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Conserved domains on  [gi|736167230|ref|XP_010764828|]
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PREDICTED: protein cereblon [Notothenia coriiceps]

Protein Classification

CRBN_C_like domain-containing protein( domain architecture ID 13561126)

CRBN_C_like domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CRBN_C_like cd15777
Thalidomide-binding C-terminal domain of cereblon (CRBN) and similar protein domains; Cereblon ...
 94-195 3.63e-52

Thalidomide-binding C-terminal domain of cereblon (CRBN) and similar protein domains; Cereblon is part of an E3 ubiquitin ligase complex, together with damaged DNA-binding protein 1 (DDB1), CUL4A and ROC1. Cereblon interacts directly with DDB1, although the C-terminal domain characterized here does not contribute to that interaction. Ubiquination of cellular targets by this complex increases levels of FGF8 and FGF10, which was shown to affect the development of limbs and auditory vesicles in embryogenesis. The C-terminal domain of Cereblon was shown to contain the binding site for thalidomide and its analogs, a class of teratogenic drugs that exhibit an antiproliferative effect on myelomas. Mutations in CRBN, some of which map onto the C-terminal domain, were associated with autosomal recessive mental retardation, which may have to do with interactions between CRBN and ion channels in the brain.


:

Pssm-ID: 276940  Cd Length: 101  Bit Score: 163.18  E-value: 3.63e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736167230  94 LCCKQCQdTEITTKTEIFSLSLNGPMAAYVNPHGYVHETLTVYKTNNLNLVGRPSTLHSWFPGYAWTIAQCRTCGSHMGW 173
Cdd:cd15777    1 LLCRSCG-APITRKSDIFSMSGEGHVHTFVNPHGYVFEIGTFSKAPGCALVGPPSTEFSWFPGYAWTIALCARCGSHLGW 79

                         90       100
                 ....*....|....*....|..
gi 736167230 174 RFTATKKHLSPPRFWGLTRSAL 195
Cdd:cd15777   80 KFTAVEKNLSPKSFYGLILDRL 101
LON_substr_bdg super family cl47207
ATP-dependent protease La (LON) substrate-binding domain; This domain has been shown to be ...
 19-90 1.90e-08

ATP-dependent protease La (LON) substrate-binding domain; This domain has been shown to be part of the PUA superfamily. This domain represents a general protein and polypeptide interaction domain for the ATP-dependent serine peptidase, LON, Peptidase_S16, pfam05362. ATP-dependent Lon proteases are conserved in all living organizms and catalyze rapid turnover of short-lived regulatory proteins and many damaged or denatured proteins.


The actual alignment was detected with superfamily member pfam02190:

Pssm-ID: 481547 [Multi-domain]  Cd Length: 195  Bit Score: 52.34  E-value: 1.90e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 736167230   19 ALYDSESLMNRVKKQLHEWDENLKDDSLpTNAVDFSYRVAACLPIDDALRLQLLKIGSAIQRLRCELDIMDR 90
Cdd:pfam02190 125 LVKELIEKLRRLLKLLLPLELLLKIKDI-ENPGRLADLVAAILPLSPEEKQELLETLDVKERLEKVLELLNR 195
 
Name Accession Description Interval E-value
CRBN_C_like cd15777
Thalidomide-binding C-terminal domain of cereblon (CRBN) and similar protein domains; Cereblon ...
 94-195 3.63e-52

Thalidomide-binding C-terminal domain of cereblon (CRBN) and similar protein domains; Cereblon is part of an E3 ubiquitin ligase complex, together with damaged DNA-binding protein 1 (DDB1), CUL4A and ROC1. Cereblon interacts directly with DDB1, although the C-terminal domain characterized here does not contribute to that interaction. Ubiquination of cellular targets by this complex increases levels of FGF8 and FGF10, which was shown to affect the development of limbs and auditory vesicles in embryogenesis. The C-terminal domain of Cereblon was shown to contain the binding site for thalidomide and its analogs, a class of teratogenic drugs that exhibit an antiproliferative effect on myelomas. Mutations in CRBN, some of which map onto the C-terminal domain, were associated with autosomal recessive mental retardation, which may have to do with interactions between CRBN and ion channels in the brain.


