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Conserved domains on  [gi|2323579627|ref|NP_001400301|]
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telomeric repeat-binding factor 1 isoform 12 [Homo sapiens]

Protein Classification

telomere repeat binding factor family protein( domain architecture ID 10252328)

telomere repeat binding factor (TRF) family protein binds directly to the telomeric double-stranded TTAGGG repeat through its SANT (SWI3, ADA2, N-CoR and TFIIIB)/Myb-like DNA-binding domain, and negatively regulates telomere length

CATH:  1.20.58.1880
Gene Ontology:  GO:0042162|GO:0000723|GO:0006355|GO:0003700|GO:0003677|GO:0010833
PubMed:  8882580|12757977|15608118|22244753
SCOP:  4000317

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TRFH super family cl02779
Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain ...
 76-232 1.46e-81

Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH. Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains.


The actual alignment was detected with superfamily member cd00280:

Pssm-ID: 413471  Cd Length: 200  Bit Score: 248.13  E-value: 1.46e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2323579627  76 GWMLDFLCLSLCRAFRDGRSEDFRRTRNSAE--------------------------------DAQFENDERITPLESAL 123
Cdd:cd00280    10 RWVLDFYFHSACRAFREGRYEDFRRTRDIAEallvgplkltatqlktlrimqflsriaegknlDCQFENDEELTPLESAL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2323579627 124 MIWGSIEKEHDK---LHEEIQNLIKIQAIAVCMENGNFKEAEEVFERIFGDPNSHMPfKSKLLMIISQKDTFHSFFQHFS 200
Cdd:cd00280    90 MVLESIEKEFSLpetLHEEIRKLIKEQAVAVCMENGEFKKAEEVLKRLFSDPESQKL-RMKLLMIIREKDPAHPVLQNFS 168

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2323579627 201 YNHMMEKIKSYVNYVLSEKSSTFLMKAAAKVV 232
Cdd:cd00280   169 YSHFMQKMKSYVELVLDEKESPFLLKAAAKVV 200
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 329-377 8.08e-20

Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human telomere repeat binding factors, TRF1 and TRF2, function as part of the 6 component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminal (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA binding proteins (TRF2, TRF1, and POT1) and 3 recruited proteins that bind to one or more of these DNA-binding proteins (RAP1, TIN2, TPP1). Schizosaccharomyces pombe TAZ1 is an orthlog and binds RAP1. Human TRF1 and TRF2 bind double-stranded DNA. hTRF2 consists of a basic N-terminus, a TRF homology domain, the RAP1 binding motif (RBM), the TIN2 binding motif (TBM) and a myb-like DNA binding domain, SANT, named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. Tandem copies of the domain bind telomeric DNA tandem repeats as part of the capping complex. The single myb-like domain of TRF-type proteins is similar to the tandem myb_like domains found in yeast RAP1.


:

Pssm-ID: 212558 [Multi-domain]  Cd Length: 50  Bit Score: 81.84  E-value: 8.08e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2323579627 329 QAWLWEEDKNLRSGVRKYGEGNWSKILLHYKF-NNRTSVMLKDRWRTMKK 377
Cdd:cd11660     1 RKWTDEEDEALVEGVEKYGVGNWAKILKDYFFvNNRTSVDLKDKWRNLKK 50
 
Name Accession Description Interval E-value
TRFH cd00280
Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain ...
 76-232 1.46e-81

Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH. Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains.


Pssm-ID: 238174  Cd Length: 200  Bit Score: 248.13  E-value: 1.46e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2323579627  76 GWMLDFLCLSLCRAFRDGRSEDFRRTRNSAE--------------------------------DAQFENDERITPLESAL 123
Cdd:cd00280    10 RWVLDFYFHSACRAFREGRYEDFRRTRDIAEallvgplkltatqlktlrimqflsriaegknlDCQFENDEELTPLESAL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2323579627 124 MIWGSIEKEHDK---LHEEIQNLIKIQAIAVCMENGNFKEAEEVFERIFGDPNSHMPfKSKLLMIISQKDTFHSFFQHFS 200
Cdd:cd00280    90 MVLESIEKEFSLpetLHEEIRKLIKEQAVAVCMENGEFKKAEEVLKRLFSDPESQKL-RMKLLMIIREKDPAHPVLQNFS 168

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2323579627 201 YNHMMEKIKSYVNYVLSEKSSTFLMKAAAKVV 232
Cdd:cd00280   169 YSHFMQKMKSYVELVLDEKESPFLLKAAAKVV 200
TRF pfam08558
Telomere repeat binding factor (TRF); Telomere repeat binding factor (TRF) family proteins are ...
 77-210 1.30e-27

Telomere repeat binding factor (TRF); Telomere repeat binding factor (TRF) family proteins are important for the regulation of telomere stability. The two related human TRF proteins hTRF1 and hTRF2 form homodimers and bind directly to telomeric TTAGGG repeats via the myb DNA binding domain pfam00249 at the carboxy terminus. TRF1 is implicated in telomere length regulation and TRF2 in telomere protection. Other telomere complex associated proteins are recruited through their interaction with either TRF1 or TRF2. The fission yeast protein Taz1p (telomere-associated in Schizosaccharomyces pombe) has similarity to both hTRF1 and hTRF2 and may perform the dual functions of TRF1 and TRF2 at fission yeast telomeres. This domain is composed of multiple alpha helices arranged in a solenoid conformation similar to TPR repeats. The fungal members have now also been found to carry two double strand telomeric repeat binding factors.


