NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|6321305|ref|NP_011382|]
View 

Itc1p [Saccharomyces cerevisiae S288C]

Protein Classification

WAC_Acf1_DNA_bd and DDT domain-containing protein( domain architecture ID 12107267)

protein containing domains WAC_Acf1_DNA_bd, DDT, and WSD

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
WAC_Acf1_DNA_bd pfam10537
ATP-utilizing chromatin assembly and remodelling N-terminal; ACF (for ATP-utilizing chromatin ...
 24-124 3.89e-46

ATP-utilizing chromatin assembly and remodelling N-terminal; ACF (for ATP-utilizing chromatin assembly and remodelling factor) is a chromatin-remodelling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. The WAC (WSTF/Acf1/cbp146) domain is an approximately 110-residue module present at the N-termini of Acf1-related proteins in a variety of organizms. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA.


:

Pssm-ID: 463140  Cd Length: 101  Bit Score: 160.80  E-value: 3.89e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321305      24 QVWHIEETGEWFSSYEEFLERFDFYTRHHFTCEITGTSCLTFFQALDSEETQFKYVEDRFPLKLREPVARFLHFNGIRRL 103
Cdd:pfam10537    1 EVFVIPLTGEIFRDYEEYLERLDLYNQRIWSCEITGKSNLTYFEALESEEKARKKLEEKFPESLREPVLRLVQFSTRSRL 80

                           90       100
                   ....*....|....*....|.
gi 6321305     104 DALVEKVYARFKNDFFPGEVV 124
Cdd:pfam10537   81 DDLVDDVYEEFKDRFFPGEEV 101
DDT smart00571
domain in different transcription and chromosome remodeling factors;
423-483 5.01e-16

domain in different transcription and chromosome remodeling factors;


:

Pssm-ID: 214726  Cd Length: 63  Bit Score: 73.44  E-value: 5.01e-16
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6321305      423 FDSFGKLLQAYQFLNTFGSKICLSHF--SLDQFITSLKCTDPYELKGEVVLVNIRTQTSKEQE 483
Cdd:smart00571    1 NEAFGDLLMVYEFLRSFGKVLGLSPFraTLEDFIAALKCRDQNGLLTEVHVVLLRAILKDEGE 63
WSD super family cl21412
Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined ...
 869-952 4.69e-03

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.


The actual alignment was detected with superfamily member pfam15613:

Pssm-ID: 464775 [Multi-domain]  Cd Length: 69  Bit Score: 36.74  E-value: 4.69e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321305     869 RLKPLGLDRYGNRYFWLDhngvpfpqypagmnetpksnnslsYHSGRLLIQGPKASSAKFFLNVSD-EQLSNWQkirNSE 947
Cdd:pfam15613    2 RSLPLGRDRRYNRYWWFD------------------------PGTGRLFVESPSDGEWGVYSSKEQlDALIASL---NPR 54


                   ....*
gi 6321305     948 GISEA 952
Cdd:pfam15613   55 GVRES 59
 
Name Accession Description Interval E-value
WAC_Acf1_DNA_bd pfam10537
ATP-utilizing chromatin assembly and remodelling N-terminal; ACF (for ATP-utilizing chromatin ...
 24-124 3.89e-46

ATP-utilizing chromatin assembly and remodelling N-terminal; ACF (for ATP-utilizing chromatin assembly and remodelling factor) is a chromatin-remodelling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. The WAC (WSTF/Acf1/cbp146) domain is an approximately 110-residue module present at the N-termini of Acf1-related proteins in a variety of organizms. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA.


Pssm-ID: 463140  Cd Length: 101  Bit Score: 160.80  E-value: 3.89e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321305      24 QVWHIEETGEWFSSYEEFLERFDFYTRHHFTCEITGTSCLTFFQALDSEETQFKYVEDRFPLKLREPVARFLHFNGIRRL 103
Cdd:pfam10537    1 EVFVIPLTGEIFRDYEEYLERLDLYNQRIWSCEITGKSNLTYFEALESEEKARKKLEEKFPESLREPVLRLVQFSTRSRL 80

                           90       100
                   ....*....|....*....|.
gi 6321305     104 DALVEKVYARFKNDFFPGEVV 124
Cdd:pfam10537   81 DDLVDDVYEEFKDRFFPGEEV 101
DDT smart00571
domain in different transcription and chromosome remodeling factors;
423-483 5.01e-16

domain in different transcription and chromosome remodeling factors;


Pssm-ID: 214726  Cd Length: 63  Bit Score: 73.44  E-value: 5.01e-16
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6321305      423 FDSFGKLLQAYQFLNTFGSKICLSHF--SLDQFITSLKCTDPYELKGEVVLVNIRTQTSKEQE 483
Cdd:smart00571    1 NEAFGDLLMVYEFLRSFGKVLGLSPFraTLEDFIAALKCRDQNGLLTEVHVVLLRAILKDEGE 63
DDT pfam02791
DDT domain; The DDT domain is named after (DNA binding homeobox and Different Transcription ...
 424-476 1.90e-11

DDT domain; The DDT domain is named after (DNA binding homeobox and Different Transcription factors) and is approximately 60 residues in length. Along with the WHIM motifs, it comprises an entirely alpha helical module found in diverse eukaryotic chromatin proteins. Based on the structure of Ioc3, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. In particular, the DDT domain, in combination with the WHIM1 and WHIM2 motifs form the SLIDE domain binding pocket.


