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Conserved domains on  [gi|210147417|ref|NP_001017752|]
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splicing regulator SDE2 [Danio rerio]

Protein Classification

Ubl1_cv_Nsp3_N-like and Telomere_Sde2_2 domain-containing protein( domain architecture ID 13219224)

Ubl1_cv_Nsp3_N-like and Telomere_Sde2_2 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SDE2_2C pfam13297
Replication stress response SDE2 C-terminal; This domain represents the C-terminal region of ...
 388-460 8.41e-28

Replication stress response SDE2 C-terminal; This domain represents the C-terminal region of the Replication stress response SDE2, a genome surveillance factor. It contains the DNA-binding SAP domain, frequently found in proteins involved in DNA repair. SDE2 C-terminal domain must be cleaved from its N-terminal at a diglycine motif within the ubiquitin-like fold, after Proliferating cell nuclear antigen (PCNA) interaction. This generates a functional protein that negatively regulates damage-inducible PCNA monoubiquitination, which then is proteolytically degraded to allow S phase progression and replication fork recovery in response to DNA damage.


:

Pssm-ID: 463835  Cd Length: 80  Bit Score: 105.43  E-value: 8.41e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 210147417  388 EEKSQVLSQVEDPLDLLSVSGPEQLEALGLERLKKELMERGMKCGGTLQERAARLFSVKGLTPDQIDPSLLAK 460
Cdd:pfam13297   8 DKGSKSEVEKAAHIDLDAFSSAEELEALGLDRLKEALMALGLKCGGTLEERAARLFSVKGLALDEIDPKLFAK 80
Ubl1_cv_Nsp3_N-like super family cl28922
first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV ...
 14-140 1.08e-23

first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV non-structural protein 3 (Nsp3) and related proteins; This ubiquitin-like (Ubl) domain (Ubl1) is found at the N-terminus of coronavirus Nsp3, a large multi-functional multi-domain protein which is an essential component of the replication/transcription complex (RTC). The functions of Ubl1 in CoVs are related to single-stranded RNA (ssRNA) binding and to interacting with the nucleocapsid (N) protein. SARS-CoV Ubl1 has been shown to bind ssRNA having AUA patterns, and since the 5'-UTR of the SARS-CoV genome has a number of AUA repeats, it may bind there. In mouse hepatitis virus (MHV), this Ubl1 domain binds the cognate N protein. Adjacent to Ubl1 is a Glu-rich acidic region (also referred to as hypervariable region, HVR); Ubl1 together with HVR has been called Nsp3a. Currently, the function of HVR in CoVs is unknown. This model corresponds to one of two Ubl domains in Nsp3; the other is located N-terminal to the papain-like protease (PLpro) and is not represented by this model.


The actual alignment was detected with superfamily member pfam13019:

Pssm-ID: 475130  Cd Length: 165  Bit Score: 97.08  E-value: 1.08e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 210147417   14 NLTVAPDSTVSDLIDHFTVKNGVSLTDFYV---SSNGRLSRSNDLLQSGVV----------YRLEPRLCGGKGGFGSMLR 80
Cdd:pfam13019  18 SLTLPSTATVSDLTDRLSSRLPESLLSSLIlttTSNKQLAPSSDTPLSSLLsssadgtflsLRLSVRLRGGKGGFGSQLR 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 210147417   81 ALGAQI--EKTTNRE---ACRDLSGRRLRDVNHEKEMAEWLKKQADR---EAEKEQRRLERIQRKLAE 140
Cdd:pfam13019  98 AAGGRMssKKKSNGEnndSCRNLDGRRLRTVNEAKALAEYLASKPEMdkkEKEARRKRWEAVVEAAEK 165
 
Name Accession Description Interval E-value
SDE2_2C pfam13297
Replication stress response SDE2 C-terminal; This domain represents the C-terminal region of ...
 388-460 8.41e-28

Replication stress response SDE2 C-terminal; This domain represents the C-terminal region of the Replication stress response SDE2, a genome surveillance factor. It contains the DNA-binding SAP domain, frequently found in proteins involved in DNA repair. SDE2 C-terminal domain must be cleaved from its N-terminal at a diglycine motif within the ubiquitin-like fold, after Proliferating cell nuclear antigen (PCNA) interaction. This generates a functional protein that negatively regulates damage-inducible PCNA monoubiquitination, which then is proteolytically degraded to allow S phase progression and replication fork recovery in response to DNA damage.