Pssm-ID: 400735  Cd Length: 212  Bit Score: 108.26  E-value: 1.30e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2323579627  77 WMLDFLCLSLCRAFRDGRSE-----------DFRRTRNSAE--------------------------------------- 106
Cdd:pfam08558   3 WVLDNLSTQLLRALREGPYTdvlaivsepdsEFRESFDILEslfertkklystrspllspsilkiresyimqtlrrinlg 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2323579627 107 ---DAQFENDErITPLESALMIWGSIEKEHDKL---HEEIQNLIKIQAIAVCMENGNFKEAEEVFERIFGDPNSHM---- 176
Cdd:pfam08558  83 tflDSVFGNLE-VGFLELAENFLDIFCPEDGKLlkpQGVLYLDLKTQAYIVALKEGPFKSASEILDKLFPDDLADIlkqr 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2323579627 177 -----------------PFKSKLLMIISQKDTFHSFFQHFSYNHMMEKIKS 210
Cdd:pfam08558 162 ndklltpsetdfverckKRREKLLNIINEKDPYHPLLQNFSWESFLKELLS 212
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 329-377 8.08e-20

Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human telomere repeat binding factors, TRF1 and TRF2, function as part of the 6 component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminal (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA binding proteins (TRF2, TRF1, and POT1) and 3 recruited proteins that bind to one or more of these DNA-binding proteins (RAP1, TIN2, TPP1). Schizosaccharomyces pombe TAZ1 is an orthlog and binds RAP1. Human TRF1 and TRF2 bind double-stranded DNA. hTRF2 consists of a basic N-terminus, a TRF homology domain, the RAP1 binding motif (RBM), the TIN2 binding motif (TBM) and a myb-like DNA binding domain, SANT, named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. Tandem copies of the domain bind telomeric DNA tandem repeats as part of the capping complex. The single myb-like domain of TRF-type proteins is similar to the tandem myb_like domains found in yeast RAP1.


Pssm-ID: 212558 [Multi-domain]  Cd Length: 50  Bit Score: 81.84  E-value: 8.08e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2323579627 329 QAWLWEEDKNLRSGVRKYGEGNWSKILLHYKF-NNRTSVMLKDRWRTMKK 377
Cdd:cd11660     1 RKWTDEEDEALVEGVEKYGVGNWAKILKDYFFvNNRTSVDLKDKWRNLKK 50
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
328-377 7.11e-09

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 51.46  E-value: 7.11e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2323579627  328 RQAWLWEEDKNLRSGVRKYGEGNWSKILLHykFNNRTSVMLKDRWRTMKK 377
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGKNNWEKIAKE--LPGRTAEQCRERWRNLLK 48
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 328-376 2.48e-08

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 459731 [Multi-domain]  Cd Length: 46  Bit Score: 49.81  E-value: 2.48e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2323579627 328 RQAWLWEEDKNLRSGVRKYGeGNWSKILLHykFNNRTSVMLKDRWRTMK 376
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLG-NRWKKIAKL--LPGRTDNQCKNRWQNYL 46
 
Name Accession Description Interval E-value
TRFH cd00280
Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain ...
 76-232 1.46e-81

Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH. Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains.


Pssm-ID: 238174  Cd Length: 200  Bit Score: 248.13  E-value: 1.46e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2323579627  76 GWMLDFLCLSLCRAFRDGRSEDFRRTRNSAE--------------------------------DAQFENDERITPLESAL 123
Cdd:cd00280    10 RWVLDFYFHSACRAFREGRYEDFRRTRDIAEallvgplkltatqlktlrimqflsriaegknlDCQFENDEELTPLESAL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2323579627 124 MIWGSIEKEHDK---LHEEIQNLIKIQAIAVCMENGNFKEAEEVFERIFGDPNSHMPfKSKLLMIISQKDTFHSFFQHFS 200
Cdd:cd00280    90 MVLESIEKEFSLpetLHEEIRKLIKEQAVAVCMENGEFKKAEEVLKRLFSDPESQKL-RMKLLMIIREKDPAHPVLQNFS 168

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2323579627 201 YNHMMEKIKSYVNYVLSEKSSTFLMKAAAKVV 232
Cdd:cd00280   169 YSHFMQKMKSYVELVLDEKESPFLLKAAAKVV 200
TRF pfam08558
Telomere repeat binding factor (TRF); Telomere repeat binding factor (TRF) family proteins are ...
 77-210 1.30e-27

