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7  structures 578  species 0  interactions 2101  sequences 44  architectures

Family: PCO_ADO (PF07847)

Summary: PCO_ADO

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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.

PCO_ADO Provide feedback

This entry includes cysteine oxidases (PCOs) from plants and 2-aminoethanethiol dioxygenases (ADOs) from animals [1, 2].

Literature references

  1. Weits DA, Giuntoli B, Kosmacz M, Parlanti S, Hubberten HM, Riegler H, Hoefgen R, Perata P, van Dongen JT, Licausi F;, Nat Commun. 2014;5:3425.: Plant cysteine oxidases control the oxygen-dependent branch of the N-end-rule pathway. PUBMED:24599061 EPMC:24599061

  2. Dominy JE Jr, Simmons CR, Hirschberger LL, Hwang J, Coloso RM, Stipanuk MH;, J Biol Chem. 2007;282:25189-25198.: Discovery and characterization of a second mammalian thiol dioxygenase, cysteamine dioxygenase. PUBMED:17581819 EPMC:17581819


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012864

This entry includes cysteine oxidases (PCOs) from plants and 2-aminoethanethiol dioxygenases (ADOs) from animals. PCOs oxidize N-terminal cysteine residues, thus preparing the protein for N-end rule pathway-mediated proteasomal degradation [ PUBMED:24599061 ]. ADO is responsible for endogenous cysteamine dioxygenase activity [ PUBMED:17581819 ].

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...

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
(20)
Full
(2101)
Representative proteomes UniProt
(3662)
RP15
(317)
RP35
(1061)
RP55
(1781)
RP75
(2327)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(20)
Full
(2101)
Representative proteomes UniProt
(3662)
RP15
(317)
RP35
(1061)
RP55
(1781)
RP75
(2327)
Alignment:
Format:
Order:
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
(20)
Full
(2101)
Representative proteomes UniProt
(3662)
RP15
(317)
RP35
(1061)
RP55
(1781)
RP75
(2327)
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: Pfam-B_6051 (release 14.0)
Previous IDs: DUF1637;
Type: Family
Sequence Ontology: SO:0100021
Author: Fenech M
Number in seed: 20
Number in full: 2101
Average length of the domain: 186.10 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 70.66 %

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 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.5
Model length: 201
Family (HMM) version: 14
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 PCO_ADO domain has been found. There are 7 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
A0A0N7KHR4 View 3D Structure Click here
A0A0P0UZ10 View 3D Structure Click here
A0A0P0VI76 View 3D Structure Click here
A0A0P0W6N2 View 3D Structure Click here
A0A0P0XBC2 View 3D Structure Click here
A0A0P0XKS7 View 3D Structure Click here
A0A0R0G3S8 View 3D Structure Click here
A0A0R0H125 View 3D Structure Click here
A0A1D6I1W8 View 3D Structure Click here
A0A1D6JHH7 View 3D Structure Click here
A0A1D6KGM0 View 3D Structure Click here
A0A1D6KHR6 View 3D Structure Click here
A0A1D6KZ78 View 3D Structure Click here
A0A1D6ME85 View 3D Structure Click here
A0A1D6MI11 View 3D Structure Click here
A0A1D6NB34 View 3D Structure Click here
A0A368UIC4 View 3D Structure Click here
A4HT14 View 3D Structure Click here
B6T568 View 3D Structure Click here
B7EUY2 View 3D Structure Click here
C4JC20 View 3D Structure Click here
C6TGT8 View 3D Structure Click here
C6TMW7 View 3D Structure Click here
F1QC56 View 3D Structure Click here
F1QLC8 View 3D Structure Click here
I1JGV1 View 3D Structure Click here
I1KD54 View 3D Structure Click here
I1L5Z5 View 3D Structure Click here
I1LSG9 View 3D Structure Click here
I1LUN6 View 3D Structure Click here
I1LWJ1 View 3D Structure Click here
I1MET1 View 3D Structure Click here
I1MKY0 View 3D Structure Click here
I1N4B2 View 3D Structure Click here
I1N632 View 3D Structure Click here
I1N8C0 View 3D Structure Click here
I1N8C2 View 3D Structure Click here
K7M2I5 View 3D Structure Click here
K7M7P6 View 3D Structure Click here
Q0DFG5 View 3D Structure Click here
Q1G3U6 View 3D Structure Click here
Q2QLY7 View 3D Structure Click here
Q4DV73 View 3D Structure Click here
Q556I2 View 3D Structure Click here
Q69R46 View 3D Structure Click here
Q6PDY2 View 3D Structure Click here
Q6Z242 View 3D Structure Click here
Q84SV1 View 3D Structure Click here
Q8IAA1 View 3D Structure Click here
Q8LGJ5 View 3D Structure Click here
Q96SZ5 View 3D Structure Click here
Q9LXG9 View 3D Structure Click here
Q9LXT4 View 3D Structure Click here
Q9SJI9 View 3D Structure Click here
Q9VSD8 View 3D Structure Click here

Family Structural Model

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;