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Conserved domains on  [gi|504875954|ref|WP_015063056|]
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MULTISPECIES: Mov34/MPN/PAD-1 family protein [Enterobacteriaceae]

Protein Classification

MPN domain-containing protein( domain architecture ID 46114)

MPN domain-containing protein contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, which is involved in zinc ion coordination; similar to components of the COP9 signalosome (CSN) complex that acts as a regulator of the ubiquitin conjugation pathway

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MPN super family cl13996
Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) ...
 29-121 8.01e-16

Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function.


The actual alignment was detected with superfamily member TIGR02256:

Pssm-ID: 472685  Cd Length: 131  Bit Score: 69.56  E-value: 8.01e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504875954   29 YRQINKNMPEAFGVLIGSKDlvAEHFKIVDVTVPQQGDRCSRMSFTLMDPEHQCIVDRYYHDSGGELVYRGTWHTHPEGI 108
Cdd:TIGR02256   9 YRQWHDLSTETGGVLIGERR--GAHAVITKISEPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEWHTHPEDQ 86

                          90
                  ....*....|...
gi 504875954  109 PYASNVDVRDWKK 121
Cdd:TIGR02256  87 PEPSWTDRRSWRT 99
 
Name Accession Description Interval E-value
ICE_VC0181 TIGR02256
integrative and conjugative element protein, VC0181 family; This uncharacterized protein is ...
 29-121 8.01e-16

integrative and conjugative element protein, VC0181 family; This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.


Pssm-ID: 131309  Cd Length: 131  Bit Score: 69.56  E-value: 8.01e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504875954   29 YRQINKNMPEAFGVLIGSKDlvAEHFKIVDVTVPQQGDRCSRMSFTLMDPEHQCIVDRYYHDSGGELVYRGTWHTHPEGI 108
Cdd:TIGR02256   9 YRQWHDLSTETGGVLIGERR--GAHAVITKISEPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEWHTHPEDQ 86

                          90
                  ....*....|...
gi 504875954  109 PYASNVDVRDWKK 121
Cdd:TIGR02256  87 PEPSWTDRRSWRT 99
Prok-JAB pfam14464
Prokaryotic homologs of the JAB domain; These are metalloenzymes that function as the ...
 37-139 1.59e-07

Prokaryotic homologs of the JAB domain; These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signaling and protein turnover pathways in eukaryotes. Prokaryotic JAB domains are predicted to have a similar role in their cognates of the ubiquitin modification pathway. The domain is widely found in bacteria, archaea and phages where they are present in several gene contexts in addition to those that correspond to the prokaryotic cognates of the eukaryotic Ub pathway. Other contexts in which JAB domains are present include gene neighbor associations with ubiquitin fold domains in cysteine and siderophore biosynthesis, and phage tail morphogenesis, where they are shown or predicted to process the associated ubiquitin. A distinct family, the RadC-like JAB domains are widespread in bacteria and are predicted to function as nucleases. In halophilic archaea the JAB domain shows strong gene-neighborhood associations with a nucleotidyltransferase suggesting a role in nucleotide metabolism.


Pssm-ID: 464179  Cd Length: 113  Bit Score: 47.11  E-value: 1.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504875954   37 PEAFGVLIGsKDLVAEHFKIVDVTVPQQgdrcsrmSFTLMDPEHQCIVDRYYHDSGGELVyrGTWHTHPEGIPYASNVDV 116
Cdd:pfam14464  18 LECCGILLG-NELESQSVRVIPLVNPMR-------NRFEIDPGDSLRRVKAARERGLELV--GIYHSHPGGPAYPSETDR 87

                          90       100
                  ....*....|....*....|...
gi 504875954  117 RDWKKCKernqdkqLFFIIIGTE 139
Cdd:pfam14464  88 RDAAGPL-------PSYVIGGRA 103
MPN_like cd08070
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ...
 38-117 1.93e-06

Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.


Pssm-ID: 163701  Cd Length: 128  Bit Score: 44.56  E-value: 1.93e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504875954  38 EAFGVLIGSKDLVAEHFKIVdvtVPQQGDRCSRMSFTLMDPEHQCIVDRYYHDSGGELVyrGTWHTHPEGIPYASNVDVR 117
Cdd:cd08070   18 ECCGLLLGKGGGVTAIVTEV---YPVRNVAESPRRRFEIDPAEQLAAQREARERGLEVV--GIYHSHPDGPARPSETDLR 92
JAB_MPN smart00232
JAB/MPN domain; Domain in Jun kinase activation domain binding protein and proteasomal ...
 38-116 1.42e-05

JAB/MPN domain; Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.


Pssm-ID: 214573  Cd Length: 135  Bit Score: 42.36  E-value: 1.42e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504875954    38 EAFGVLIGSKDlvAEHFKIVDV-TVPQQGDRcSRMSFTLMDPEHQCIVDRYYHDSGGELVyrGTWHTHPEGIPYASNVDV 116
Cdd:smart00232  23 EVCGVLLGKSN--KDRPEVKEVfAVPNEPQD-DSVQEYDEDYSHLMDEELKKVNKDLEIV--GWYHSHPDESPFPSEVDV 97
Rri1 COG1310
Proteasome lid subunit RPN8/RPN11, contains Jab1/MPN domain metalloenzyme (JAMM) motif ...
 38-117 4.80e-05

