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Conserved domains on  [gi|18379271|ref|NP_565271|]
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plant UBX domain-containing protein 2 [Arabidopsis thaliana]

Protein Classification

PUB domain-containing protein( domain architecture ID 12964531)

PUB domain-containing protein may bind AAA ATPase domains; also contains a UBX (ubiquitin regulatory domain X) domain

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
UBX_UBXN6 cd16119
Ubiquitin regulatory domain X (UBX) found in UBX domain protein 6 (UBXN6) and similar proteins; ...
 354-434 3.50e-25

Ubiquitin regulatory domain X (UBX) found in UBX domain protein 6 (UBXN6) and similar proteins; UBXN6, also termed UBX domain-containing protein 1 (UBXD1), and UBXDC2, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN6 acts as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. Unlike other p97 cofactors that binds the N-domain of p97 through their UBX domain, UBXN6 binds p97 in two regions, at the p97 C terminus via a PUB domain and at the p97 N-domain with a short linear interaction motif termed VIM. Its UBX domain is not functional for the binding of p97. The UBXN6-p97 complex regulates the endolysosomal sorting of ubiquitylated plasma membrane protein caveolin-1 (CAV1), as well as the trafficking of ERGIC-53-containing vesicles by controlling the interaction of transport factors with the cytoplasmic tail of ERGIC-53. In addition, UBXN6 is a regulatory component of endoplasmic reticulum-associated degradation (ERAD) that may modulate the adaptor binding to p97.


:

Pssm-ID: 340536  Cd Length: 73  Bit Score: 98.02  E-value: 3.50e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18379271 354 SMIRVQFPDGVVLQGVFAPWEPTFALYEFVSSALKEPSLQFELLDPVLVKRRViphtpapgqKPITLEDEELVPSALIRF 433
Cdd:cd16119   2 TLIRVRFPDGVILQGTFYAREKLSAVREFVREALANDWLPFELVTPGGQKLTD---------EDATLAELGLVPAALLNF 72


                .
gi 18379271 434 R 434
Cdd:cd16119  73 S 73
PUB cd09212
PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins; The PUB domain is found in p97 adaptor ...
 175-264 7.50e-21

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.


:

Pssm-ID: 198416  Cd Length: 96  Bit Score: 87.05  E-value: 7.50e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18379271 175 SGKPSESSIDVLLRLFKNIVKEPENAKFRKVRMSNAKIKEAIGDVAGGVELLELVGFELKEENDEIWAVMDVPSEEQsiL 254
Cdd:cd09212   9 DLEAFKEALKTLLKILDNILSNPTEEKYRRIRLSNKAFQEKVLPVPGGLELLLALGFVEETESGESFLVLPDDADVD--L 86

                        90
                ....*....|
gi 18379271 255 INKVVGYLEK 264
Cdd:cd09212  87 LKDAKAALEE 96
 
Name Accession Description Interval E-value
UBX_UBXN6 cd16119
Ubiquitin regulatory domain X (UBX) found in UBX domain protein 6 (UBXN6) and similar proteins; ...
 354-434 3.50e-25

Ubiquitin regulatory domain X (UBX) found in UBX domain protein 6 (UBXN6) and similar proteins; UBXN6, also termed UBX domain-containing protein 1 (UBXD1), and UBXDC2, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN6 acts as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. Unlike other p97 cofactors that binds the N-domain of p97 through their UBX domain, UBXN6 binds p97 in two regions, at the p97 C terminus via a PUB domain and at the p97 N-domain with a short linear interaction motif termed VIM. Its UBX domain is not functional for the binding of p97. The UBXN6-p97 complex regulates the endolysosomal sorting of ubiquitylated plasma membrane protein caveolin-1 (CAV1), as well as the trafficking of ERGIC-53-containing vesicles by controlling the interaction of transport factors with the cytoplasmic tail of ERGIC-53. In addition, UBXN6 is a regulatory component of endoplasmic reticulum-associated degradation (ERAD) that may modulate the adaptor binding to p97.


