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 66472548   7 VLALCENTTEVFLDVSKLLITYADNILRNPNEEKYRSIRIGNPTFSTKLLPVKGAVECLFEMGFEEAETHLVFPRSASVE 86
Cdd:cd10459   1 VRLLEENSEDVFLEASEALLTYANNILRNPNDPKYRSIRLDNPVFSTKLLPARGAIECLFEMGFVEDEDRLFLPRNASLE 80

                        90
                ....*....|...
gi 66472548  87 KLRQVRETIAAER 99
Cdd:cd10459  81 KLQDLRDLLAAER 93

Rad4 transglutaminase-like domain;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 66472548   323 WTEVYSQSQRRWIHCDPC------ENACDKPLLYEvgwgKK---LSYILAFSKDQVA-DVTWRYS 377
Cdd:pfam03835  39 WVEVFNPETKKWISVDPLvlktieLKSKFEPRIAE----KAlnvMTYVVAFDSDGGAkDVTRRYC 99

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 66472548   7 VLALCENTTEVFLDVSKLLITYADNILRNPNEEKYRSIRIGNPTFSTKLLPVKGAVECLFEMGFEEAETHLVFPRSASVE 86
Cdd:cd10459   1 VRLLEENSEDVFLEASEALLTYANNILRNPNDPKYRSIRLDNPVFSTKLLPARGAIECLFEMGFVEDEDRLFLPRNASLE 80

                        90
                ....*....|...
gi 66472548  87 KLRQVRETIAAER 99
Cdd:cd10459  81 KLQDLRDLLAAER 93

Transglutaminase-like superfamily; This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologs of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66472548   262 RVENHFCH--TCQLSTRFPRYNNPEKLLETRKGRCGEWANCFTLLCRALGLEARYIWDSTD----------HVWTEVYSQ 329
Cdd:pfam01841  20 AIYDYVRKniTYDLPGRSPGDGDAEEFLFTGKGDCEDFASLFVALLRALGIPARYVTGYLRgpdtvrggdaHAWVEVYLP 99

                          90
                  ....*....|
gi 66472548   330 sQRRWIHCDP 339
Cdd:pfam01841 100 -GYGWVPVDP 108

domain in protein kinases, N-glycanases and other nuclear proteins;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 66472548     21 VSKLLITYADNILRNPNEEKyrsiriGNPTFSTKLLPVKGAVECLFEMGFEEAETHLVF 79
Cdd:smart00580   1 SVRDLLRALRNILHHPREEK------GNPAIKERLGPVPGGFELYFTVGFPRLLISEVY 53

Transglutaminase-like enzyme, putative cysteine protease [Posttranslational modification, protein turnover, chaperones];

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 66472548 282 NPEKLLETRKGRCGEWANCFTLLCRALGLEARYI------------WDSTD-HVWTEVYSQsQRRWIHCDP 339
Cdd:COG1305 104 TALETLERRRGVCRDFAHLLVALLRALGIPARYVsgylpgepppggGRADDaHAWVEVYLP-GAGWVPFDP 173

DNA repair protein rad4; All proteins in this family for which functions are known are involved in targeting nucleotide excision repair to specific regions of the genome.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66472548   323 WTEVYSQSQRRWIHCD-------PCENACDKPLlyevgwGKKLSYILAFSKDQ-VADVTWRYsCKHPEVLSRRTQVQ--- 391
Cdd:TIGR00605 373 WVEVFIEQEEKWVCVDavhsgvvPKGVTCFEPA------TLMMTYVFAYDRDGyVKDVTRRY-CDQWSTKVRKRRVEkad 445

                          90       100       110
                  ....*....|....*....|....*....|..
gi 66472548   392 --ETWLLHMLNKLnAERQQFLGAERKQQLLQR 421
Cdd:TIGR00605 446 fgETWFRPIFGAL-HKRKRTIDDIEDQEFLRR 476

