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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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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 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

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 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

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
(26)
Full
(14438)
Representative proteomes UniProt
(25306)
RP15
(2810)
RP35
(6793)
RP55
(11535)
RP75
(15353)
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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.

Format an alignment

  Seed
(26)
Full
(14438)
Representative proteomes UniProt
(25306)
RP15
(2810)
RP35
(6793)
RP55
(11535)
RP75
(15353)
Alignment:
Format:
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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
(26)
Full
(14438)
Representative proteomes UniProt
(25306)
RP15
(2810)
RP35
(6793)
RP55
(11535)
RP75
(15353)
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_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

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 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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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
A0A0N7KJV4 View 3D Structure Click here
A0A0P0WSW9 View 3D Structure Click here
A0A0P0X2C5 View 3D Structure Click here
A0A0P0XWI9 View 3D Structure Click here
A0A0R0K5E1 View 3D Structure Click here
A0A0R4IER2 View 3D Structure Click here
A0A0R4IIS6 View 3D Structure Click here
A0A0R4J2H6 View 3D Structure Click here
A0A0R4J3Q1 View 3D Structure Click here
A0A0R4J5N9 View 3D Structure Click here
A0A0R4J8E6 View 3D Structure Click here
A0A1D6DUW9 View 3D Structure Click here
A0A1D6FIR9 View 3D Structure Click here
A0A1D6G9P0 View 3D Structure Click here
A0A1D6GIA1 View 3D Structure Click here
A0A1D6GLV9 View 3D Structure Click here
A0A1D6J5G8 View 3D Structure Click here
A0A1D6JGZ2 View 3D Structure Click here
A0A1D6LII6 View 3D Structure Click here
A0A1D6LLK8 View 3D Structure Click here
A0A1D6MBH7 View 3D Structure Click here
A0A1D6MST6 View 3D Structure Click here
A0A1D6QKF2 View 3D Structure Click here
A0A1D8PFZ8 View 3D Structure Click here
A0A1D8PNA8 View 3D Structure Click here
A0A1P8BGX5 View 3D Structure Click here
A0A2R8Q5H4 View 3D Structure Click here
A1Z6K7 View 3D Structure Click here
A1Z8U0 View 3D Structure Click here
A3BYB2 View 3D Structure Click here
A4HWY1 View 3D Structure Click here
A4I7K3 View 3D Structure Click here
A4I9N5 View 3D Structure Click here
B0BMT2 View 3D Structure Click here
B0BMZ5 View 3D Structure Click here
B2RYM5 View 3D Structure Click here
B4FLQ8 View 3D Structure Click here
B4FSK2 View 3D Structure Click here
B4FUK9 View 3D Structure Click here
B6TWG6 View 3D Structure Click here
C6T923 View 3D Structure Click here
C6TC72 View 3D Structure Click here
C6TIT4 View 3D Structure Click here
C6TN20 View 3D Structure Click here
D3ZI16 View 3D Structure Click here
D4A7T9 View 3D Structure Click here
D4AC36 View 3D Structure Click here
D4AEH3 View 3D Structure Click here
E7F3M4 View 3D Structure Click here
F1QHE5 View 3D Structure Click here
F4JC55 View 3D Structure Click here
F7EUU4 View 3D Structure Click here
G3V6H2 View 3D Structure Click here
I1JI63 View 3D Structure Click here
I1JVP4 View 3D Structure Click here
I1K5M0 View 3D Structure Click here
I1K935 View 3D Structure Click here
I1KFU0 View 3D Structure Click here
I1KIY6 View 3D Structure Click here
I1KMT7 View 3D Structure Click here
I1L4B5 View 3D Structure Click here
I1LMP2 View 3D Structure Click here
I1LMP4 View 3D Structure Click here
I1M1N6 View 3D Structure Click here
I1M5R8 View 3D Structure Click here
I1M5U8 View 3D Structure Click here
I1M8K6 View 3D Structure Click here
I1MCE8 View 3D Structure Click here
I1MEX0 View 3D Structure Click here
I1MZ47 View 3D Structure Click here
I1N504 View 3D Structure Click here
K7K687 View 3D Structure Click here
K7TNP5 View 3D Structure Click here
K7UWW6 View 3D Structure Click here
K7V686 View 3D Structure Click here
K7W637 View 3D Structure Click here
O00303 View 3D Structure Click here
