NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1734327777|ref|NP_001360308|]
View 

Ubiquitin-like domain-containing protein [Caenorhabditis elegans]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RING0_parkin cd21382
RING finger-like zinc-binding domain 0 of parkin; Parkin, also called Parkinson juvenile ...
 104-182 9.57e-27

RING finger-like zinc-binding domain 0 of parkin; Parkin, also called Parkinson juvenile disease protein 2, is a RBR (RING1-BRcat-Rcat)-type E3 ubiquitin-protein ligase that is associated with recessive early onset Parkinson's disease (PD), and exerts a protective effect against dopamine-induced alpha-synuclein-dependent cell toxicity. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Parkin functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. It is involved in regulating mitochondrial quality control. Its activation is a key regulatory event in the pathway to the clearance of depolarized or damaged mitochondria. Parkin contains an N-terminal ubiquitin-like domain, an acid linker, a RING finger-like domain 0 (RING0), and a C-terminal RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. This model represents RING0 of parkin.


:

Pssm-ID: 412057  Cd Length: 84  Bit Score: 98.84  E-value: 9.57e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734327777 104 FYVWCKN-CDDVKRGKLRVYCQKCSSTSVLVKSEPQNWSDVLKSKRIPAVCEECCTPGLFAEFKFKCLA----CNDPAAA 178
Cdd:cd21382     1 FYVYCKGpCKKVQPGKLRVRCATCKQGAFTLDRGPSCWDDVLIPNRISGVCQSPDCPGTRAEFYFKCAShptsDKDTSVA 80


                  ....
gi 1734327777 179 LTHV 182
Cdd:cd21382    81 LNLI 84
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 13-77 3.20e-03

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: 35.26  E-value: 3.20e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1734327777  13 KTGQRRNLTLNINITGNIEDLTKDVEKLTEIPSDELEVVFCGKKLSKSTIMRDLSLTPATQIMLL 77
Cdd:cd17039     4 KTLDGKTYTVEVDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKELKDDKTLSDYGIKDGSTIHLV 68
 
Name Accession Description Interval E-value
RING0_parkin cd21382
RING finger-like zinc-binding domain 0 of parkin; Parkin, also called Parkinson juvenile ...
 104-182 9.57e-27

RING finger-like zinc-binding domain 0 of parkin; Parkin, also called Parkinson juvenile disease protein 2, is a RBR (RING1-BRcat-Rcat)-type E3 ubiquitin-protein ligase that is associated with recessive early onset Parkinson's disease (PD), and exerts a protective effect against dopamine-induced alpha-synuclein-dependent cell toxicity. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Parkin functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. It is involved in regulating mitochondrial quality control. Its activation is a key regulatory event in the pathway to the clearance of depolarized or damaged mitochondria. Parkin contains an N-terminal ubiquitin-like domain, an acid linker, a RING finger-like domain 0 (RING0), and a C-terminal RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. This model represents RING0 of parkin.


Pssm-ID: 412057  Cd Length: 84  Bit Score: 98.84  E-value: 9.57e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734327777 104 FYVWCKN-CDDVKRGKLRVYCQKCSSTSVLVKSEPQNWSDVLKSKRIPAVCEECCTPGLFAEFKFKCLA----CNDPAAA 178
Cdd:cd21382     1 FYVYCKGpCKKVQPGKLRVRCATCKQGAFTLDRGPSCWDDVLIPNRISGVCQSPDCPGTRAEFYFKCAShptsDKDTSVA 80


                  ....
gi 1734327777 179 LTHV 182
Cdd:cd21382    81 LNLI 84
zf-RING_12 pfam17976
RING/Ubox like zinc-binding domain; This is a RING zinc finger domain found in parkin proteins. ...
 103-171 8.29e-15

RING/Ubox like zinc-binding domain; This is a RING zinc finger domain found in parkin proteins. Parkin consists of a ubiquitin-like (Ubl) domain and a 60-amino acid linker followed by this domain RING0 and three additional zinc finger domains characteriztic of the RBR family. RING0 binds two coordinated zinc atoms at each extremity of the domain with a hairpin. Deletion of RING0 massively derepressed parkin activity supporting the role of RING0 in autoinhibition, point mutations in RING0 (Phe146 to Ala) or RING2 (Phe463 to Ala) both increased parkin activity. The REP (repressor element of parkin) and RING0 domains play a preeminent role in repressing parkin ligase activity through their interactions with RING1 and RING2, respectively.


