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Conserved domains on  [gi|3123034|sp|Q15011|]
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RecName: Full=Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein; AltName: Full=Methyl methanesulfonate (MMF)-inducible fragment protein 1

Protein Classification

ubiquitin family protein( domain architecture ID 13019299)

ubiquitin family protein belongs to an diverse class of protein modifier and gene expression regulatory proteins that participate in a number of cellular processes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ubl_HERP1 cd17118
ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress ...
 9-86 2.49e-47

ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP1 and similar proteins; HERP1, also termed homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (HERPUD1), or methyl methanesulfonate (MMF)-inducible fragment protein 1 (MIF1), is an endoplasmic reticulum (ER) integral membrane protein containing an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. HERP1 is a component of the ER quality control (ERQC) system, also called ER-associated degradation (ERAD), which is involved in ubiquitin-dependent degradation of misfolded ER proteins. It promotes the degradation of ER-resident Ca2+ channels. It is also involved in ubiquitin ligase HRD1-dependent protein degradation at the ER. Moreover, HERP1 plays a role in regulating the cell cycle, apoptosis and steroid hormone biosynthesis in mouse granulosa cells.


:

Pssm-ID: 340638  Cd Length: 78  Bit Score: 155.72  E-value: 2.49e-47
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 3123034    9 PVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVC 86
Cdd:cd17118   1 EVTLLIKSPSQRHEDLELRGDRGWTVRRLKTQLRREYPDHPPEQEQRLIYSGKLLLDHLYLREVLPKDEERHVLHLVC 78
 
Name Accession Description Interval E-value
Ubl_HERP1 cd17118
ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress ...
 9-86 2.49e-47

ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP1 and similar proteins; HERP1, also termed homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (HERPUD1), or methyl methanesulfonate (MMF)-inducible fragment protein 1 (MIF1), is an endoplasmic reticulum (ER) integral membrane protein containing an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. HERP1 is a component of the ER quality control (ERQC) system, also called ER-associated degradation (ERAD), which is involved in ubiquitin-dependent degradation of misfolded ER proteins. It promotes the degradation of ER-resident Ca2+ channels. It is also involved in ubiquitin ligase HRD1-dependent protein degradation at the ER. Moreover, HERP1 plays a role in regulating the cell cycle, apoptosis and steroid hormone biosynthesis in mouse granulosa cells.


Pssm-ID: 340638  Cd Length: 78  Bit Score: 155.72  E-value: 2.49e-47
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 3123034    9 PVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVC 86
Cdd:cd17118   1 EVTLLIKSPSQRHEDLELRGDRGWTVRRLKTQLRREYPDHPPEQEQRLIYSGKLLLDHLYLREVLPKDEERHVLHLVC 78
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
 10-86 5.91e-14

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 66.51  E-value: 5.91e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3123034      10 VTLLVKSPNQRHRDLELSGDrgWSVGHLKAHLSRVYpERPrPEDQRLIYSGKLLLDHQCLRDLLPKQEkrHVLHLVC 86
Cdd:smart00213   1 IELTVKTLDGKTITLEVKPS--DTVSELKEKIAELT-GIP-PEQQRLIYKGKVLEDDRTLADYGIQDG--STIHLVL 71
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 12-89 3.27e-10

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 55.64  E-value: 3.27e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 3123034     12 LLVKspNQRHRDLELSGDRGWSVGHLKAHLSRVypERPRPEDQRLIYSGKLLLDHQCLRDLlpKQEKRHVLHLVCNVK 89
Cdd:pfam00240   1 ITVK--TLDGKKITLEVDPTDTVLELKEKIAEK--EGVPPEQQRLIYSGKVLEDDQTLGEY--GIEDGSTIHLVLRQR 72
 
Name Accession Description Interval E-value
Ubl_HERP1 cd17118
ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress ...
 9-86 2.49e-47

ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP1 and similar proteins; HERP1, also termed homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (HERPUD1), or methyl methanesulfonate (MMF)-inducible fragment protein 1 (MIF1), is an endoplasmic reticulum (ER) integral membrane protein containing an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. HERP1 is a component of the ER quality control (ERQC) system, also called ER-associated degradation (ERAD), which is involved in ubiquitin-dependent degradation of misfolded ER proteins. It promotes the degradation of ER-resident Ca2+ channels. It is also involved in ubiquitin ligase HRD1-dependent protein degradation at the ER. Moreover, HERP1 plays a role in regulating the cell cycle, apoptosis and steroid hormone biosynthesis in mouse granulosa cells.


Pssm-ID: 340638  Cd Length: 78  Bit Score: 155.72  E-value: 2.49e-47
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 3123034    9 PVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVC 86
Cdd:cd17118   1 EVTLLIKSPSQRHEDLELRGDRGWTVRRLKTQLRREYPDHPPEQEQRLIYSGKLLLDHLYLREVLPKDEERHVLHLVC 78
Ubl_HERP cd01790
ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress ...
 10-85 1.03e-37

ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP; HERP is an endoplasmic reticulum (ER) integral membrane protein containing an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. The Ubl domain is required for the degradation of HERP itself as well as for HERP-mediated anti-apoptotic effects. HERP is induced by the ER stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. There are two types of HERP, HERP1 and HERP2, which are encoded by the HERPUD1 and HERPUD2 genes, respectively.