O00487 View 3D Structure Click here
O01974 View 3D Structure Click here
O04202 View 3D Structure Click here
O14187 View 3D Structure Click here
O15372 View 3D Structure Click here
O24412 View 3D Structure Click here
O35593 View 3D Structure Click here
O35864 View 3D Structure Click here
O43060 View 3D Structure Click here
O61792 View 3D Structure Click here
O74440 View 3D Structure Click here
O76577 View 3D Structure Click here
O88545 View 3D Structure Click here
O94454 View 3D Structure Click here
O95630 View 3D Structure Click here
P26270 View 3D Structure Click here
P26516 View 3D Structure Click here
P34369 View 3D Structure Click here
P41878 View 3D Structure Click here
P41883 View 3D Structure Click here
P43588 View 3D Structure Click here
P46736 View 3D Structure Click here
P46737 View 3D Structure Click here
P51665 View 3D Structure Click here
P91001 View 3D Structure Click here
Q08723 View 3D Structure Click here
Q08CH3 View 3D Structure Click here
Q0DGB3 View 3D Structure Click here
Q0JKN5 View 3D Structure Click here
Q12468 View 3D Structure Click here
Q18967 View 3D Structure Click here
Q2QLZ5 View 3D Structure Click here
Q2QM04 View 3D Structure Click here
Q3TV65 View 3D Structure Click here
Q4CK98 View 3D Structure Click here
Q4CMJ7 View 3D Structure Click here
Q4CUS2 View 3D Structure Click here
Q4CYA0 View 3D Structure Click here
Q4CYA6 View 3D Structure Click here
Q4D3R6 View 3D Structure Click here
Q4DDT1 View 3D Structure Click here
Q4DG61 View 3D Structure Click here
Q4DH98 View 3D Structure Click here
Q4DKG4 View 3D Structure Click here
Q4DL11 View 3D Structure Click here
Q4DPM7 View 3D Structure Click here
Q4DQZ2 View 3D Structure Click here
Q4DXR1 View 3D Structure Click here
Q4V8E2 View 3D Structure Click here
Q54C49 View 3D Structure Click here
Q54C92 View 3D Structure Click here
Q54PF3 View 3D Structure Click here
Q54Q40 View 3D Structure Click here
Q54UD0 View 3D Structure Click here
Q54WI8 View 3D Structure Click here
Q54Z40 View 3D Structure Click here
Q59PG6 View 3D Structure Click here
Q5ADU3 View 3D Structure Click here
Q5AG96 View 3D Structure Click here
Q5PNU3 View 3D Structure Click here
Q5PR67 View 3D Structure Click here
Q5QLJ2 View 3D Structure Click here
Q5RGA4 View 3D Structure Click here
Q5VVJ2 View 3D Structure Click here
Q5Z816 View 3D Structure Click here
Q60EW3 View 3D Structure Click here
Q69Z66 View 3D Structure Click here
Q6AXJ2 View 3D Structure Click here
Q6NKP9 View 3D Structure Click here
Q6P2Q9 View 3D Structure Click here
Q6P9U8 View 3D Structure Click here
Q6PC30 View 3D Structure Click here
Q6TH47 View 3D Structure Click here
Q6ZKM2 View 3D Structure Click here
Q75M19 View 3D Structure Click here
Q76N33 View 3D Structure Click here
Q7L5N1 View 3D Structure Click here
Q7M757 View 3D Structure Click here
Q7XMI6 View 3D Structure Click here
Q86IJ1 View 3D Structure Click here
Q8H936 View 3D Structure Click here
Q8I2X0 View 3D Structure Click here
Q8I323 View 3D Structure Click here
Q8ID28 View 3D Structure Click here
Q8LAZ7 View 3D Structure Click here
Q8N594 View 3D Structure Click here
Q8R424 View 3D Structure Click here
Q8RW94 View 3D Structure Click here
Q8T295 View 3D Structure Click here
Q8VYB5 View 3D Structure Click here
Q8W1P0 View 3D Structure Click here
Q8W206 View 3D Structure Click here
Q91WK2 View 3D Structure Click here
Q92905 View 3D Structure Click here
Q942M1 View 3D Structure Click here
Q95PZ0 View 3D Structure Click here
Q96FJ0 View 3D Structure Click here
Q99PV0 View 3D Structure Click here
Q9C5Z2 View 3D Structure Click here
Q9C774 View 3D Structure Click here
Q9CQ26 View 3D Structure Click here
Q9DCH4 View 3D Structure Click here
Q9FVU9 View 3D Structure Click here
Q9LT08 View 3D Structure Click here
Q9P371 View 3D Structure Click here
Q9SDD1 View 3D Structure Click here
Q9SSD2 View 3D Structure Click here
Q9T0I6 View 3D Structure Click here
Q9U9Q4 View 3D Structure Click here
Q9UT48 View 3D Structure Click here
Q9V3H2 View 3D Structure Click here
Q9VA71 View 3D Structure Click here
Q9VCY3 View 3D Structure Click here
Q9VKJ1 View 3D Structure Click here
Q9VN50 View 3D Structure Click here
Q9XZ58 View 3D Structure Click here
R4GEX4 View 3D Structure Click here