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12062  structures 6431  species 0  interactions 36558  sequences 445  architectures

Family: Proteasome (PF00227)

Summary: Proteasome subunit

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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 16 members:

AAT Asparaginase_2 CBAH DUF1933 DUF3700 G_glu_transpept GATase_2 GATase_4 GATase_6 GATase_7 IMP_cyclohyd Penicil_amidase Peptidase_C69 Phospholip_B Proteasome Proteasome_A_N

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
(154)
Full
(36558)
Representative proteomes UniProt
(88178)
RP15
(6756)
RP35
(17204)
RP55
(30541)
RP75
(43999)
Jalview View  View  View  View  View  View  View 
HTML View             
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
(154)
Full
(36558)
Representative proteomes UniProt
(88178)
RP15
(6756)
RP35
(17204)
RP55
(30541)
RP75
(43999)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(154)
Full
(36558)
Representative proteomes UniProt
(88178)
RP15
(6756)
RP35
(17204)
RP55
(30541)
RP75
(43999)
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: Prosite
Previous IDs: proteasome;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A , Valas RE
Number in seed: 154
Number in full: 36558
Average length of the domain: 170.60 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 71.43 %

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 22.4 22.4
Trusted cut-off 22.4 22.4
Noise cut-off 22.3 22.3
Model length: 190
Family (HMM) version: 28
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

Selections

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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 Proteasome domain has been found. There are 12062 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
A0A0G2JSL0 View 3D Structure Click here
A0A0R0GQN2 View 3D Structure Click here
A0A0R0JFH3 View 3D Structure Click here
A0A0R0K0T7 View 3D Structure Click here
A0A0R0LAF9 View 3D Structure Click here
A0A0R4ISC7 View 3D Structure Click here
A0A0R4J2M8 View 3D Structure Click here
A0A0R4J321 View 3D Structure Click here
A0A0R4J3L5 View 3D Structure Click here
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A0A1D6F4W1 View 3D Structure Click here
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A0A1D6FVJ7 View 3D Structure Click here
A0A1D6G9P9 View 3D Structure Click here
A0A1D6GK60 View 3D Structure Click here
A0A1D6H2M0 View 3D Structure Click here
A0A1D6HE64 View 3D Structure Click here
A0A1D6HE74 View 3D Structure Click here
A0A1D6I145 View 3D Structure Click here
A0A1D6I5L5 View 3D Structure Click here
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A0A1D6I8L7 View 3D Structure Click here
A0A1D6IJH2 View 3D Structure Click here
A0A1D6IJH2 View 3D Structure Click here
A0A1D6IL23 View 3D Structure Click here
A0A1D6KJT7 View 3D Structure Click here
A0A1D6KK93 View 3D Structure Click here
A0A1D6LJL1 View 3D Structure Click here
A0A1D6LKR2 View 3D Structure Click here
A0A1D6LQX4 View 3D Structure Click here
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A0A1D6N827 View 3D Structure Click here
A0A1D6N969 View 3D Structure Click here
A0A1D6NV82 View 3D Structure Click here
A0A1D6NVT9 View 3D Structure Click here
A0A1D6P3Y5 View 3D Structure Click here
A0A1D6P3Y5 View 3D Structure Click here
A0A1D6PJW1 View 3D Structure Click here
A0A1D6PUM4 View 3D Structure Click here
A0A1D6Q5L0 View 3D Structure Click here
A0A1D6Q5L0 View 3D Structure Click here
A0A1D8PJ20 View 3D Structure Click here
A0A1D8PK85 View 3D Structure Click here
A0A1D8PLK1 View 3D Structure Click here
A0A1D8PNC8 View 3D Structure Click here
A0A1D8PQW1 View 3D Structure Click here
A0A1D8PRB6 View 3D Structure Click here
A0A1D8PRH6 View 3D Structure Click here
A0A1D8PSS4 View 3D Structure Click here
A0A1D8PTY6 View 3D Structure Click here
A0A1D8PU67 View 3D Structure Click here
A0A2R8PYA0 View 3D Structure Click here
A0A381MU64 View 3D Structure Click here
A0A5K1K7U1 View 3D Structure Click here
A0AQH0 View 3D Structure Click here
A3FMB9 View 3D Structure Click here
A4HSQ5 View 3D Structure Click here
A4HUT6 View 3D Structure Click here
A4HV47 View 3D Structure Click here
A4HVX3 View 3D Structure Click here
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A4I357 View 3D Structure Click here
A4I384 View 3D Structure Click here
A4IAL6 View 3D Structure Click here
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A5LHX3 View 3D Structure Click here
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B0R027 View 3D Structure Click here
B0R027 View 3D Structure Click here
B3DG31 View 3D Structure Click here
B4F7U0 View 3D Structure Click here
B4F822 View 3D Structure Click here
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C0PFF5 View 3D Structure Click here
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C6SV91 View 3D Structure Click here
C6SW24 View 3D Structure Click here
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C6SY85 View 3D Structure Click here
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C6TH59 View 3D Structure Click here
D3Z8J0 View 3D Structure Click here
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F1QR78 View 3D Structure Click here
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H1ACL9 View 3D Structure Click here
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I1J717 View 3D Structure Click here
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I1MA63 View 3D Structure Click here
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I1MN39 View 3D Structure Click here
I1MXX5 View 3D Structure Click here
I1N318 View 3D Structure Click here
I1N783 View 3D Structure Click here
I1NC65 View 3D Structure Click here
K7MS03 View 3D Structure Click here
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M0R7C4 View 3D Structure Click here
O09061 View 3D Structure Click here
O14250 View 3D Structure Click here
O14818 View 3D Structure Click here
O17586 View 3D Structure Click here
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O35955 View 3D Structure Click here
O43063 View 3D Structure Click here
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O48551 View 3D Structure Click here
O55234 View 3D Structure Click here
O57330 View 3D Structure Click here
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P12881 View 3D Structure Click here
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P70195 View 3D Structure Click here
P90868 View 3D Structure Click here
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P99026 View 3D Structure Click here
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Q09583 View 3D Structure Click here
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Q09841 View 3D Structure Click here
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Q0J006 View 3D Structure Click here
Q10329 View 3D Structure Click here
Q10KF0 View 3D Structure Click here
Q1LWY1 View 3D Structure Click here
Q23237 View 3D Structure Click here
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Q2FZ29 View 3D Structure Click here
Q42134 View 3D Structure Click here
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Q4DW25 View 3D Structure Click here
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Q4KM35 View 3D Structure Click here
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Q54BC8 View 3D Structure Click here
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Q54QR2 View 3D Structure Click here
Q54XM7 View 3D Structure Click here
Q556Q0 View 3D Structure Click here
Q55D66 View 3D Structure Click here
Q55DY7 View 3D Structure Click here
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Q55G04 View 3D Structure Click here
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Q58634 View 3D Structure Click here
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Q60177 View 3D Structure Click here
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Q86A21 View 3D Structure Click here
Q8BG41 View 3D Structure Click here
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Q8I261 View 3D Structure Click here
Q8I496 View 3D Structure Click here
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Q8IAR3 View 3D Structure Click here
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Q8IJT1 View 3D Structure Click here
Q8IK90 View 3D Structure Click here
Q8IKC9 View 3D Structure Click here
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Q8LD27 View 3D Structure Click here
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Q8TAA3 View 3D Structure Click here
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Q99436 View 3D Structure Click here
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Q9N599 View 3D Structure Click here
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