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12351  structures 6613  species 0  interactions 39483  sequences 458  architectures

Family: Proteasome (PF00227)

Summary: Proteasome subunit

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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.

Proteasome subunit Provide feedback

The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologues vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is encoded by more than 14 genes [1]. Recently evidence of two novel groups of bacterial proteasomes was proposed. The first is Anbu, which is sparsely distributed among cyanobacteria and proteobacteria [1]. The second is call beta-proteobacteria proteasome homologue (BPH) [1].

Literature references

  1. Valas RE, Bourne PE; , J Mol Evol. 2008;66:494-504.: Rethinking proteasome evolution: two novel bacterial proteasomes. PUBMED:18389302 EPMC:18389302

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001353

The proteasome (or macropain) ( EC ) [ PUBMED:7682410 , PUBMED:2643381 , PUBMED:1317508 , PUBMED:7697118 , PUBMED:8882582 ] is a multicatalytic proteinase complex in eukaryotes and archaea, and in some bacteria, that is involved in an ATP/ubiquitin-dependent non-lysosomal proteolytic pathway. In eukaryotes the 20S proteasome is composed of 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700kDa. Proteasome subunits can be classified on the basis of sequence similarities into two groups, alpha (A) and beta (B). The proteasome consists of four stacked rings composed of alpha/beta/beta/alpha subunits. There are seven different alpha subunits and seven different beta subunits [ PUBMED:9087403 ]. Three of the seven beta subunits are peptidases, each with a different specificity. Subunit beta1c (MEROPS identifier T01.010) has a preference for cleaving glutaminyl bonds ("peptidyl-glutamyl-like" or "caspase-like"), subunit beta2c (MEROPS identifier T01.011) has a preference for cleaving arginyl and lysyl bonds ("trypsin-like"), and subunit beta5c (MEROPS identifier T01.012) cleaves after hydrophobic amino acids ("chymotrypsin-like") [ PUBMED:2535672 ]. The proteasome subunits are related to N-terminal nucleophile hydrolases, and the catalytic subunits have an N-terminal threonine nucleophile.

ATP-dependent protease complexes are present in all three kingdoms of life, where they rid the cell of misfolded or damaged proteins and control the level of certain regulatory proteins. They include the proteasome in Eukaryotes, Archaea, and Actinomycetales and the HslVU (ClpQY, clpXP) complex in other eubacteria. Genes homologues to eubacterial HslU (ClpY, clpX) have also been demonstrated in to be present in the genome of trypanosomatid protozoa [ PUBMED:12446803 ].

The prokaryotic ATP-dependent proteasome is coded for by the heat-shock locus VU (HslVU). It consists of HslV, a peptidase, and HslU ( INTERPRO ), the ATPase and chaperone belonging to the AAA/Clp/Hsp100 family. The crystal structure of Thermotoga maritima HslV has been determined to 2.1-A resolution. The structure of the dodecameric enzyme is well conserved compared to those from Escherichia coli and Haemophilus influenzae [ PUBMED:12646382 , PUBMED:12823960 ].

This entry contains threonine peptidases and non-peptidase homologues belong to MEROPS peptidase family T1 (proteasome family, clan PB(T)). The family consists of the protease components of the archaeal and bacterial proteasomes and the alpha and beta subunits of the eukaryotic proteasome.

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 NTN (CL0052), which has the following description:

In the N-terminal nucleophile aminohydrolases (Ntn hydrolases) the N-terminal residue provides two catalytic groups, nucleophile and proton donor. These enzymes use the side chain of the amino-terminal residue, incorporated in a beta-sheet, as the nucleophile in the catalytic attack at the carbonyl carbon. The nucleophile is cysteine in GAT, serine in penicillin acylase, and threonine in the proteasome. All the enzymes share an unusual fold in which the nucleophile and other catalytic groups occupy equivalent sites. This fold provides both the capacity for nucleophilic attack and the possibility of autocatalytic processing [1].

The clan contains the following 17 members:

AAT Asparaginase_2 CarA_N CBAH DUF3700 G_glu_transpept GATase_2 GATase_4 GATase_6 GATase_7 IMP_cyclohyd Penicil_amidase Peptidase_C69 Phospholip_B Proteasome Proteasome_A_N TANGO2


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.

Representative proteomes UniProt
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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.

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Representative proteomes UniProt

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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.

Representative proteomes UniProt
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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...


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: Prosite
Previous IDs: proteasome;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A , Valas RE
Number in seed: 153
Number in full: 39483
Average length of the domain: 170.9 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 71.53 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.4 22.4
Trusted cut-off 22.4 22.4
Noise cut-off 22.3 22.3
Model length: 190
Family (HMM) version: 29
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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


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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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The tree shows the occurrence of this domain across different species. More...


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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 Proteasome domain has been found. There are 12351 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
A0A044QPC2 View 3D Structure Click here
A0A044R3U9 View 3D Structure Click here
A0A044RBU3 View 3D Structure Click here
A0A044RDY9 View 3D Structure Click here
A0A044SGW9 View 3D Structure Click here
A0A044STH6 View 3D Structure Click here
A0A044SXA4 View 3D Structure Click here
A0A044TBP3 View 3D Structure Click here
A0A044UD64 View 3D Structure Click here
A0A044UEZ7 View 3D Structure Click here
A0A044UQS0 View 3D Structure Click here
A0A044V9J7 View 3D Structure Click here
A0A077YWJ6 View 3D Structure Click here
A0A077YZS4 View 3D Structure Click here
A0A077Z059 View 3D Structure Click here
A0A077Z2P7 View 3D Structure Click here
A0A077Z7L4 View 3D Structure Click here
A0A077Z826 View 3D Structure Click here
A0A077Z894 View 3D Structure Click here
A0A077ZAD9 View 3D Structure Click here
A0A077ZAK6 View 3D Structure Click here
A0A077ZAR9 View 3D Structure Click here
A0A077ZAW8 View 3D Structure Click here
A0A077ZDP8 View 3D Structure Click here
A0A0D2DTB7 View 3D Structure Click here
A0A0D2F8W7 View 3D Structure Click here
A0A0D2G0Y3 View 3D Structure Click here
A0A0D2G4C2 View 3D Structure Click here
A0A0D2GCK9 View 3D Structure Click here
A0A0D2GEY6 View 3D Structure Click here
A0A0D2GG75 View 3D Structure Click here
A0A0D2GH05 View 3D Structure Click here
A0A0D2GHL9 View 3D Structure Click here
A0A0D2GIC6 View 3D Structure Click here
A0A0D2GPK0 View 3D Structure Click here
A0A0D2GPT4 View 3D Structure Click here
A0A0D2GR38 View 3D Structure Click here
A0A0D2GWP3 View 3D Structure Click here
A0A0G2JSL0 View 3D Structure Click here
A0A0H3GLF6 View 3D Structure Click here