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283  structures 1520  species 0  interactions 14438  sequences 322  architectures

Family: JAB (PF01398)

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

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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 signalling and protein turnover pathways in eukaryotes [7]. Versions of the domain in prokaryotic cognates of the ubiquitin-modification pathway are shown to have a similar role, and the archael protein from Haloferax volcanii is found to cleave ubiquitin-like small archaeal modifier proteins (SAMP1/2) from protein conjugates [8,9].

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

  9. Hepowit NL, Uthandi S, Miranda HV, Toniutti M, Prunetti L, Olivarez O, De Vera IM, Fanucci GE, Chen S, Maupin-Furlow JA;, Mol Microbiol. 2012;86:971-987.: Archaeal JAB1/MPN/MOV34 metalloenzyme (HvJAMM1) cleaves ubiquitin-like small archaeal modifier proteins (SAMPs) from protein-conjugates. PUBMED:22970855 EPMC:22970855

Internal database links

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 ].

The archaeal (H. volcanii) JAMM domain containing protein, HvJAMM1, cleaves ubiquitin-like small archaeal modifier proteins (SAMP1/2) from protein conjugates [ PUBMED:22970855 ]. The bacterial JAMM domain containing protein QbsD from Pseudomonas fluorescens cleaves the C-terminal amino acid residues of the sulfur carrier protein QbsE prior to the formation of the carboxy-terminal thiocarboxylate [ PUBMED:17209031 ].

Gene Ontology

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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 has the following description:

This superfamily includes a number of proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits, regulators of transcription factors and ubiquitination-assisting protein families. In eukaryotes and in prokaryotic cognates of the ubiquitin-based modification pathway, they function as ubiquitin isopeptidases/ deubiquitinases. JAB domains are also found in diverse metabolic pathways in prokaryotes such as siderophore and cysteine biosynthesis. Other distinct versions of the JAB domain, such as RadC are predicted to function as nucleases. Structurally, the JAB domain is related to the nucleotide deaminase and binds a Zinc ion in a similar structural location.

The clan contains the following 7 members:

fvmJAB_N JAB NPL4 Prok-JAB RadC Toxin-JAB1 UPF0172


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.

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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.

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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
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A , Iyer LM , Burroughs AM , Aravind L
Number in seed: 26
Number in full: 14438
Average length of the domain: 111.00 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 21.10 %

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 22.5 22.5
Trusted cut-off 22.5 22.5
Noise cut-off 22.4 22.4
Model length: 118
Family (HMM) version: 23
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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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 283 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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