Telomere repeat binding factor (TRF); Telomere repeat binding factor (TRF) family proteins are important for the regulation of telomere stability. The two related human TRF proteins hTRF1 and hTRF2 form homodimers and bind directly to telomeric TTAGGG repeats via the myb DNA binding domain pfam00249 at the carboxy terminus. TRF1 is implicated in telomere length regulation and TRF2 in telomere protection. Other telomere complex associated proteins are recruited through their interaction with either TRF1 or TRF2. The fission yeast protein Taz1p (telomere-associated in Schizosaccharomyces pombe) has similarity to both hTRF1 and hTRF2 and may perform the dual functions of TRF1 and TRF2 at fission yeast telomeres. This domain is composed of multiple alpha helices arranged in a solenoid conformation similar to TPR repeats. The fungal members have now also been found to carry two double strand telomeric repeat binding factors.


Pssm-ID: 400735  Cd Length: 212  Bit Score: 108.26  E-value: 1.30e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2323579627  77 WMLDFLCLSLCRAFRDGRSE-----------DFRRTRNSAE--------------------------------------- 106
Cdd:pfam08558   3 WVLDNLSTQLLRALREGPYTdvlaivsepdsEFRESFDILEslfertkklystrspllspsilkiresyimqtlrrinlg 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2323579627 107 ---DAQFENDErITPLESALMIWGSIEKEHDKL---HEEIQNLIKIQAIAVCMENGNFKEAEEVFERIFGDPNSHM---- 176
Cdd:pfam08558  83 tflDSVFGNLE-VGFLELAENFLDIFCPEDGKLlkpQGVLYLDLKTQAYIVALKEGPFKSASEILDKLFPDDLADIlkqr 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2323579627 177 -----------------PFKSKLLMIISQKDTFHSFFQHFSYNHMMEKIKS 210
Cdd:pfam08558 162 ndklltpsetdfverckKRREKLLNIINEKDPYHPLLQNFSWESFLKELLS 212
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 329-377 8.08e-20

Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human telomere repeat binding factors, TRF1 and TRF2, function as part of the 6 component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminal (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA binding proteins (TRF2, TRF1, and POT1) and 3 recruited proteins that bind to one or more of these DNA-binding proteins (RAP1, TIN2, TPP1). Schizosaccharomyces pombe TAZ1 is an orthlog and binds RAP1. Human TRF1 and TRF2 bind double-stranded DNA. hTRF2 consists of a basic N-terminus, a TRF homology domain, the RAP1 binding motif (RBM), the TIN2 binding motif (TBM) and a myb-like DNA binding domain, SANT, named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. Tandem copies of the domain bind telomeric DNA tandem repeats as part of the capping complex. The single myb-like domain of TRF-type proteins is similar to the tandem myb_like domains found in yeast RAP1.


Pssm-ID: 212558 [Multi-domain]  Cd Length: 50  Bit Score: 81.84  E-value: 8.08e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2323579627 329 QAWLWEEDKNLRSGVRKYGEGNWSKILLHYKF-NNRTSVMLKDRWRTMKK 377
Cdd:cd11660     1 RKWTDEEDEALVEGVEKYGVGNWAKILKDYFFvNNRTSVDLKDKWRNLKK 50
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 330-376 4.08e-09

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.


Pssm-ID: 238096 [Multi-domain]  Cd Length: 45  Bit Score: 51.81  E-value: 4.08e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2323579627 330 AWLWEEDKNLRSGVRKYGEGNWSKILLHykFNNRTSVMLKDRWRTMK 376
Cdd:cd00167     1 PWTEEEDELLLEAVKKYGKNNWEKIAKE--LPGRTPKQCRERWRNLL 45
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
328-377 7.11e-09

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 51.46  E-value: 7.11e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2323579627  328 RQAWLWEEDKNLRSGVRKYGEGNWSKILLHykFNNRTSVMLKDRWRTMKK 377
Cdd:smart00717   1 KGEWTEEEDELLIELVKKYGKNNWEKIAKE--LPGRTAEQCRERWRNLLK 48
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 328-376 2.48e-08

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 459731 [Multi-domain]  Cd Length: 46  Bit Score: 49.81  E-value: 2.48e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2323579627 328 RQAWLWEEDKNLRSGVRKYGeGNWSKILLHykFNNRTSVMLKDRWRTMK 376
Cdd:pfam00249   1 RGPWTPEEDELLLEAVEKLG-NRWKKIAKL--LPGRTDNQCKNRWQNYL 46
Myb_DNA-bind_6 pfam13921
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 331-375 8.42e-03

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 372817 [Multi-domain]  Cd Length: 60  Bit Score: 34.59  E-value: 8.42e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2323579627 331 WLWEEDKNLRSGVRKYGeGNWSKILLHykFNNRTSVMLKDRWRTM 375
Cdd:pfam13921   1 WTEEEDEKLLKLVEKYG-NDWKQIAKE--LGRRTPKQCFDRWRRK 42
 
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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