Pssm-ID: 465600  Cd Length: 73  Bit Score: 67.15  E-value: 8.29e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734327777 103 SFYVWCKN-CDDVKRGKLRVYCQKCSSTSVLVKSEPQNWSDVLKSKRIPAVCEECCTPGLFAEFKFKCLA 171
Cdd:pfam17976   1 SFYVYCKSpCKSIQPGKLRVRCSTCKQGTLTLDRGPSCWDDVLIPNRITGVCQSPDCEGTVAEFYFKCAA 70
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 13-77 3.20e-03

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: 35.26  E-value: 3.20e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1734327777  13 KTGQRRNLTLNINITGNIEDLTKDVEKLTEIPSDELEVVFCGKKLSKSTIMRDLSLTPATQIMLL 77
Cdd:cd17039     4 KTLDGKTYTVEVDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKELKDDKTLSDYGIKDGSTIHLV 68
 
Name Accession Description Interval E-value
RING0_parkin cd21382
RING finger-like zinc-binding domain 0 of parkin; Parkin, also called Parkinson juvenile ...
 104-182 9.57e-27

RING finger-like zinc-binding domain 0 of parkin; Parkin, also called Parkinson juvenile disease protein 2, is a RBR (RING1-BRcat-Rcat)-type E3 ubiquitin-protein ligase that is associated with recessive early onset Parkinson's disease (PD), and exerts a protective effect against dopamine-induced alpha-synuclein-dependent cell toxicity. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Parkin functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. It is involved in regulating mitochondrial quality control. Its activation is a key regulatory event in the pathway to the clearance of depolarized or damaged mitochondria. Parkin contains an N-terminal ubiquitin-like domain, an acid linker, a RING finger-like domain 0 (RING0), and a C-terminal RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. This model represents RING0 of parkin.


Pssm-ID: 412057  Cd Length: 84  Bit Score: 98.84  E-value: 9.57e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734327777 104 FYVWCKN-CDDVKRGKLRVYCQKCSSTSVLVKSEPQNWSDVLKSKRIPAVCEECCTPGLFAEFKFKCLA----CNDPAAA 178
Cdd:cd21382     1 FYVYCKGpCKKVQPGKLRVRCATCKQGAFTLDRGPSCWDDVLIPNRISGVCQSPDCPGTRAEFYFKCAShptsDKDTSVA 80


                  ....
gi 1734327777 179 LTHV 182
Cdd:cd21382    81 LNLI 84
zf-RING_12 pfam17976
RING/Ubox like zinc-binding domain; This is a RING zinc finger domain found in parkin proteins. ...
 103-171 8.29e-15

RING/Ubox like zinc-binding domain; This is a RING zinc finger domain found in parkin proteins. Parkin consists of a ubiquitin-like (Ubl) domain and a 60-amino acid linker followed by this domain RING0 and three additional zinc finger domains characteriztic of the RBR family. RING0 binds two coordinated zinc atoms at each extremity of the domain with a hairpin. Deletion of RING0 massively derepressed parkin activity supporting the role of RING0 in autoinhibition, point mutations in RING0 (Phe146 to Ala) or RING2 (Phe463 to Ala) both increased parkin activity. The REP (repressor element of parkin) and RING0 domains play a preeminent role in repressing parkin ligase activity through their interactions with RING1 and RING2, respectively.


Pssm-ID: 465600  Cd Length: 73  Bit Score: 67.15  E-value: 8.29e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1734327777 103 SFYVWCKN-CDDVKRGKLRVYCQKCSSTSVLVKSEPQNWSDVLKSKRIPAVCEECCTPGLFAEFKFKCLA 171
Cdd:pfam17976   1 SFYVYCKSpCKSIQPGKLRVRCSTCKQGTLTLDRGPSCWDDVLIPNRITGVCQSPDCEGTVAEFYFKCAA 70
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 13-77 3.20e-03

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: 35.26  E-value: 3.20e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1734327777  13 KTGQRRNLTLNINITGNIEDLTKDVEKLTEIPSDELEVVFCGKKLSKSTIMRDLSLTPATQIMLL 77
Cdd:cd17039     4 KTLDGKTYTVEVDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKELKDDKTLSDYGIKDGSTIHLV 68
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH