Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase; This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it participates in transcriptional regulation events in androgen receptor-dependent gene activation. In prostate tumors, the levels of uH2A are dramatically decreased, thus 2A-DUB serving as a cancer-related marker.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149028235 252 KFQPFNVAVSSNVLFLLDFHCHLTRSEVVGYLGGRWDINNQMLTVLRAFPCRSRL--GDPDTAATVEEEIHQVLFLRGLS 329
Cdd:cd08067    1 KIQPFKVTVSSNALLLMDFHCHLTTSEVIGYLGGTWDPNTQNLTILQAFPCRSRLtgLDCEMDPVSETEIRESLESRGLS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149028235 330 LVGWYHSHPHSPAAPSLQDIDAQMEYQLRLQGSNNGFQPCLALLCSPYYSGNPGPESKICPFWVMPPPEQRPSDYGIPMD 409
Cdd:cd08067   81 VVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPPPENRPNEYGVPML 160

                        170       180
                 ....*....|....*....|....*..
gi 149028235 410 VEMAYVQDSFLTNDVLQEMMMLVEFYK 436
Cdd:cd08067  161 MSYTVSQDEFLTQDVLKELRWLVEFYR 187

Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase; This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it participates in transcriptional regulation events in androgen receptor-dependent gene activation. In prostate tumors, the levels of uH2A are dramatically decreased, thus 2A-DUB serving as a cancer-related marker.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149028235 252 KFQPFNVAVSSNVLFLLDFHCHLTRSEVVGYLGGRWDINNQMLTVLRAFPCRSRL--GDPDTAATVEEEIHQVLFLRGLS 329
Cdd:cd08067    1 KIQPFKVTVSSNALLLMDFHCHLTTSEVIGYLGGTWDPNTQNLTILQAFPCRSRLtgLDCEMDPVSETEIRESLESRGLS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149028235 330 LVGWYHSHPHSPAAPSLQDIDAQMEYQLRLQGSNNGFQPCLALLCSPYYSGNPGPESKICPFWVMPPPEQRPSDYGIPMD 409
Cdd:cd08067   81 VVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPPPENRPNEYGVPML 160

                        170       180
                 ....*....|....*....|....*..
gi 149028235 410 VEMAYVQDSFLTNDVLQEMMMLVEFYK 436
Cdd:cd08067  161 MSYTVSQDEFLTQDVLKELRWLVEFYR 187

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149028235 278 EVVGYLGGRWDINNqmlTVLRAFPCRSRLG--------DPDTAATVEEEIHQvlflRGLSLVGWYHSHPHSPAAPSLQDI 349
Cdd:COG1310   23 ECCGLLLGKGGGDK---RVTRVYPARNVAEspetrfeiDPEDLLAAEREARE----RGLEIVGIYHSHPDGPAYPSETDR 95

                 ....*.
gi 149028235 350 dAQMEY 355
Cdd:COG1310   96 -AQAAW 100

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 149028235  278 EVVGYLGGRWDINNQMLTVLRAFPCRSR-LGDP-DTAATVEEeihqvLFLRGLSLVGWYHSHPHSPAAPSLQDID 350
Cdd:pfam14464  19 ECCGILLGNELESQSVRVIPLVNPMRNRfEIDPgDSLRRVKA-----ARERGLELVGIYHSHPGGPAYPSETDRR 88

Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase; This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it participates in transcriptional regulation events in androgen receptor-dependent gene activation. In prostate tumors, the levels of uH2A are dramatically decreased, thus 2A-DUB serving as a cancer-related marker.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149028235 252 KFQPFNVAVSSNVLFLLDFHCHLTRSEVVGYLGGRWDINNQMLTVLRAFPCRSRL--GDPDTAATVEEEIHQVLFLRGLS 329
Cdd:cd08067    1 KIQPFKVTVSSNALLLMDFHCHLTTSEVIGYLGGTWDPNTQNLTILQAFPCRSRLtgLDCEMDPVSETEIRESLESRGLS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149028235 330 LVGWYHSHPHSPAAPSLQDIDAQMEYQLRLQGSNNGFQPCLALLCSPYYSGNPGPESKICPFWVMPPPEQRPSDYGIPMD 409
Cdd:cd08067   81 VVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPPPENRPNEYGVPML 160

