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Conserved domains on  [gi|457867145|ref|NP_001263987|]
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ERCC6-PGBD3 fusion protein isoform 1 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DDE_Tnp_1_7 pfam13843
Transposase IS4;
609-967 1.62e-118

Transposase IS4;


:

Pssm-ID: 433521  Cd Length: 349  Bit Score: 368.16  E-value: 1.62e-118
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 457867145   609 TPTEILELFLDDEVIELIVKYSNLYACSKGVHLGLTSSEFKCFLGIIFLSGYVSVPRRRMFWEQRTDVHNVLVSAAMRRD 688
Cdd:pfam13843    1 DPVELFELFLDDEIIARIVRETNLYAKQKYKWLPLTAEELMAFLGLLILMGDVRLPSVEDYWSTKMFYGNPGLRDAMSRE 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 457867145   689 RFETIFSNLHVADNANLDP-VDKFSKLRPLISKLNERCMKFVPNETYFSFDEFMVPYFGRHGCKQFIRGKPIRFGYKFWC 767
Cdd:pfam13843   81 RFEFLLSALHFADNPTRKAeTDKLGKIRPLIDYLNENMQKVYRPSQTLVLDESLILFKGRVPFKQYLPGKPRKNGIKLHV 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 457867145   768 GATCL-GYICWFQPYQGKNPNTKHEEY-GVGASLVLQFSEALTEAHpgqYHFVFNNFFTSIALLDKLSSMGHQATGTVRK 845
Cdd:pfam13843  161 LCDAQtGYIIALELYEGPARNGRNSRQlGKRNALVLRLTEPLQGQG---RHVYFDNFYTSLDLAQELAKKGTYATGTLRK 237
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 457867145   846 DHiDRVPleSDVaLKKKERGTFDYRIDGKgNIVCRWNDNSVVTVASSgagIHPLCLVSRYSQKLKKkiqVQQPNMIKVYN 925
Cdd:pfam13843  238 NR-YGLP--KDL-TQQLPPGSILARYGGP-LMLFKWRRRKVVLLLST---FSSDCLVYSKERSGQK---IARPKLVEDYN 306
                          330       340       350       360
                   ....*....|....*....|....*....|....*....|...
gi 457867145   926 QFMGGVDRADENIDKYRASIRG-KKWYSSPLLFCFELVLQNAW 967
Cdd:pfam13843  307 QAKGAVDRHDQLLAAYRVSRKGsKKWYKRVFIFLLNIAVVNAY 349
cc_ERCC-6_N cd21397
coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 ...
83-159 4.86e-32

coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 (ERCC-6) and related proteins; This model represents a coiled-coil domain located near the N-terminus of ERCC-6 and related proteins. ERCC-6 (also known as Cockayne syndrome group B, CSB) is a DNA-binding protein important in eukaryotic transcription-coupled repair (TCR). TCR is a well-conserved sub-pathway of nucleotide excision repair (NER) that preferentially removes DNA lesions from the template strand blocking translocation of RNA polymerase II (Pol II). In a model for TCR, the processing Pol II encounters the lesion on the transcribed DNA strand and stalls; it is then displaced by the TCR-initiation complex which includes ERCC-6, ERCC-8, UVSSA and USP7; TCR-specific factors then access the lesion for the DNA damage incision process. The N-terminal region, the ATPase domain and the C-terminal region of ERCC-6 all directly contribute to DNA association and catalytic activity. The ATPase domain functions in concert with either the N- or C-terminal region to mediate UV-induced chromatin association. The N-terminal region prevents ERCC-6 from stably associating with chromatin under normal growth conditions, and the C-terminal region of ERCC-6 promotes stable chromatin association in the presence of lesion-stalled transcription. In addition to this coiled-coil domain, the N-terminal region of ERCC-6 includes two lysine residues subject to SUMOylation, a nucleolar localization signal NoLS1, and a nuclear localization signal NLS1. ERCC-6 also includes a SWI/SNF-like ATPase domain, a nucleotide-binding domain and a ubiquitin-binding domain. This coiled-coil domain binds magnesium. This domain family does not include Saccharomyces cerevisiae RAD26, and Schizosaccharomyces pombe Rhp26.