Pssm-ID: 276940  Cd Length: 101  Bit Score: 163.18  E-value: 3.63e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736167230  94 LCCKQCQdTEITTKTEIFSLSLNGPMAAYVNPHGYVHETLTVYKTNNLNLVGRPSTLHSWFPGYAWTIAQCRTCGSHMGW 173
Cdd:cd15777    1 LLCRSCG-APITRKSDIFSMSGEGHVHTFVNPHGYVFEIGTFSKAPGCALVGPPSTEFSWFPGYAWTIALCARCGSHLGW 79

                         90       100
                 ....*....|....*....|..
gi 736167230 174 RFTATKKHLSPPRFWGLTRSAL 195
Cdd:cd15777   80 KFTAVEKNLSPKSFYGLILDRL 101
Yippee-Mis18 pfam03226
Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; This family includes both ...
 94-195 1.17e-09

Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; This family includes both Yippee-type proteins and Mis18 kinetochore proteins. Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of a small complex with Mis18-binding protein. Mis18-alpha is found to interact with DNA de-methylases through a Leu-rich region located at its carboxyl terminus. This entry also includes the CULT domain proteins such as Cereblon.


Pssm-ID: 427204  Cd Length: 99  Bit Score: 53.48  E-value: 1.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736167230   94 LCCKQCQdTEITTKTEIFSlslngpMAAYVNphgyvhetLTVYK--TNNLNLVGRPSTLHSWFPGYAWTIAQCRTCGSHM 171
Cdd:pfam03226   3 FQCKRCN-TILGDSLALVS------SGRELN--------TIVLKkvTRNVVVGKELVTSESGFDDCTYSPLFCAGCGAVL 67

                          90       100
                  ....*....|....*....|....*
gi 736167230  172 GWRFTATKKHLSPPR-FWGLTRSAL 195
Cdd:pfam03226  68 GRKYRSTPEELDYKRgLFCLETDAI 92
LON_substr_bdg pfam02190
ATP-dependent protease La (LON) substrate-binding domain; This domain has been shown to be ...
 19-90 1.90e-08

ATP-dependent protease La (LON) substrate-binding domain; This domain has been shown to be part of the PUA superfamily. This domain represents a general protein and polypeptide interaction domain for the ATP-dependent serine peptidase, LON, Peptidase_S16, pfam05362. ATP-dependent Lon proteases are conserved in all living organizms and catalyze rapid turnover of short-lived regulatory proteins and many damaged or denatured proteins.


Pssm-ID: 426647 [Multi-domain]  Cd Length: 195  Bit Score: 52.34  E-value: 1.90e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 736167230   19 ALYDSESLMNRVKKQLHEWDENLKDDSLpTNAVDFSYRVAACLPIDDALRLQLLKIGSAIQRLRCELDIMDR 90
Cdd:pfam02190 125 LVKELIEKLRRLLKLLLPLELLLKIKDI-ENPGRLADLVAAILPLSPEEKQELLETLDVKERLEKVLELLNR 195
 
Name Accession Description Interval E-value
CRBN_C_like cd15777
Thalidomide-binding C-terminal domain of cereblon (CRBN) and similar protein domains; Cereblon ...
 94-195 3.63e-52

Thalidomide-binding C-terminal domain of cereblon (CRBN) and similar protein domains; Cereblon is part of an E3 ubiquitin ligase complex, together with damaged DNA-binding protein 1 (DDB1), CUL4A and ROC1. Cereblon interacts directly with DDB1, although the C-terminal domain characterized here does not contribute to that interaction. Ubiquination of cellular targets by this complex increases levels of FGF8 and FGF10, which was shown to affect the development of limbs and auditory vesicles in embryogenesis. The C-terminal domain of Cereblon was shown to contain the binding site for thalidomide and its analogs, a class of teratogenic drugs that exhibit an antiproliferative effect on myelomas. Mutations in CRBN, some of which map onto the C-terminal domain, were associated with autosomal recessive mental retardation, which may have to do with interactions between CRBN and ion channels in the brain.