                        170       180
                 ....*....|....*....|....*..
gi 149028235 410 VEMAYVQDSFLTNDVLQEMMMLVEFYK 436
Cdd:cd08067  161 MSYTVSQDEFLTQDVLKELRWLVEFYR 187

Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic; This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). 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. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor proteins, including p53, p27, and Smad4. Over-expression of CSN5 has been implicated in cancer initiation and progression. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. It is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity; it is targeted to DNA damage foci after irradiation. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. It is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene and serves as a marker in prostate tumors.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149028235 265 LFLLDFHCHL-TRSEVVGYLGGRWDINNQMLTVLR---AFPCrsrlgdPDTAATVE-EEIHQVLFLRGLSLVGWYHSHPH 339
Cdd:cd08058    3 LLKMLQHAESnTGIEVMGLLCGELTHNEFTDKHVIvpkQSAG------PDSCTGENvEELFNVQTGRPLLVVGWYHSHPT 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 149028235 340 SPAAPSLQDIDAQMEYQLRLQGSnngfqpcLALLCSPYYSGNPGPESKI 388
Cdd:cd08058   77 FTAWLSSVDIHTQASYQLMLPEA-------IAIVVSPKHRNKDTGIFRL 118

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149028235 278 EVVGYLGGRwdINNQMLTVLRAFPCRSRLG--------DPDTAATVEEEIHQvlflRGLSLVGWYHSHPHSPAAPSLQDI 349
Cdd:cd08070   18 ECCGLLLGK--GGGVTAIVTEVYPVRNVAEsprrrfeiDPAEQLAAQREARE----RGLEVVGIYHSHPDGPARPSETDL 91

                 ....*.
gi 149028235 350 dAQMEY 355
Cdd:cd08070   92 -RLAWP 96

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149028235 275 TRSEVVGYLGGRWDINNQMLTVLRAFPCRSRLGDPDTAATveEEIHQVLFLRGLSLVGWYHSHPHSPAAPSLQDIDAQME 354
Cdd:cd07767   12 NGKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWFL--MYLDFKKLNAGLRIVGWYHTHPKPSCFLSPNDLATHEL 89

                 ....*...
gi 149028235 355 YQLRLQGS 362
Cdd:cd07767   90 FQRYFPEK 97

Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex; BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-containing complex and is essential for the integrity of the complex. There are studies suggesting that MERIT40/NBA1 ties BRCA1 complex integrity, DSB recognition, and ubiquitin chain activities to the DNA damage response. It has also been shown that BRCA1-containing complex resembles the lid complex of the 26S proteasome.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149028235 258 VAVSSNVLFLLDFHCHLT-RSEVVGYLGGRWDINNQMLTVLR---AFPCRSRLGD---------PD--TAATVEEEIHQV 322
Cdd:cd08068    4 VHLSADVYLVCLTHALSTeKEEVMGLLIGEIEVSKKGEEVAIvhiSAVIILRRSDkrkdrveisPEqlSAASTEAERLTE 83

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 149028235 323 LFLRGLSLVGWYHSHPHSPAAPSLQDIDAQMEYQL 357
Cdd:cd08068   84 ETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQM 118

Mov34/MPN/PAD-1 family; AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, all of which are components of ESCRT-III, suggested to be required for EGFR down-regulation. The function of AMSH-LP has not been elucidated; however, it exhibits two fundamentally distinct features from AMSH: first, there is a substitution in the critical amino acid residue in the SH3-binding motif (SBM) in the human AMSH-LP, but not in its mouse ortholog, and lacks STAM-binding ability; second, AMSH-LP lacks the ability to interact with CHMP proteins. It is therefore likely that AMSH and AMSH-LP play different roles on early endosomes.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 149028235 307 GDPDTAATV-EEEIHQVLFLRGLSLVGWYHSHPHSPAAPSLQDIDAQMEYQLRLQGSnngfqpcLALLCSPYY 378
Cdd:cd08066   53 GTSDSCQTTnEEELFDFQDQHDLITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEA-------IAIVCAPKY 118