:

Pssm-ID: 411064 [Multi-domain]  Cd Length: 77  Bit Score: 119.24  E-value: 4.86e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 457867145   83 VEPSAQALELQGLGVDVYDQDVLEQGVLQQVDNAIHEASRASQLVDVEKEYRSVLDDLTSCTTSLRQINKIIEQLSP 159
Cdd:cd21397     1 VPESDQASELQGLGVDVYDQDEFEQGVLQQVDQAIAEEEEERRKKDAEKELKSVLDDIRSVKQDLEHIEKVLEQLEP 77
C1 super family cl00040
protein kinase C conserved region 1 (C1 domain) superfamily; The C1 domain is a cysteine-rich ...
1019-1055 4.77e-03

protein kinase C conserved region 1 (C1 domain) superfamily; The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains. It contains the motif HX12CX2CXnCX2CX4HX2CX7C, where C and H are cysteine and histidine, respectively; X represents other residues; and n is either 13 or 14. C1 has a globular fold with two separate Zn(2+)-binding sites. It was originally discovered as lipid-binding modules in protein kinase C (PKC) isoforms. C1 domains that bind and respond to phorbol esters (PE) and diacylglycerol (DAG) are referred to as typical, and those that do not respond to PE and DAG are deemed atypical. A C1 domain may also be referred to as PKC or non-PKC C1, based on the parent protein's activity. Most C1 domain-containing non-PKC proteins act as lipid kinases and scaffolds, except PKD which acts as a protein kinase. PKC C1 domains play roles in membrane translocation and activation of the enzyme.


The actual alignment was detected with superfamily member smart00109:

Pssm-ID: 412127  Cd Length: 50  Bit Score: 36.29  E-value: 4.77e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|...
gi 457867145   1019 INHVIVKQGKQTRCAECHK------NTTFRCEKCDVALHVKCS 1055
Cdd:smart00109    1 HKHVFRTFTKPTFCCVCRKsiwgsfKQGLRCSECKVKCHKKCA 43
 
Name Accession Description Interval E-value
DDE_Tnp_1_7 pfam13843
Transposase IS4;
609-967 1.62e-118

Transposase IS4;


Pssm-ID: 433521  Cd Length: 349  Bit Score: 368.16  E-value: 1.62e-118
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 457867145   609 TPTEILELFLDDEVIELIVKYSNLYACSKGVHLGLTSSEFKCFLGIIFLSGYVSVPRRRMFWEQRTDVHNVLVSAAMRRD 688
Cdd:pfam13843    1 DPVELFELFLDDEIIARIVRETNLYAKQKYKWLPLTAEELMAFLGLLILMGDVRLPSVEDYWSTKMFYGNPGLRDAMSRE 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 457867145   689 RFETIFSNLHVADNANLDP-VDKFSKLRPLISKLNERCMKFVPNETYFSFDEFMVPYFGRHGCKQFIRGKPIRFGYKFWC 767
Cdd:pfam13843   81 RFEFLLSALHFADNPTRKAeTDKLGKIRPLIDYLNENMQKVYRPSQTLVLDESLILFKGRVPFKQYLPGKPRKNGIKLHV 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 457867145   768 GATCL-GYICWFQPYQGKNPNTKHEEY-GVGASLVLQFSEALTEAHpgqYHFVFNNFFTSIALLDKLSSMGHQATGTVRK 845
Cdd:pfam13843  161 LCDAQtGYIIALELYEGPARNGRNSRQlGKRNALVLRLTEPLQGQG---RHVYFDNFYTSLDLAQELAKKGTYATGTLRK 237
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 457867145   846 DHiDRVPleSDVaLKKKERGTFDYRIDGKgNIVCRWNDNSVVTVASSgagIHPLCLVSRYSQKLKKkiqVQQPNMIKVYN 925
Cdd:pfam13843  238 NR-YGLP--KDL-TQQLPPGSILARYGGP-LMLFKWRRRKVVLLLST---FSSDCLVYSKERSGQK---IARPKLVEDYN 306
                          330       340       350       360
                   ....*....|....*....|....*....|....*....|...
gi 457867145   926 QFMGGVDRADENIDKYRASIRG-KKWYSSPLLFCFELVLQNAW 967
Cdd:pfam13843  307 QAKGAVDRHDQLLAAYRVSRKGsKKWYKRVFIFLLNIAVVNAY 349
cc_ERCC-6_N cd21397
coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 ...
83-159 4.86e-32

coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 (ERCC-6) and related proteins; This model represents a coiled-coil domain located near the N-terminus of ERCC-6 and related proteins. ERCC-6 (also known as Cockayne syndrome group B, CSB) is a DNA-binding protein important in eukaryotic transcription-coupled repair (TCR). TCR is a well-conserved sub-pathway of nucleotide excision repair (NER) that preferentially removes DNA lesions from the template strand blocking translocation of RNA polymerase II (Pol II). In a model for TCR, the processing Pol II encounters the lesion on the transcribed DNA strand and stalls; it is then displaced by the TCR-initiation complex which includes ERCC-6, ERCC-8, UVSSA and USP7; TCR-specific factors then access the lesion for the DNA damage incision process. The N-terminal region, the ATPase domain and the C-terminal region of ERCC-6 all directly contribute to DNA association and catalytic activity. The ATPase domain functions in concert with either the N- or C-terminal region to mediate UV-induced chromatin association. The N-terminal region prevents ERCC-6 from stably associating with chromatin under normal growth conditions, and the C-terminal region of ERCC-6 promotes stable chromatin association in the presence of lesion-stalled transcription. In addition to this coiled-coil domain, the N-terminal region of ERCC-6 includes two lysine residues subject to SUMOylation, a nucleolar localization signal NoLS1, and a nuclear localization signal NLS1. ERCC-6 also includes a SWI/SNF-like ATPase domain, a nucleotide-binding domain and a ubiquitin-binding domain. This coiled-coil domain binds magnesium. This domain family does not include Saccharomyces cerevisiae RAD26, and Schizosaccharomyces pombe Rhp26.


Pssm-ID: 411064 [Multi-domain]  Cd Length: 77  Bit Score: 119.24  E-value: 4.86e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 457867145   83 VEPSAQALELQGLGVDVYDQDVLEQGVLQQVDNAIHEASRASQLVDVEKEYRSVLDDLTSCTTSLRQINKIIEQLSP 159
Cdd:cd21397     1 VPESDQASELQGLGVDVYDQDEFEQGVLQQVDQAIAEEEEERRKKDAEKELKSVLDDIRSVKQDLEHIEKVLEQLEP 77
C1 smart00109
Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains); Some bind phorbol ...
1019-1055 4.77e-03

Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains); Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.


Pssm-ID: 197519  Cd Length: 50  Bit Score: 36.29  E-value: 4.77e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|...
gi 457867145   1019 INHVIVKQGKQTRCAECHK------NTTFRCEKCDVALHVKCS 1055
Cdd:smart00109    1 HKHVFRTFTKPTFCCVCRKsiwgsfKQGLRCSECKVKCHKKCA 43
 
Name Accession Description Interval E-value
DDE_Tnp_1_7 pfam13843
Transposase IS4;
609-967 1.62e-118

Transposase IS4;


