PNGase/UBA or UBX (PUB) domain of plant Ubiquitin-associated (UBA) domain containing proteins; The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover. This family contains only plant UBA domain-containing proteins.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79532073 209 LRSLRRNHKDeDPRITRRVFETLLTIVRNVAKKPDEERYRRIRLKNRLFHERVGRYKEGIEFMELCGFKRVEGSEFLSLS 288
Cdd:cd10461   1 LVDLKKAHKD-DPDAVKTAFQTLLTYLGNVAKNPDEEKFRRIRLTNAAFQERVGALRGGIEFLELCGFERDEGDEALVLP 79

                        90       100
                ....*....|....*....|....*...
gi 79532073 289 KRDSDINRLRDAAFLLNSASANPFFGLL 316
Cdd:cd10461  80 RDKVDMALLNTAGAELNSAINNPFFGVL 107

PNGase/UBA or UBX (PUB) domain of plant Ubiquitin-associated (UBA) domain containing proteins; The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover. This family contains only plant UBA domain-containing proteins.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79532073 209 LRSLRRNHKDeDPRITRRVFETLLTIVRNVAKKPDEERYRRIRLKNRLFHERVGRYKEGIEFMELCGFKRVEGSEFLSLS 288
Cdd:cd10461   1 LVDLKKAHKD-DPDAVKTAFQTLLTYLGNVAKNPDEEKFRRIRLTNAAFQERVGALRGGIEFLELCGFERDEGDEALVLP 79

                        90       100
                ....*....|....*....|....*...
gi 79532073 289 KRDSDINRLRDAAFLLNSASANPFFGLL 316
Cdd:cd10461  80 RDKVDMALLNTAGAELNSAINNPFFGVL 107

PUB domain; The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain. This domain is also found on other proteins linked to the ubiquitin-proteasome system.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 79532073   228 FETLLTIVRNVAKKPDEERYRRIRLKNRLFHERVGRYKEGIEFMELCGFKRVEGSEFLSLS 288
Cdd:pfam09409   8 LETLLKYLNNILSNPNEEKYRKIRLSNKAFQEKVLPLEGALELLLAIGFEKEDEEEFLLLE 68

PNGase/UBA or UBX (PUB) domain of plant Ubiquitin-associated (UBA) domain containing proteins; The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover. This family contains only plant UBA domain-containing proteins.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79532073 209 LRSLRRNHKDeDPRITRRVFETLLTIVRNVAKKPDEERYRRIRLKNRLFHERVGRYKEGIEFMELCGFKRVEGSEFLSLS 288
Cdd:cd10461   1 LVDLKKAHKD-DPDAVKTAFQTLLTYLGNVAKNPDEEKFRRIRLTNAAFQERVGALRGGIEFLELCGFERDEGDEALVLP 79

                        90       100
                ....*....|....*....|....*...
gi 79532073 289 KRDSDINRLRDAAFLLNSASANPFFGLL 316
Cdd:cd10461  80 RDKVDMALLNTAGAELNSAINNPFFGVL 107

PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins; The PUB domain is found in p97 adaptor proteins such as PNGase, UBXD1 (UBX domain-containing protein 1), and RNF31 (RING finger protein 31). It functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The p97, a type II AAA+ ATPase, is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The PUB domain in UBX-domain protein 1 (UBXD1), which is widely expressed in higher eukaryotes (except for fungi) and which is involved in substrate recruitment to p97, interacts strongly with the C-terminus of p97. Peptide:N-glycanase (PNGase), a deglycosylating enzyme that functions in proteasome-dependent degradation of misfolded glycoproteins which are translocated from the endoplasmic reticulum (ER) to the cytosol during ERAD, associates with the ubiquitin-proteasome system proteins mediated by the N-terminal PUB domain. PNGase is present in all eukaryotic organisms; however, the yeast PNGase ortholog does not contain the PUB domain. The RNF31 protein, also known as HOIP or Zibra, contains an N-terminal PUB domain similar to those in PNGase and UBXD1, suggesting its association with p97.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79532073 217 KDEDPRITRRVFETLLTIVRNVAKKPDEERYRRIRLKNRLFHERVGRYKEGIEFMELCGFKRV-EGSEFLSLSKRDSDIN 295
Cdd:cd09212   6 SNNDLEAFKEALKTLLKILDNILSNPTEEKYRRIRLSNKAFQEKVLPVPGGLELLLALGFVEEtESGESFLVLPDDADVD 85

                        90
                ....*....|.
gi 79532073 296 RLRDAAFLLNS 306
Cdd:cd09212  86 LLKDAKAALEE 96

PNGase/UBA or UBX (PUB) domain of Ubiquitin-associated (UBA) domain containing proteins; The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 79532073 209 LRSLRRNHKDEDPRITRRVFETLLTIVRNVAKKPDEERYRRIRLKNRLFHERVGRYKEGIEFMELCGFKRVEGSEF 284
Cdd:cd10462   1 CNNLKKEYKDTDKQGLMTCLNTLRTYISNAHDHPLEEKYKKIRKENKAFVSKVLIFEGAIEILLACGFEDTGDFLF 76