Pssm-ID: 276940  Cd Length: 101  Bit Score: 163.18  E-value: 3.63e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736167230  94 LCCKQCQdTEITTKTEIFSLSLNGPMAAYVNPHGYVHETLTVYKTNNLNLVGRPSTLHSWFPGYAWTIAQCRTCGSHMGW 173
Cdd:cd15777    1 LLCRSCG-APITRKSDIFSMSGEGHVHTFVNPHGYVFEIGTFSKAPGCALVGPPSTEFSWFPGYAWTIALCARCGSHLGW 79

                         90       100
                 ....*....|....*....|..
gi 736167230 174 RFTATKKHLSPPRFWGLTRSAL 195
Cdd:cd15777   80 KFTAVEKNLSPKSFYGLILDRL 101
RLR_C_like cd15803
C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors, Cereblon (CRBN), and ...
 94-195 3.25e-20

C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors, Cereblon (CRBN), and similar protein domains; Retinoic acid-inducible gene (RIG)-I-like Receptors (RLRs) are cytoplasmic RNA receptors that recognize non-self RNA and act as molecular sensors to detect viral pathogens. They play crucial roles in innate antiviral responses, including the production of proinflammatory cytokines and type I interferon. There are three RLRs in vertebrates, RIG-I, LGP2, and MDA5. They are characterized by a central DExD/H-box helicase domain and a C-terminal domain, both of which are responsible for binding viral RNA. Cereblon is part of an E3 ubiquitin ligase complex, together with damaged DNA binding protein 1 (DDB1), CUL4A and ROC1. Cereblon interacts directly with DDB1, although the C-terminal domain characterized here does not contribute to that interaction. The C-terminal domain of Cereblon was shown to contain the binding site for thalidomide and its analogs, a class of teratogenic drugs that exhibit an antiproliferative effect on myelomas. Mutations in CRBN, some of which map onto the C-terminal domain, were associated with autosomal recessive mental retardation, which may have to do with interactions between CRBN and ion channels in the brain. RLRs and Cereblon contain a common conserved zinc binding site in their C-terminal domains.


Pssm-ID: 276941  Cd Length: 84  Bit Score: 81.03  E-value: 3.25e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736167230  94 LCCKQCQDTeITTKTEIFSLSLNgpmaayvnphgyvheTLTVYK---TNNLNLVGRPSTLHSWFPGYAWTIAQCRTCGSH 170
Cdd:cd15803    1 LLCKNCSAL-ACTGEDIRVIELC---------------HHVVYKpafKNNYNVIGRPSTVHKWFDGYAWGIISCKICSSH 64

                         90       100
                 ....*....|....*....|....*
gi 736167230 171 MGWRFTATKKhlsppRFWGLTRSAL 195
Cdd:cd15803   65 WGWHFTYKPQ-----KLPVLKRESF 84
Yippee-Mis18 pfam03226
Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; This family includes both ...
 94-195 1.17e-09

Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; This family includes both Yippee-type proteins and Mis18 kinetochore proteins. Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of a small complex with Mis18-binding protein. Mis18-alpha is found to interact with DNA de-methylases through a Leu-rich region located at its carboxyl terminus. This entry also includes the CULT domain proteins such as Cereblon.


Pssm-ID: 427204  Cd Length: 99  Bit Score: 53.48  E-value: 1.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736167230   94 LCCKQCQdTEITTKTEIFSlslngpMAAYVNphgyvhetLTVYK--TNNLNLVGRPSTLHSWFPGYAWTIAQCRTCGSHM 171
Cdd:pfam03226   3 FQCKRCN-TILGDSLALVS------SGRELN--------TIVLKkvTRNVVVGKELVTSESGFDDCTYSPLFCAGCGAVL 67

                          90       100
                  ....*....|....*....|....*
gi 736167230  172 GWRFTATKKHLSPPR-FWGLTRSAL 195
Cdd:pfam03226  68 GRKYRSTPEELDYKRgLFCLETDAI 92
LON_substr_bdg pfam02190
ATP-dependent protease La (LON) substrate-binding domain; This domain has been shown to be ...
 19-90 1.90e-08

ATP-dependent protease La (LON) substrate-binding domain; This domain has been shown to be part of the PUA superfamily. This domain represents a general protein and polypeptide interaction domain for the ATP-dependent serine peptidase, LON, Peptidase_S16, pfam05362. ATP-dependent Lon proteases are conserved in all living organizms and catalyze rapid turnover of short-lived regulatory proteins and many damaged or denatured proteins.


Pssm-ID: 426647 [Multi-domain]  Cd Length: 195  Bit Score: 52.34  E-value: 1.90e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 736167230   19 ALYDSESLMNRVKKQLHEWDENLKDDSLpTNAVDFSYRVAACLPIDDALRLQLLKIGSAIQRLRCELDIMDR 90
Cdd:pfam02190 125 LVKELIEKLRRLLKLLLPLELLLKIKDI-ENPGRLADLVAAILPLSPEEKQELLETLDVKERLEKVLELLNR 195
 
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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