Pssm-ID: 340536  Cd Length: 73  Bit Score: 98.02  E-value: 3.50e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18379271 354 SMIRVQFPDGVVLQGVFAPWEPTFALYEFVSSALKEPSLQFELLDPVLVKRRViphtpapgqKPITLEDEELVPSALIRF 433
Cdd:cd16119   2 TLIRVRFPDGVILQGTFYAREKLSAVREFVREALANDWLPFELVTPGGQKLTD---------EDATLAELGLVPAALLNF 72


                .
gi 18379271 434 R 434
Cdd:cd16119  73 S 73
PUB cd09212
PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins; The PUB domain is found in p97 adaptor ...
 175-264 7.50e-21

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.


Pssm-ID: 198416  Cd Length: 96  Bit Score: 87.05  E-value: 7.50e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18379271 175 SGKPSESSIDVLLRLFKNIVKEPENAKFRKVRMSNAKIKEAIGDVAGGVELLELVGFELKEENDEIWAVMDVPSEEQsiL 254
Cdd:cd09212   9 DLEAFKEALKTLLKILDNILSNPTEEKYRRIRLSNKAFQEKVLPVPGGLELLLALGFVEETESGESFLVLPDDADVD--L 86

                        90
                ....*....|
gi 18379271 255 INKVVGYLEK 264
Cdd:cd09212  87 LKDAKAALEE 96
PUB pfam09409
PUB domain; The PUB (also known as PUG) domain is found in peptide N-glycanase where it ...
 177-251 3.32e-16

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.


Pssm-ID: 462790  Cd Length: 80  Bit Score: 73.07  E-value: 3.32e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18379271   177 KPSESSIDVLLRLFKNIVKEPENAKFRKVRMSNAKIKEAIGDVAGGVELLELVGFELKEENDeiWAVMDVPSEEQ 251
Cdd:pfam09409   2 EKVKEALETLLKYLNNILSNPNEEKYRKIRLSNKAFQEKVLPLEGALELLLAIGFEKEDEEE--FLLLEEESLKQ 74
PUG smart00580
domain in protein kinases, N-glycanases and other nuclear proteins;
182-248 2.46e-11

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


Pssm-ID: 197798  Cd Length: 57  Bit Score: 58.85  E-value: 2.46e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18379271    182 SIDVLLRLFKNIVKEPENAKfrkvrmSNAKIKEAIGDVAGGVELLELVGFELKeendEIWAVMDVPS 248
Cdd:smart00580   1 SVRDLLRALRNILHHPREEK------GNPAIKERLGPVPGGFELYFTVGFPRL----LISEVYTLPK 57
UBX pfam00789
UBX domain; This domain is present in ubiquitin-regulatory proteins and is a general ...
 356-435 1.24e-03

UBX domain; This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module.


Pssm-ID: 395637 [Multi-domain]  Cd Length: 80  Bit Score: 37.66  E-value: 1.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18379271   356 IRVQFPDGVVLQGVFAPWEPTFALYEFVSSALKEPSLQFELLDPvlVKRRVIphtpAPGQKPITLEDEELVPSALIRFRP 435
Cdd:pfam00789   7 LQIRLPDGSRLVRRFNSSDKLQTVYDFVDSNRYDDLEPFSLNTP--FPRRPL----TDLDYSKTLKEAGLLPNSTLVLEP 80
UBX smart00166
Domain present in ubiquitin-regulatory proteins; Present in FAF1 and Shp1p.
 353-429 1.84e-03

Domain present in ubiquitin-regulatory proteins; Present in FAF1 and Shp1p.