Pssm-ID: 340488  Cd Length: 78  Bit Score: 130.83  E-value: 1.03e-37
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 3123034   10 VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLL--PKQEKRHVLHLV 85
Cdd:cd01790   1 VTLVVKSPNQRIQDLTVNCTLGWTVLKLKEHLSEVYPSKPLPEDQKLIYSGKLLEDHQTLKDVLreDDPEQVHTVHLV 78
Ubl_HERP2 cd17119
ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress ...
 9-85 9.05e-29

ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP2 and similar proteins; HERP2, also termed homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 2 protein (HERPUD2), is an endoplasmic reticulum (ER) integral membrane protein containing an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. It is homologous to HERP1, and could be involved in the unfolded protein response (UPR) pathway. It regulates the ubiquitin ligase HRD1-dependent protein degradation at the ER.


Pssm-ID: 340639  Cd Length: 77  Bit Score: 107.05  E-value: 9.05e-29
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3123034    9 PVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLV 85
Cdd:cd17119   1 PVTLVIKAPNQKYDDQTINCFLNWTVEKLKSHLSKVYPSKPSTKDQRLVYSGRLLPDHLQLKDILRKQDEYHMVHLV 77
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
 10-86 5.91e-14

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 66.51  E-value: 5.91e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3123034      10 VTLLVKSPNQRHRDLELSGDrgWSVGHLKAHLSRVYpERPrPEDQRLIYSGKLLLDHQCLRDLLPKQEkrHVLHLVC 86
Cdd:smart00213   1 IELTVKTLDGKTITLEVKPS--DTVSELKEKIAELT-GIP-PEQQRLIYKGKVLEDDRTLADYGIQDG--STIHLVL 71
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 12-89 3.27e-10

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 55.64  E-value: 3.27e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 3123034     12 LLVKspNQRHRDLELSGDRGWSVGHLKAHLSRVypERPRPEDQRLIYSGKLLLDHQCLRDLlpKQEKRHVLHLVCNVK 89
Cdd:pfam00240   1 ITVK--TLDGKKITLEVDPTDTVLELKEKIAEK--EGVPPEQQRLIYSGKVLEDDQTLGEY--GIEDGSTIHLVLRQR 72
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 12-85 1.81e-08

ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. Polyubiquitination signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation.


Pssm-ID: 340559 [Multi-domain]  Cd Length: 68  Bit Score: 50.67  E-value: 1.81e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3123034   12 LLVKSPNQRHRDLELSGDrgWSVGHLKAHLSRVYPerPRPEDQRLIYSGKLLLDHQCLRDLlpKQEKRHVLHLV 85
Cdd:cd17039   1 ITVKTLDGKTYTVEVDPD--DTVADLKEKIEEKTG--IPVEQQRLIYNGKELKDDKTLSDY--GIKDGSTIHLV 68
Ubl_Dsk2p_like cd16106
ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein ...
 10-85 1.38e-05

ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein Dsk2p and similar proteins; The family contains several fungal multiubiquitin receptors, including Saccharomyces cerevisiae Dsk2p and Schizosaccharomyces pombe Dph1p, both of which have been characterized as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. They interact with the proteasome through their N-terminal ubiquitin-like domain (Ubl) and with ubiquitin (Ub) through their C-terminal Ub-associated domain (UBA). S. cerevisiae Dsk2p is a nuclear-enriched protein that may involve in the ubiquitin-proteasome proteolytic pathway through interacting with K48-linked polyubiquitin and the proteasome. Moreover, it has been implicated in spindle pole duplication through assisting in Cdc31 assembly into the new spindle pole body (SPB). S. pombe Dph1p is an ubiquitin (Ub0 receptor working in concert with the class V myosin, Myo52, to target the degradation of the S. pombe CLIP-170 homolog, Tip1. It also can protect Ub chains against disassembly by deubiquitinating enzymes.


Pssm-ID: 340523 [Multi-domain]  Cd Length: 73  Bit Score: 42.63  E-value: 1.38e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3123034   10 VTLLVKSPNQRHRDLELSGDrgWSVGHLK-AHLSRVYPErprPEDQRLIYSGKLLLDHQCLRDLlpKQEKRHVLHLV 85
Cdd:cd16106   1 IKVTVKCSNGKKFTVEVEPD--ATVLELKeLIAEKSDIP---AEQQRLIYKGKILKDEETLSSY--KIQDGHTVHLV 70
Ubl_Rad23 cd01805
ubiquitin-like (Ubl) domain found in the Rad23 protein family; The Rad23 family includes the ...
 10-84 1.04e-03

ubiquitin-like (Ubl) domain found in the Rad23 protein family; The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry an ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. The Ubl domain is responsible for the binding to proteasome. The UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates, which suggests Rad23 proteins might be involved in certain pathways of Ub metabolism. Both the Ubl domain and the XPC-binding domain are necessary for efficient NER function of Rad23 proteins.


Pssm-ID: 340503 [Multi-domain]  Cd Length: 72  Bit Score: 37.54  E-value: 1.04e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 3123034   10 VTLLVKSPNQRHRDLELSGDRgwSVGHLKAHLSRVYPERPrPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHL 84
Cdd:cd01805   1 MKITFKTLQQQTFEIEVEPSD--TVLELKEKIEQEQGDFP-ASGQKLIYSGKVLKDDKTLSEYNIKEKDFVVVMV 72
 
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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