PNGase/UBA or UBX (PUB) domain of UBXD1; This PUB domain is found in p97 adaptor protein UBXD1 (UBX domain-containing protein 1, also called UBXD6). It functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The PUB domain in UBX-domain protein 1 (UBXD1), which is widely expressed in higher eukaryotes, except for fungi, and which is involved in substrate recruitment to p97, interacts strongly with the C-terminus of p97. UBXD1 also interacts with HRD1 and HERP, both components of the ERAD pathway, via p97. It is possibly involved in aggresome formation; aggresomes are perinuclear compartments that contain misfolded proteins colocalized with centrosome markers.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79532073 229 ETLLTIVRNVAKKPDEERYRRIRLKNRLFHERVGRYKEGIEFMELCGFKRVEGS------EFLSLSKrDSDINRLRDAAF 302
Cdd:cd10460  19 DTLCKYLENIIDHPDEEKYRKIRLSNKVFQEKVLPVEGALEFLEAAGFEEKTLPeqedeeDFLVLSE-ECDIDSLELAKD 97

                ....*
gi 79532073 303 LLNSA 307
Cdd:cd10460  98 LLQSL 102

UBA1 domain found in Saccharomyces cerevisiae ubiquitin carboxyl-terminal hydrolase 14 (scUBP14) and similar proteins; scUBP14, also called deubiquitinating enzyme 14, glucose-induced degradation protein 6, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is the yeast ortholog of human Isopeptidase T (USP5), a deubiquitinating enzyme known to bind the 29-linked polyubiquitin chains. scUBP14 has been identified as a K29-linked polyubiquitin binding protein as well. It is involved in K29-linked polyubiquitin metabolism by binding to the 29-linked Ub4 resin and serving as an internal positive control in budding yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain.

                        10        20        30
                ....*....|....*....|....*....|....*..
gi 79532073  16 LLKELEDMGFSMARAAWALHHSGNSSLEAAVNWIIDH 52
Cdd:cd14296   3 AVSQLMSMGFSENAAKRALYYTGNSSVEAAMNWLFEH 39

UBA1 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 (spUBP14) and similar proteins; spUBP14, also called deubiquitinating enzyme 14, UBA domain-containing protein 2, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, functions as a deubiquitinating enzyme that is involved in protein degradation in fission yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 79532073  13 NHGLLKELEDMGFSMARAAWALHHSGNSSLEAAVNWIIDH 52
Cdd:cd14385   1 NAEALAQLLGMGFPEVRCKKALLATGNSDAEAAMNWLFEH 40

UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins; VP13D is a chorea-acanthocytosis (CHAC)-similar protein encoded by gene VPS13D. it contains two putative domains, ubiquitin-associated (UBA) domain and lectin domain of ricin B chain profile (ricin-B-lectin), suggesting it may interact with, and be involved in the trafficking of, proteins modified with ubiquitin and/or carbohydrate molecules. Further investigation is required.

                        10        20        30
                ....*....|....*....|....*....|....*.
gi 79532073  17 LKELEDMGFSMARAAWALHHSGNsSLEAAVNWIIDH 52
Cdd:cd14306   1 VAKLMELGFPEEDCIRALRACGG-NVEEAANWLLEN 35

UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5); UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin (Ub)-binding sites including an N-terminal zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. ZnF domain binds the proximal ubiquitin. UBP domain forms the active site. UBA domains are involved in binding linear or K48-linked polyubiquitin. This model corresponds to the UBA1 domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 79532073  12 VNHGLLKELEDMGFSMARAAWALHHSGNSSLEAAVNWIIDHENESQF 58
Cdd:cd14383   2 LDESVIIQLVEMGFPMDACRKAVYYTGNSGAEAAMNWVMSHMDDPDF 48

PNGase/UBA or UBX (PUB) domain of the P97 adaptor protein Peptide:N-glycanase (PNGase); This PUB (PNGase/UBA or UBX) domain is found in the p97 adaptor protein PNGase (Peptide:N-glycanase). The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. Peptide:N-glycanase (PNGase), a deglycosylating enzyme that functions in proteasome-dependent degradation of misfolded glycoproteins which are translocated from the endoplasmic reticulum (ER) to the cytosol during ERAD, associates with the ubiquitin-proteasome system proteins mediated by the N-terminal PUB domain. PNGase is present in all eukaryotic organisms; however, the yeast PNGase ortholog does not contain the PUB domain. The mammalian PNGase binds a considerable number of proteins via its PUB domain; these include ERAD E3 enzyme, the autocrine motility factor receptor (AMFR or gp78), SAKS and Derlin-1.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79532073 229 ETLLTIVRNVAKKPDEERYRRIRLKNRLFHERVGRYKEGIEFMELCGFkrVEGSEFLSLSkRDSDINRLRDAAFLLNSAS 308
Cdd:cd10459  17 EALLTYANNILRNPNDPKYRSIRLDNPVFSTKLLPARGAIECLFEMGF--VEDEDRLFLP-RNASLEKLQDLRDLLAAER 93

UBA domain found in ubiquitin-associated and SH3 domain-containing protein B (UBS3B) and similar proteins; UBS3B, or Cbl-interacting protein p70, suppressor of T-cell receptor signaling 1 (Sts-1), T-cell ubiquitin ligand 2 (TULA-2), or tyrosine-protein phosphatase STS1/TULA2, is ubiquitously expressed in mammalian tissues in a variety of cell types. It exhibits high phosphatase activity, but demonstrates no proapoptotic activity. It negatively regulates the tyrosine kinase Zap-70 activation and T cell receptor (TCR) signaling pathways that modulate T cell activation. Moreover, UBS3B acts as a Cbl- and ubiquitin-interacting protein that inhibits endocytosis of epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor.