Pssm-ID: 197552 [Multi-domain]  Cd Length: 77  Bit Score: 36.90  E-value: 1.84e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18379271    353 RSMIRVQFPDGVVLQGVFAPWEPTFALYEFVSSALKEPSLQFELLDPvlVKRRVIphTPAPGQKpiTLEDEELVPSA 429
Cdd:smart00166   1 VCRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALGDGNDPFTLNSP--FPRRTF--TKDDYSK--KLLELALLPSS 71
 
Name Accession Description Interval E-value
UBX_UBXN6 cd16119
Ubiquitin regulatory domain X (UBX) found in UBX domain protein 6 (UBXN6) and similar proteins; ...
 354-434 3.50e-25

Ubiquitin regulatory domain X (UBX) found in UBX domain protein 6 (UBXN6) and similar proteins; UBXN6, also termed UBX domain-containing protein 1 (UBXD1), and UBXDC2, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN6 acts as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. Unlike other p97 cofactors that binds the N-domain of p97 through their UBX domain, UBXN6 binds p97 in two regions, at the p97 C terminus via a PUB domain and at the p97 N-domain with a short linear interaction motif termed VIM. Its UBX domain is not functional for the binding of p97. The UBXN6-p97 complex regulates the endolysosomal sorting of ubiquitylated plasma membrane protein caveolin-1 (CAV1), as well as the trafficking of ERGIC-53-containing vesicles by controlling the interaction of transport factors with the cytoplasmic tail of ERGIC-53. In addition, UBXN6 is a regulatory component of endoplasmic reticulum-associated degradation (ERAD) that may modulate the adaptor binding to p97.


Pssm-ID: 340536  Cd Length: 73  Bit Score: 98.02  E-value: 3.50e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18379271 354 SMIRVQFPDGVVLQGVFAPWEPTFALYEFVSSALKEPSLQFELLDPVLVKRRViphtpapgqKPITLEDEELVPSALIRF 433
Cdd:cd16119   2 TLIRVRFPDGVILQGTFYAREKLSAVREFVREALANDWLPFELVTPGGQKLTD---------EDATLAELGLVPAALLNF 72


                .
gi 18379271 434 R 434
Cdd:cd16119  73 S 73
PUB cd09212
PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins; The PUB domain is found in p97 adaptor ...
 175-264 7.50e-21

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.


Pssm-ID: 198416  Cd Length: 96  Bit Score: 87.05  E-value: 7.50e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18379271 175 SGKPSESSIDVLLRLFKNIVKEPENAKFRKVRMSNAKIKEAIGDVAGGVELLELVGFELKEENDEIWAVMDVPSEEQsiL 254
Cdd:cd09212   9 DLEAFKEALKTLLKILDNILSNPTEEKYRRIRLSNKAFQEKVLPVPGGLELLLALGFVEETESGESFLVLPDDADVD--L 86

                        90
                ....*....|
gi 18379271 255 INKVVGYLEK 264
Cdd:cd09212  87 LKDAKAALEE 96
UBX2_UBXN9 cd16118
Ubiquitin regulatory domain X (UBX) 2 found in UBX domain protein 9 (UBXN9, UBXD9, or ASPSCR1) ...
 356-435 3.58e-17

Ubiquitin regulatory domain X (UBX) 2 found in UBX domain protein 9 (UBXN9, UBXD9, or ASPSCR1) and similar proteins; UBXN9, also termed tether containing UBX domain for GLUT4 (TUG), or alveolar soft part sarcoma chromosomal region candidate gene 1 protein (ASPSCR1), or alveolar soft part sarcoma locus (ASPL), or renal papillary cell carcinoma protein 17 (RCC17), belongs to the UBXD family of proteins that contains two ubiquitin regulatory domains X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, UBXN9 contains an N-terminal ubiquitin-like (Ubl) domain. UBXN9 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. However, high-affinity interacting protein ASPL efficiently promotes p97 hexamer disassembly, resulting in the formation of stable p97:ASPL heterotetramers; the extended UBX domain (eUBX) in ASPL is critical for p97 hexamer disassembly and facilitates the assembly of p97:ASPL heterotetramers.UBXN9 is involved in insulin-stimulated redistribution of the glucose transporter GLUT4, assembly of the Golgi apparatus. In addition to GLUT4, UBXN9 also controls vesicle translocation by interacting with insulin-regulated aminopeptidase (IRAP), a transmembrane aminopeptidase. UBXN9 and its budding yeast ortholog, Ubx4p, are multifunctional proteins that share some, but not all functions. Yeast Ubx4p is important for endoplasmic reticulum-associated protein degradation (ERAD) but UBXN9 appears not to share this function.


Pssm-ID: 340535  Cd Length: 74  Bit Score: 75.68  E-value: 3.58e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18379271 356 IRVQFPDGVVLQGVFAPWEPTFALYEFVSSALKEPSLQFELldpvlvkrrvipHTPAPGQ----KPITLEDEELVPSALI 431
Cdd:cd16118   3 IRVQFPDRLVLQAFFRPLETVRALYDFVKSHLADPDLPFYL------------YTTPPKRvlkdKNKTLYQAGLVPAALV 70


                ....
gi 18379271 432 RFRP 435
Cdd:cd16118  71 YFGL 74
PUB pfam09409
PUB domain; The PUB (also known as PUG) domain is found in peptide N-glycanase where it ...
 177-251 3.32e-16

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.


Pssm-ID: 462790  Cd Length: 80  Bit Score: 73.07  E-value: 3.32e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18379271   177 KPSESSIDVLLRLFKNIVKEPENAKFRKVRMSNAKIKEAIGDVAGGVELLELVGFELKEENDeiWAVMDVPSEEQ 251
Cdd:pfam09409   2 EKVKEALETLLKYLNNILSNPNEEKYRKIRLSNKAFQEKVLPLEGALELLLAIGFEKEDEEE--FLLLEEESLKQ 74
PUB_WLM cd10463
PNGase/UBA or UBX (PUB) domain of the Wss1p-like metalloprotease (WLM) family; The PUB domain ...
 181-232 8.59e-12

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.


Pssm-ID: 198421  Cd Length: 96  Bit Score: 61.25  E-value: 8.59e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 18379271 181 SSIDVLLRLFKNIVKEPENAKFRKVRMSNAKIKEAIGDVAGGVELLELVGFE 232
Cdd:cd10463  16 SALQTLFKILGNAIEHPNEDKFRRLRKSNPAFQRRVARFPGAVELLLAAGFA 67
PUG smart00580
domain in protein kinases, N-glycanases and other nuclear proteins;
182-248 2.46e-11

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


Pssm-ID: 197798  Cd Length: 57  Bit Score: 58.85  E-value: 2.46e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18379271    182 SIDVLLRLFKNIVKEPENAKfrkvrmSNAKIKEAIGDVAGGVELLELVGFELKeendEIWAVMDVPS 248
Cdd:smart00580   1 SVRDLLRALRNILHHPREEK------GNPAIKERLGPVPGGFELYFTVGFPRL----LISEVYTLPK 57
PUB_UBA_plant cd10461
PNGase/UBA or UBX (PUB) domain of plant Ubiquitin-associated (UBA) domain containing proteins; ...
 185-239 5.65e-11

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.


Pssm-ID: 198419  Cd Length: 107  Bit Score: 59.37  E-value: 5.65e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 18379271 185 VLLRLFKNIVKEPENAKFRKVRMSNAKIKEAIGDVAGGVELLELVGFElKEENDE 239
Cdd:cd10461  21 TLLTYLGNVAKNPDEEKFRRIRLTNAAFQERVGALRGGIEFLELCGFE-RDEGDE 74
PUB_UBXD1 cd10460
PNGase/UBA or UBX (PUB) domain of UBXD1; This PUB domain is found in p97 adaptor protein ...
 180-253 1.15e-09

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.