Proteasome lid subunit RPN8/RPN11, contains Jab1/MPN domain metalloenzyme (JAMM) motif [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440921  Cd Length: 127  Bit Score: 40.67  E-value: 4.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504875954  38 EAFGVLIGSKD---LVAEHFKIVDVtvpqqgDRCSRMSFTlMDPEHQCIVDRYYHDSGGELVyrGTWHTHPEGIPYASNV 114
Cdd:COG1310   23 ECCGLLLGKGGgdkRVTRVYPARNV------AESPETRFE-IDPEDLLAAEREARERGLEIV--GIYHSHPDGPAYPSET 93


                 ...
gi 504875954 115 DVR 117
Cdd:COG1310   94 DRA 96
 
Name Accession Description Interval E-value
ICE_VC0181 TIGR02256
integrative and conjugative element protein, VC0181 family; This uncharacterized protein is ...
 29-121 8.01e-16

integrative and conjugative element protein, VC0181 family; This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.


Pssm-ID: 131309  Cd Length: 131  Bit Score: 69.56  E-value: 8.01e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504875954   29 YRQINKNMPEAFGVLIGSKDlvAEHFKIVDVTVPQQGDRCSRMSFTLMDPEHQCIVDRYYHDSGGELVYRGTWHTHPEGI 108
Cdd:TIGR02256   9 YRQWHDLSTETGGVLIGERR--GAHAVITKISEPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEWHTHPEDQ 86

                          90
                  ....*....|...
gi 504875954  109 PYASNVDVRDWKK 121
Cdd:TIGR02256  87 PEPSWTDRRSWRT 99
Prok-JAB pfam14464
Prokaryotic homologs of the JAB domain; These are metalloenzymes that function as the ...
 37-139 1.59e-07

Prokaryotic homologs of the JAB domain; These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signaling and protein turnover pathways in eukaryotes. Prokaryotic JAB domains are predicted to have a similar role in their cognates of the ubiquitin modification pathway. The domain is widely found in bacteria, archaea and phages where they are present in several gene contexts in addition to those that correspond to the prokaryotic cognates of the eukaryotic Ub pathway. Other contexts in which JAB domains are present include gene neighbor associations with ubiquitin fold domains in cysteine and siderophore biosynthesis, and phage tail morphogenesis, where they are shown or predicted to process the associated ubiquitin. A distinct family, the RadC-like JAB domains are widespread in bacteria and are predicted to function as nucleases. In halophilic archaea the JAB domain shows strong gene-neighborhood associations with a nucleotidyltransferase suggesting a role in nucleotide metabolism.


Pssm-ID: 464179  Cd Length: 113  Bit Score: 47.11  E-value: 1.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504875954   37 PEAFGVLIGsKDLVAEHFKIVDVTVPQQgdrcsrmSFTLMDPEHQCIVDRYYHDSGGELVyrGTWHTHPEGIPYASNVDV 116
Cdd:pfam14464  18 LECCGILLG-NELESQSVRVIPLVNPMR-------NRFEIDPGDSLRRVKAARERGLELV--GIYHSHPGGPAYPSETDR 87

                          90       100
                  ....*....|....*....|...
gi 504875954  117 RDWKKCKernqdkqLFFIIIGTE 139
Cdd:pfam14464  88 RDAAGPL-------PSYVIGGRA 103
MPN_like cd08070
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ...
 38-117 1.93e-06

Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.


Pssm-ID: 163701  Cd Length: 128  Bit Score: 44.56  E-value: 1.93e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504875954  38 EAFGVLIGSKDLVAEHFKIVdvtVPQQGDRCSRMSFTLMDPEHQCIVDRYYHDSGGELVyrGTWHTHPEGIPYASNVDVR 117
Cdd:cd08070   18 ECCGLLLGKGGGVTAIVTEV---YPVRNVAESPRRRFEIDPAEQLAAQREARERGLEVV--GIYHSHPDGPARPSETDLR 92
JAB_MPN smart00232
JAB/MPN domain; Domain in Jun kinase activation domain binding protein and proteasomal ...
 38-116 1.42e-05

JAB/MPN domain; Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.


Pssm-ID: 214573  Cd Length: 135  Bit Score: 42.36  E-value: 1.42e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504875954    38 EAFGVLIGSKDlvAEHFKIVDV-TVPQQGDRcSRMSFTLMDPEHQCIVDRYYHDSGGELVyrGTWHTHPEGIPYASNVDV 116
Cdd:smart00232  23 EVCGVLLGKSN--KDRPEVKEVfAVPNEPQD-DSVQEYDEDYSHLMDEELKKVNKDLEIV--GWYHSHPDESPFPSEVDV 97
Rri1 COG1310
Proteasome lid subunit RPN8/RPN11, contains Jab1/MPN domain metalloenzyme (JAMM) motif ...
 38-117 4.80e-05

Proteasome lid subunit RPN8/RPN11, contains Jab1/MPN domain metalloenzyme (JAMM) motif [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440921  Cd Length: 127  Bit Score: 40.67  E-value: 4.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504875954  38 EAFGVLIGSKD---LVAEHFKIVDVtvpqqgDRCSRMSFTlMDPEHQCIVDRYYHDSGGELVyrGTWHTHPEGIPYASNV 114
Cdd:COG1310   23 ECCGLLLGKGGgdkRVTRVYPARNV------AESPETRFE-IDPEDLLAAEREARERGLEIV--GIYHSHPDGPAYPSET 93


                 ...
gi 504875954 115 DVR 117
Cdd:COG1310   94 DRA 96
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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