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 66472548   7 VLALCENTTEVFLDVSKLLITYADNILRNPNEEKYRSIRIGNPTFSTKLLPVKGAVECLFEMGFEEAETHLVFPRSASVE 86
Cdd:cd10459   1 VRLLEENSEDVFLEASEALLTYANNILRNPNDPKYRSIRLDNPVFSTKLLPARGAIECLFEMGFVEDEDRLFLPRNASLE 80

                        90
                ....*....|...
gi 66472548  87 KLRQVRETIAAER 99
Cdd:cd10459  81 KLQDLRDLLAAER 93

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 66472548   8 LALCENTTEVFLDVSKLLITYADNILRNPNEEKYRSIRIGNPTFSTKLLPVKGAVECLFEMGFEEA----ETHLVFPRSA 83
Cdd:cd09212   3 ALRSNNDLEAFKEALKTLLKILDNILSNPTEEKYRRIRLSNKAFQEKVLPVPGGLELLLALGFVEEtesgESFLVLPDDA 82

                        90
                ....*....|....
gi 66472548  84 SVEKLRQVRETIAA 97
Cdd:cd09212  83 DVDLLKDAKAALEE 96

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 66472548  10 LCENTTEVFLDVsKLLITYADNILRNPNEEKYRSIRIGNPTFSTKLLPVKGAVECLFEMGFEE--------AETHLVFPR 81
Cdd:cd10460   7 LNKDREKVEECV-DTLCKYLENIIDHPDEEKYRKIRLSNKVFQEKVLPVEGALEFLEAAGFEEktlpeqedEEDFLVLSE 85

                        90
                ....*....|..
gi 66472548  82 SASVEKLRQVRE 93
Cdd:cd10460  86 ECDIDSLELAKD 97

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 66472548  25 LITYADNILRNPNEEKYRSIRIGNPTFSTKLLPVKGAVECLFEMGFEEAET--HLVFPRsasvEKLRQVRETIAAE 98
Cdd:cd10461  22 LLTYLGNVAKNPDEEKFRRIRLTNAAFQERVGALRGGIEFLELCGFERDEGdeALVLPR----DKVDMALLNTAGA 93

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
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 66472548  23 KLLITYADNILRNPNEEKYRSIRIGNPTFSTKLLPVKGAVECLFEMGFEEAETHLVFPRS 82
Cdd:cd10462  21 NTLRTYISNAHDHPLEEKYKKIRKENKAFVSKVLIFEGAIEILLACGFEDTGDFLFIINK 80

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 66472548  24 LLITYADNILRNPNEEKYRSIRIGNPTFSTKLLPVKGAVECLFEMGFEE 72
Cdd:cd10463  20 TLFKILGNAIEHPNEDKFRRLRKSNPAFQRRVARFPGAVELLLAAGFAE 68

Rad4 transglutaminase-like domain;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 66472548   323 WTEVYSQSQRRWIHCDPC------ENACDKPLLYEvgwgKK---LSYILAFSKDQVA-DVTWRYS 377
Cdd:pfam03835  39 WVEVFNPETKKWISVDPLvlktieLKSKFEPRIAE----KAlnvMTYVVAFDSDGGAkDVTRRYC 99

PNGase/UBA or UBX (PUB) domain of the RNF31 (or HOIP) protein; This PUB domain is found in the p97 adaptor protein RNF31 (RING finger protein 31). 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 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. RNF31 functions in a complex with another RING-finger protein (HOIL-IL), displaying E3 ubiquitin-protein ligase activity, and forming linear ubiquitin chain assembly complex (LUBAC) through linkages between the N- and C-termini of ubiquitin. LUBAC has been shown to activate the NF-kappaB pathway.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 66472548  28 YADNILrNPNEEKY-RSIRIGNPTFSTKLLPVKGAVECLFEMGF-EEAETHLVFPRSAS---VEKLRQV 91
Cdd:cd10464  30 YGRNLL-SPGRPKFwRSVKFSNPVFRTKVDAVQGGRNVLSLYGYtESQPDGLSFPDDVEepdISKVAKV 97