Pssm-ID: 463835  Cd Length: 80  Bit Score: 105.43  E-value: 8.41e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 210147417  388 EEKSQVLSQVEDPLDLLSVSGPEQLEALGLERLKKELMERGMKCGGTLQERAARLFSVKGLTPDQIDPSLLAK 460
Cdd:pfam13297   8 DKGSKSEVEKAAHIDLDAFSSAEELEALGLDRLKEALMALGLKCGGTLEERAARLFSVKGLALDEIDPKLFAK 80
Sde2_N_Ubi pfam13019
Silencing defective 2 N-terminal ubiquitin domain; Sde2 (silencing defective 2) is a ...
 14-140 1.08e-23

Silencing defective 2 N-terminal ubiquitin domain; Sde2 (silencing defective 2) is a ubiquitin-fold-containing splicing regulator that supports splicing of selected pre-mRNAs in an intron-specific manner in Schizosaccharomyces pombe. Both fission yeast and human Sde2 are translated as inactive precursor proteins harbouring the ubiquitin-fold domain linked through an invariant GGKGG motif to a C-terminal domain. The Sde2 protein has a ubiquitin-fold at its N-terminus, which must be cleaved by the ubiquitin-specific proteases (USPs) Ubp5 and Ubp15. After cleavage, the C-terminal domain of Sde2, which starts with a lysine, gets incorporated into the spliceosome. This entry represents the ubiquitin fold N-terminal domain found in Sde2 proteins.


Pssm-ID: 372432  Cd Length: 165  Bit Score: 97.08  E-value: 1.08e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 210147417   14 NLTVAPDSTVSDLIDHFTVKNGVSLTDFYV---SSNGRLSRSNDLLQSGVV----------YRLEPRLCGGKGGFGSMLR 80
Cdd:pfam13019  18 SLTLPSTATVSDLTDRLSSRLPESLLSSLIlttTSNKQLAPSSDTPLSSLLsssadgtflsLRLSVRLRGGKGGFGSQLR 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 210147417   81 ALGAQI--EKTTNRE---ACRDLSGRRLRDVNHEKEMAEWLKKQADR---EAEKEQRRLERIQRKLAE 140
Cdd:pfam13019  98 AAGGRMssKKKSNGEnndSCRNLDGRRLRTVNEAKALAEYLASKPEMdkkEKEARRKRWEAVVEAAEK 165
 
Name Accession Description Interval E-value
SDE2_2C pfam13297
Replication stress response SDE2 C-terminal; This domain represents the C-terminal region of ...
 388-460 8.41e-28

Replication stress response SDE2 C-terminal; This domain represents the C-terminal region of the Replication stress response SDE2, a genome surveillance factor. It contains the DNA-binding SAP domain, frequently found in proteins involved in DNA repair. SDE2 C-terminal domain must be cleaved from its N-terminal at a diglycine motif within the ubiquitin-like fold, after Proliferating cell nuclear antigen (PCNA) interaction. This generates a functional protein that negatively regulates damage-inducible PCNA monoubiquitination, which then is proteolytically degraded to allow S phase progression and replication fork recovery in response to DNA damage.


Pssm-ID: 463835  Cd Length: 80  Bit Score: 105.43  E-value: 8.41e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 210147417  388 EEKSQVLSQVEDPLDLLSVSGPEQLEALGLERLKKELMERGMKCGGTLQERAARLFSVKGLTPDQIDPSLLAK 460
Cdd:pfam13297   8 DKGSKSEVEKAAHIDLDAFSSAEELEALGLDRLKEALMALGLKCGGTLEERAARLFSVKGLALDEIDPKLFAK 80
Sde2_N_Ubi pfam13019
Silencing defective 2 N-terminal ubiquitin domain; Sde2 (silencing defective 2) is a ...
 14-140 1.08e-23

Silencing defective 2 N-terminal ubiquitin domain; Sde2 (silencing defective 2) is a ubiquitin-fold-containing splicing regulator that supports splicing of selected pre-mRNAs in an intron-specific manner in Schizosaccharomyces pombe. Both fission yeast and human Sde2 are translated as inactive precursor proteins harbouring the ubiquitin-fold domain linked through an invariant GGKGG motif to a C-terminal domain. The Sde2 protein has a ubiquitin-fold at its N-terminus, which must be cleaved by the ubiquitin-specific proteases (USPs) Ubp5 and Ubp15. After cleavage, the C-terminal domain of Sde2, which starts with a lysine, gets incorporated into the spliceosome. This entry represents the ubiquitin fold N-terminal domain found in Sde2 proteins.


Pssm-ID: 372432  Cd Length: 165  Bit Score: 97.08  E-value: 1.08e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 210147417   14 NLTVAPDSTVSDLIDHFTVKNGVSLTDFYV---SSNGRLSRSNDLLQSGVV----------YRLEPRLCGGKGGFGSMLR 80
Cdd:pfam13019  18 SLTLPSTATVSDLTDRLSSRLPESLLSSLIlttTSNKQLAPSSDTPLSSLLsssadgtflsLRLSVRLRGGKGGFGSQLR 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 210147417   81 ALGAQI--EKTTNRE---ACRDLSGRRLRDVNHEKEMAEWLKKQADR---EAEKEQRRLERIQRKLAE 140
Cdd:pfam13019  98 AAGGRMssKKKSNGEnndSCRNLDGRRLRTVNEAKALAEYLASKPEMdkkEKEARRKRWEAVVEAAEK 165
 
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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