Pssm-ID: 198418  Cd Length: 102  Bit Score: 55.33  E-value: 1.15e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18379271 180 ESSIDVLLRLFKNIVKEPENAKFRKVRMSNAKIKEAIGDVAGGVELLELVGFELK----EENDEIWAVMDVPSEEQSI 253
Cdd:cd10460  15 EECVDTLCKYLENIIDHPDEEKYRKIRLSNKVFQEKVLPVEGALEFLEAAGFEEKtlpeQEDEEDFLVLSEECDIDSL 92
UBX cd01767
Ubiquitin regulatory domain X (UBX) structurally similar to a beta-grasp ubiquitin-like fold; ...
 355-434 5.63e-08

Ubiquitin regulatory domain X (UBX) structurally similar to a beta-grasp ubiquitin-like fold; The UBXD family of proteins contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. Members in this family function as cofactors of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. Based on domain composition, UBXD proteins can be divided into two main groups, with and without ubiquitin-associated (UBA) domain.


Pssm-ID: 340466 [Multi-domain]  Cd Length: 74  Bit Score: 49.57  E-value: 5.63e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18379271 355 MIRVQFPDGVVLQGVFAPWEPTFALYEFVSSALKEPSLQFELLDPvlVKRRVIphTPAPGQKpiTLEDEELVPSALIRFR 434
Cdd:cd01767   1 RIQIRLPDGSRIQRRFSKSDTLQDLYDFVESNLGDSPSSFSLVTS--FPRRVL--TDEDSDK--TLEELGLTPNAVLFVE 74
PUB_PNGase cd10459
PNGase/UBA or UBX (PUB) domain of the P97 adaptor protein Peptide:N-glycanase (PNGase); This ...
 186-237 3.17e-07

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.


Pssm-ID: 198417  Cd Length: 93  Bit Score: 48.04  E-value: 3.17e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 18379271 186 LLRLFKNIVKEPENAKFRKVRMSNAKIKEAIGDVAGGVELLELVGFELKEEN 237
Cdd:cd10459  19 LLTYANNILRNPNDPKYRSIRLDNPVFSTKLLPARGAIECLFEMGFVEDEDR 70
UBX pfam00789
UBX domain; This domain is present in ubiquitin-regulatory proteins and is a general ...
 356-435 1.24e-03

UBX domain; This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module.


Pssm-ID: 395637 [Multi-domain]  Cd Length: 80  Bit Score: 37.66  E-value: 1.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18379271   356 IRVQFPDGVVLQGVFAPWEPTFALYEFVSSALKEPSLQFELLDPvlVKRRVIphtpAPGQKPITLEDEELVPSALIRFRP 435
Cdd:pfam00789   7 LQIRLPDGSRLVRRFNSSDKLQTVYDFVDSNRYDDLEPFSLNTP--FPRRPL----TDLDYSKTLKEAGLLPNSTLVLEP 80
UBX smart00166
Domain present in ubiquitin-regulatory proteins; Present in FAF1 and Shp1p.
 353-429 1.84e-03

Domain present in ubiquitin-regulatory proteins; Present in FAF1 and Shp1p.


Pssm-ID: 197552 [Multi-domain]  Cd Length: 77  Bit Score: 36.90  E-value: 1.84e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18379271    353 RSMIRVQFPDGVVLQGVFAPWEPTFALYEFVSSALKEPSLQFELLDPvlVKRRVIphTPAPGQKpiTLEDEELVPSA 429
Cdd:smart00166   1 VCRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALGDGNDPFTLNSP--FPRRTF--TKDDYSK--KLLELALLPSS 71
PUB_UBA cd10462
PNGase/UBA or UBX (PUB) domain of Ubiquitin-associated (UBA) domain containing proteins; The ...
 152-232 9.93e-03

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.


Pssm-ID: 198420  Cd Length: 100  Bit Score: 35.54  E-value: 9.93e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18379271 152 SSFEKDNNDNDKSEME---KLVVVYLSgkpsessidvllrlfkNIVKEPENAKFRKVRMSNAKIKEAIGDVAGGVELLEL 228
Cdd:cd10462   2 NNLKKEYKDTDKQGLMtclNTLRTYIS----------------NAHDHPLEEKYKKIRKENKAFVSKVLIFEGAIEILLA 65


                ....
gi 18379271 229 VGFE 232
Cdd:cd10462  66 CGFE 69
 
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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