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19  structures 451  species 2  interactions 2882  sequences 61  architectures

Family: JAB (PF01398)

Summary: JAB1/Mov34/MPN/PAD-1 ubiquitin protease

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.

JAB1/Mov34/MPN/PAD-1 ubiquitin protease Provide feedback

Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [3] and PAD-1-like domain [4] JABP1 domain [5] or JAMM domain [7]. These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signaling and protein turnover pathways in eukaryotes [7]. Versions of the domain in prokaryotic cognates of the ubiquitin-modification pathway are predicted to have a similar role [8].

Literature references

  1. Aravind L, Ponting CP; , Protein Sci 1998;7:1250-1254.: Homologues of 26S proteasome subunits are regulators of transcription and translation. PUBMED:9605331 EPMC:9605331

  2. Hershey JW, Asano K, Naranda T, Vornlocher HP, Hanachi P, Merrick WC; , Biochimie 1996;78:903-907.: Conservation and diversity in the structure of translation initiation factor EIF3 from humans and yeast. PUBMED:9150866 EPMC:9150866

  3. Hofmann K, Bucher P; , Trends Biochem Sci 1998;23:204-205.: The PCI domain: a common theme in three multiprotein complexes. PUBMED:9644972 EPMC:9644972

  4. Ponting CP, Aravind L, Schultz J, Bork P, Koonin EV; , J Mol Biol 1999;289:729-745.: Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. PUBMED:10369758 EPMC:10369758

  5. Kouranti I, McLean JR, Feoktistova A, Liang P, Johnson AE, Roberts-Galbraith RH, Gould KL;, PLoS Biol. 2010; [Epub ahead of print]: A global census of fission yeast deubiquitinating enzyme localization and interaction networks reveals distinct compartmentalization profiles and overlapping functions in endocytosis and polarity. PUBMED:20838651 EPMC:20838651

  6. Piper RC, Katzmann DJ;, Annu Rev Cell Dev Biol. 2007;23:519-547.: Biogenesis and function of multivesicular bodies. PUBMED:17506697 EPMC:17506697

  7. Verma R, Aravind L, Oania R, McDonald WH, Yates JR 3rd, Koonin EV, Deshaies RJ;, Science. 2002;298:611-615.: Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. PUBMED:12183636 EPMC:12183636

  8. Iyer LM, Burroughs AM, Aravind L; , Genome Biol. 2006;7:R60.: The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. PUBMED:16859499 EPMC:16859499


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000555

This domain is known as the MPN domain [PUBMED:9644972], PAD-1-like domain [PUBMED:10369758], JABP1 domain [PUBMED:20838651] or JAMM domain [PUBMED:12183636]. Proteins with this domain include proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. They are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signaling and protein turnover pathways in eukaryotes [PUBMED:12183636]. Versions of the domain in prokaryotic cognates of the ubiquitin-modification pathway are predicted to have a similar role [PUBMED:16859499].

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 JAB (CL0366), which contains the following 6 members:

JAB NPL4 Prok-JAB RadC Toxin-JAB1 UPF0172

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(30)
Full
(2882)
Representative proteomes NCBI
(3177)
Meta
(141)
RP15
(655)
RP35
(1015)
RP55
(1500)
RP75
(1880)
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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
(30)
Full
(2882)
Representative proteomes NCBI
(3177)
Meta
(141)
RP15
(655)
RP35
(1015)
RP55
(1500)
RP75
(1880)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(30)
Full
(2882)
Representative proteomes NCBI
(3177)
Meta
(141)
RP15
(655)
RP35
(1015)
RP55
(1500)
RP75
(1880)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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_738 (release 3.0)
Previous IDs: Mov34; JAMM;
Type: Family
Author: Finn RD, Bateman A, Iyer LM, Burroughs AM, Aravind L
Number in seed: 30
Number in full: 2882
Average length of the domain: 110.70 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 23.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 21.6
Trusted cut-off 21.6 21.6
Noise cut-off 21.5 21.5
Model length: 114
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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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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Interactions

There are 2 interactions for this family. More...

JAB PROCT

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 JAB domain has been found. There are 19 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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