11106766]. The EPR study of Arabidopsis thaliana (mouse-ear cress) alternative oxidase AOX1a shows that the enzyme contains a hydroxo-bridged mixed-valent Fe(II)/Fe(III) binuclear iron centre [PUBMED:12215444]. A catalytic cycle has been proposed that involves a di-iron centre and at least one transient protein-derived radical, most probably an invariant Tyr residue [PUBMED:11801238].

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

This family is a member of clan Ferritin (CL0044), which has the following description:

The members of this clan all share a distinctive four helical bundle. The four helices are arranged antiparallel with a left-handed twist. This helical bundle is distinguished from others by the long connection between the second and third helices. Some of the members contain a Fe or Mn dimer at the centre of the helical bundle. The ferritin fold was first described by Murzin AG and Chothia C, Cur Opin Struc Biol 1992, 2:895-903.

The clan contains the following 25 members:

Ald_deCOase AOX AurF Coat_F COQ7 DUF2202 DUF2383 DUF305 DUF3231 DUF4142 DUF4439 DUF455 DUF5623 DUF892 FA_desaturase_2 Ferritin Ferritin-like Ferritin_2 MiaE MiaE_2 Mn_catalase PaaA_PaaC Phenol_Hydrox Ribonuc_red_sm Rubrerythrin

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(119)
Full
(1598)
Representative proteomes UniProt
(2706)
NCBI
(3157)
Meta
(914)
RP15
(460)
RP35
(987)
RP55
(1356)
RP75
(1686)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(119)
Full
(1598)
Representative proteomes UniProt
(2706)
NCBI
(3157)
Meta
(914)
RP15
(460)
RP35
(987)
RP55
(1356)
RP75
(1686)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(119)
Full
(1598)
Representative proteomes UniProt
(2706)
NCBI
(3157)
Meta
(914)
RP15
(460)
RP35
(987)
RP55
(1356)
RP75
(1686)
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.

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: Pfam-B_1154 (release 4.2)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bashton M , Bateman A
Number in seed: 119
Number in full: 1598
Average length of the domain: 200.60 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 63.54 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.5 22.5
Trusted cut-off 22.6 22.6
Noise cut-off 21.6 22.4
Model length: 215
Family (HMM) version: 17
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 AOX domain has been found. There are 20 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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