Pssm-ID: 460696  Cd Length: 58  Bit Score: 60.21  E-value: 1.90e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 6321305     424 DSFGKLLQAYQFLNTFGSKICLSHFSLDQFITSLKCTD-PYELKGEVVLVNIRT 476
Cdd:pfam02791    1 EAFGDLLMVWEFLNSFGEVLGLSPFTLDDFEEALLCTEePSELLDEIHCALLKA 54
WSD pfam15613
Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined ...
 869-952 4.69e-03

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.


Pssm-ID: 464775 [Multi-domain]  Cd Length: 69  Bit Score: 36.74  E-value: 4.69e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321305     869 RLKPLGLDRYGNRYFWLDhngvpfpqypagmnetpksnnslsYHSGRLLIQGPKASSAKFFLNVSD-EQLSNWQkirNSE 947
Cdd:pfam15613    2 RSLPLGRDRRYNRYWWFD------------------------PGTGRLFVESPSDGEWGVYSSKEQlDALIASL---NPR 54


                   ....*
gi 6321305     948 GISEA 952
Cdd:pfam15613   55 GVRES 59
 
Name Accession Description Interval E-value
WAC_Acf1_DNA_bd pfam10537
ATP-utilizing chromatin assembly and remodelling N-terminal; ACF (for ATP-utilizing chromatin ...
 24-124 3.89e-46

ATP-utilizing chromatin assembly and remodelling N-terminal; ACF (for ATP-utilizing chromatin assembly and remodelling factor) is a chromatin-remodelling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. The WAC (WSTF/Acf1/cbp146) domain is an approximately 110-residue module present at the N-termini of Acf1-related proteins in a variety of organizms. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA.


Pssm-ID: 463140  Cd Length: 101  Bit Score: 160.80  E-value: 3.89e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321305      24 QVWHIEETGEWFSSYEEFLERFDFYTRHHFTCEITGTSCLTFFQALDSEETQFKYVEDRFPLKLREPVARFLHFNGIRRL 103
Cdd:pfam10537    1 EVFVIPLTGEIFRDYEEYLERLDLYNQRIWSCEITGKSNLTYFEALESEEKARKKLEEKFPESLREPVLRLVQFSTRSRL 80

                           90       100
                   ....*....|....*....|.
gi 6321305     104 DALVEKVYARFKNDFFPGEVV 124
Cdd:pfam10537   81 DDLVDDVYEEFKDRFFPGEEV 101
DDT smart00571
domain in different transcription and chromosome remodeling factors;
423-483 5.01e-16

domain in different transcription and chromosome remodeling factors;


Pssm-ID: 214726  Cd Length: 63  Bit Score: 73.44  E-value: 5.01e-16
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6321305      423 FDSFGKLLQAYQFLNTFGSKICLSHF--SLDQFITSLKCTDPYELKGEVVLVNIRTQTSKEQE 483
Cdd:smart00571    1 NEAFGDLLMVYEFLRSFGKVLGLSPFraTLEDFIAALKCRDQNGLLTEVHVVLLRAILKDEGE 63
DDT pfam02791
DDT domain; The DDT domain is named after (DNA binding homeobox and Different Transcription ...
 424-476 1.90e-11

DDT domain; The DDT domain is named after (DNA binding homeobox and Different Transcription factors) and is approximately 60 residues in length. Along with the WHIM motifs, it comprises an entirely alpha helical module found in diverse eukaryotic chromatin proteins. Based on the structure of Ioc3, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. In particular, the DDT domain, in combination with the WHIM1 and WHIM2 motifs form the SLIDE domain binding pocket.


Pssm-ID: 460696  Cd Length: 58  Bit Score: 60.21  E-value: 1.90e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 6321305     424 DSFGKLLQAYQFLNTFGSKICLSHFSLDQFITSLKCTD-PYELKGEVVLVNIRT 476
Cdd:pfam02791    1 EAFGDLLMVWEFLNSFGEVLGLSPFTLDDFEEALLCTEePSELLDEIHCALLKA 54
WSD pfam15613
Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined ...
 869-952 4.69e-03

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.


Pssm-ID: 464775 [Multi-domain]  Cd Length: 69  Bit Score: 36.74  E-value: 4.69e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321305     869 RLKPLGLDRYGNRYFWLDhngvpfpqypagmnetpksnnslsYHSGRLLIQGPKASSAKFFLNVSD-EQLSNWQkirNSE 947
Cdd:pfam15613    2 RSLPLGRDRRYNRYWWFD------------------------PGTGRLFVESPSDGEWGVYSSKEQlDALIASL---NPR 54


                   ....*
gi 6321305     948 GISEA 952
Cdd:pfam15613   55 GVRES 59
 
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