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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 186530504  178 FETLLTIVRNVAKKPDEERYRRIRLKNRLFHERVGRYKEGIEFMELCGFKRVEGSEFLSLS 238
Cdd:pfam09409   8 LETLLKYLNNILSNPNEEKYRKIRLSNKAFQEKVLPLEGALELLLAIGFEKEDEEEFLLLE 68

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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186530504 167 KDEDPRITRRVFETLLTIVRNVAKKPDEERYRRIRLKNRLFHERVGRYKEGIEFMELCGFKRV-EGSEFLSLSKRDSDIN 245
Cdd:cd09212    6 SNNDLEAFKEALKTLLKILDNILSNPTEEKYRRIRLSNKAFQEKVLPVPGGLELLLALGFVEEtESGESFLVLPDDADVD 85

                         90
                 ....*....|.
gi 186530504 246 RLRDAAFLLNS 256
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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 186530504 159 LRSLRRNHKDEDPRITRRVFETLLTIVRNVAKKPDEERYRRIRLKNRLFHERVGRYKEGIEFMELCGFKRVEGSEF 234
Cdd:cd10462    1 CNNLKKEYKDTDKQGLMTCLNTLRTYISNAHDHPLEEKYKKIRKENKAFVSKVLIFEGAIEILLACGFEDTGDFLF 76

PNGase/UBA or UBX (PUB) domain of the Wss1p-like metalloprotease (WLM) family; 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. WLM domains are found mostly in plant proteins, belonging to the Zincin-like superfamily of Zn-dependent peptidases that are linked to the ubiquitin signaling pathway through its fusion with the ubiquitin-binding PUB, ubiquitin-like, and Little Finger domains. More specifically, genetic evidence implicates the WLM family in de-SUMOylation.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 186530504 177 VFETLLTIVRNVAKKPDEERYRRIRLKNRLFHERVGRYKEGIEFMELCGFKR--VEGSEFLSLSKRD 241
Cdd:cd10463   17 ALQTLFKILGNAIEHPNEDKFRRLRKSNPAFQRRVARFPGAVELLLAAGFAEegVSGPDTYLLLRND 83

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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186530504 179 ETLLTIVRNVAKKPDEERYRRIRLKNRLFHERVGRYKEGIEFMELCGFkrVEGSEFLSLSkRDSDINRLRDAAFLLNSAS 258
Cdd:cd10459   17 EALLTYANNILRNPNDPKYRSIRLDNPVFSTKLLPARGAIECLFEMGF--VEDEDRLFLP-RNASLEKLQDLRDLLAAER 93