                        10        20        30
                ....*....|....*....|....*....|....*.
gi 79532073  17 LKELEDMGFSMARAAWALHHSGNSSLEAAVNWIIDH 52
Cdd:cd14301   3 LEVLLSMGFPKHRAEKALAATGGRSVQLASDWLLSH 38

UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13); UBP13, also called deubiquitinating enzyme 13, Isopeptidase T-3 (isoT3), ubiquitin thioesterase 13, or ubiquitin-specific-processing protease 13, is an ortholog of UBP5 implicated in catalyzing hydrolysis of various ubiquitin (Ub)-chains. It contains a zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. Due to the non-activating catalysis for K63-polyubiquitin chains, UBP13 may function differently from USP5 in cellular deubiquitination processes. Moreover, the zinc finger (ZnF) domain of USP13 cannot bind to Ub. Its tandem UBA domains can bind with different types of diUb but preferentially with K63-linked.USP13 can also regulate the protein level of CD3delta in cells via its UBA domains. This model corresponds to the UBA1 domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 79532073  11 EVNHGLLKELEDMGFSMARAAWALHHSGNSSLEAAVNWIIDHENESQF 58
Cdd:cd14384   1 DIDESSVMQLAEMGFPLEACRKAVYYTGNMGAEVAFNWIIAHMEEPDF 48

UBA1 domain found in Kip1 ubiquitination-promoting complex protein 2 (KPC2) and similar proteins; KPC2, also called ubiquitin-associated domain-containing protein 1 (UBAC1), or glialblastoma cell differentiation-related protein 1, is one of two subunits of Kip1 ubiquitination-promoting complex (KPC), a novel E3 ubiquitin-protein ligase that also contains KPC1 subunit and regulates the ubiquitin-dependent degradation of the cyclin-dependent kinase (CDK) inhibitor p27 at G1 phase. KPC2 contains a ubiquitin-like (UBL) domain and two ubiquitin-associated (UBA) domains. This model corresponds to the UBA1 domain.

                        10        20        30
                ....*....|....*....|....*....|....*..
gi 79532073  17 LKELEDMGFSMARAAWALHHSGNsSLEAAVNWIIDHE 53
Cdd:cd14303   6 LKQLTEMGFPEARATKALLLNRM-SPTQAMEWLLEHE 41

UBA domain found in eukaryotic E3 ubiquitin-protein ligase HUWE1 and similar proteins; HUWE1, also called ARF-binding protein 1 (ARF-BP1), HECT, UBA and WWE domain-containing protein 1, homologous to E6AP carboxyl terminus homologs protein 9 (HectH9), large structure of UREB1 (LASU1), Mcl-1 ubiquitin ligase E3 (Mule), upstream regulatory element-binding protein 1 (URE-B1), or URE-binding protein 1, may function as a ubiquitin-protein ligase that involves in the ubiquitination cascade that targets specific substrate proteins in proteolysis. It can ubiquitylate DNA polymerase beta (Pol beta), the major BER DNA polymerase and modulates base excision repair (BER). HUWE1 also acts as a critical mediator of both the p53-independent and p53-dependent tumor suppressor functions of ARF tumor suppressor in p53 regulation. Moreover, HUWE1 is both required and sufficient for the polyubiquitination of Mcl-1, an anti-apoptotic Bcl-2 family member involving in DNA damage-induced apoptosis. Furthermore, HUWE1 plays an important role in the regulation of Cdc6 stability after DNA damage. In addition, HUWE1 works as a partner of N-Myc oncoprotein in neural cells. It ubiquitinates N-Myc and primes it for proteasomal-mediated degradation. HUWE1 contains a ubiquitin-associated (UBA) domain, a WWE domain, and a Bcl-2 homology region 3 (BH3) domain at the N-terminus and a HECT domain at the C-terminus. WWE domain plays a role in the regulation of specific protein-protein interactions in a ubiquitin conjugation system. BH3 domain is responsible for the specific binding to Mcl-1. HECT domain involves in the inhibition of the transcriptional activity of p53 via a ubiquitin-dependent degradation pathway. It also controls neural differentiation and proliferation by destabilizing the N-Myc oncoprotein.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 79532073  12 VNHGLLKELEDMGFSMARAAWALHHSgnSSLEAAVNWIIDH 52
Cdd:cd14288   1 VNEAHLQQLMDMGFTREHALEALLHT--STLEQATEYLLTH 39