Pssm-ID: 433521  Cd Length: 349  Bit Score: 368.16  E-value: 1.62e-118
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 457867145   609 TPTEILELFLDDEVIELIVKYSNLYACSKGVHLGLTSSEFKCFLGIIFLSGYVSVPRRRMFWEQRTDVHNVLVSAAMRRD 688
Cdd:pfam13843    1 DPVELFELFLDDEIIARIVRETNLYAKQKYKWLPLTAEELMAFLGLLILMGDVRLPSVEDYWSTKMFYGNPGLRDAMSRE 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 457867145   689 RFETIFSNLHVADNANLDP-VDKFSKLRPLISKLNERCMKFVPNETYFSFDEFMVPYFGRHGCKQFIRGKPIRFGYKFWC 767
Cdd:pfam13843   81 RFEFLLSALHFADNPTRKAeTDKLGKIRPLIDYLNENMQKVYRPSQTLVLDESLILFKGRVPFKQYLPGKPRKNGIKLHV 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 457867145   768 GATCL-GYICWFQPYQGKNPNTKHEEY-GVGASLVLQFSEALTEAHpgqYHFVFNNFFTSIALLDKLSSMGHQATGTVRK 845
Cdd:pfam13843  161 LCDAQtGYIIALELYEGPARNGRNSRQlGKRNALVLRLTEPLQGQG---RHVYFDNFYTSLDLAQELAKKGTYATGTLRK 237
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 457867145   846 DHiDRVPleSDVaLKKKERGTFDYRIDGKgNIVCRWNDNSVVTVASSgagIHPLCLVSRYSQKLKKkiqVQQPNMIKVYN 925
Cdd:pfam13843  238 NR-YGLP--KDL-TQQLPPGSILARYGGP-LMLFKWRRRKVVLLLST---FSSDCLVYSKERSGQK---IARPKLVEDYN 306
                          330       340       350       360
                   ....*....|....*....|....*....|....*....|...
gi 457867145   926 QFMGGVDRADENIDKYRASIRG-KKWYSSPLLFCFELVLQNAW 967
Cdd:pfam13843  307 QAKGAVDRHDQLLAAYRVSRKGsKKWYKRVFIFLLNIAVVNAY 349
cc_ERCC-6_N cd21397
coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 ...
83-159 4.86e-32

coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 (ERCC-6) and related proteins; This model represents a coiled-coil domain located near the N-terminus of ERCC-6 and related proteins. ERCC-6 (also known as Cockayne syndrome group B, CSB) is a DNA-binding protein important in eukaryotic transcription-coupled repair (TCR). TCR is a well-conserved sub-pathway of nucleotide excision repair (NER) that preferentially removes DNA lesions from the template strand blocking translocation of RNA polymerase II (Pol II). In a model for TCR, the processing Pol II encounters the lesion on the transcribed DNA strand and stalls; it is then displaced by the TCR-initiation complex which includes ERCC-6, ERCC-8, UVSSA and USP7; TCR-specific factors then access the lesion for the DNA damage incision process. The N-terminal region, the ATPase domain and the C-terminal region of ERCC-6 all directly contribute to DNA association and catalytic activity. The ATPase domain functions in concert with either the N- or C-terminal region to mediate UV-induced chromatin association. The N-terminal region prevents ERCC-6 from stably associating with chromatin under normal growth conditions, and the C-terminal region of ERCC-6 promotes stable chromatin association in the presence of lesion-stalled transcription. In addition to this coiled-coil domain, the N-terminal region of ERCC-6 includes two lysine residues subject to SUMOylation, a nucleolar localization signal NoLS1, and a nuclear localization signal NLS1. ERCC-6 also includes a SWI/SNF-like ATPase domain, a nucleotide-binding domain and a ubiquitin-binding domain. This coiled-coil domain binds magnesium. This domain family does not include Saccharomyces cerevisiae RAD26, and Schizosaccharomyces pombe Rhp26.


Pssm-ID: 411064 [Multi-domain]  Cd Length: 77  Bit Score: 119.24  E-value: 4.86e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 457867145   83 VEPSAQALELQGLGVDVYDQDVLEQGVLQQVDNAIHEASRASQLVDVEKEYRSVLDDLTSCTTSLRQINKIIEQLSP 159
Cdd:cd21397     1 VPESDQASELQGLGVDVYDQDEFEQGVLQQVDQAIAEEEEERRKKDAEKELKSVLDDIRSVKQDLEHIEKVLEQLEP 77
C1 smart00109
Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains); Some bind phorbol ...
1019-1055 4.77e-03

Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains); Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.


Pssm-ID: 197519  Cd Length: 50  Bit Score: 36.29  E-value: 4.77e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|...
gi 457867145   1019 INHVIVKQGKQTRCAECHK------NTTFRCEKCDVALHVKCS 1055
Cdd:smart00109    1 HKHVFRTFTKPTFCCVCRKsiwgsfKQGLRCSECKVKCHKKCA 43
 
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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