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Conserved domains on  [gi|30682510|ref|NP_196480|]
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DDT domain-containing protein [Arabidopsis thaliana]

Protein Classification

WAC_Acf1_DNA_bd and DDT domain-containing protein( domain architecture ID 10565471)

protein containing domains WAC_Acf1_DNA_bd, DDT, WHIM1, and WSD

Graphical summary

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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 ...
 24-121 1.16e-34

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: 127.28  E-value: 1.16e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30682510    24 VYQVRLTNEIFRDYQLYLKRLNLYRNRVWTCKSTGKTSLSYEEALDSEKLAGKKVQT-LPRELVAPALRIIQFSTLS-LK 101
Cdd:pfam10537   2 VFVIPLTGEIFRDYEEYLERLDLYNQRIWSCEITGKSNLTYFEALESEEKARKKLEEkFPESLREPVLRLVQFSTRSrLD 81

                          90       100
                  ....*....|....*....|
gi 30682510   102 DLADKIATELQDCFFPGAEL 121
Cdd:pfam10537  82 DLVDDVYEEFKDRFFPGEEV 101
WSD pfam15613
Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined ...
 603-667 8.96e-27

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: 103.38  E-value: 8.96e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30682510   603 IRTNPLGKDRDYNRYWWF-RSNGRIFVENSDSEEWGYYTAKEELDALMGSLNRKGERELSLYTQLE 667
Cdd:pfam15613   1 IRSLPLGRDRRYNRYWWFdPGTGRLFVESPSDGEWGVYSSKEQLDALIASLNPRGVRESALKEALE 66
DDT pfam02791
DDT domain; The DDT domain is named after (DNA binding homeobox and Different Transcription ...
 298-355 8.38e-18

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: 77.55  E-value: 8.38e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 30682510   298 DCVGDLLMVWDFCTSFGRQLHLWRFSLEDFENAVCHKESNLVLIMEVHASLFRFLINE 355
Cdd:pfam02791   1 EAFGDLLMVWEFLNSFGEVLGLSPFTLDDFEEALLCTEEPSELLDEIHCALLKALVRD 58
WHIM1 pfam15612
WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and ...
 399-435 6.78e-05

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, 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 conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.


:

Pssm-ID: 464774 [Multi-domain]  Cd Length: 46  Bit Score: 40.56  E-value: 6.78e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 30682510   399 TIKRGHYGLLDPNVKLKILRELVNHITETGMFKGEID 435
Cdd:pfam15612  10 TLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEIE 46
 
Name Accession Description Interval E-value
WAC_Acf1_DNA_bd pfam10537
ATP-utilizing chromatin assembly and remodelling N-terminal; ACF (for ATP-utilizing chromatin ...
 24-121 1.16e-34

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: 127.28  E-value: 1.16e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30682510    24 VYQVRLTNEIFRDYQLYLKRLNLYRNRVWTCKSTGKTSLSYEEALDSEKLAGKKVQT-LPRELVAPALRIIQFSTLS-LK 101
Cdd:pfam10537   2 VFVIPLTGEIFRDYEEYLERLDLYNQRIWSCEITGKSNLTYFEALESEEKARKKLEEkFPESLREPVLRLVQFSTRSrLD 81

                          90       100
                  ....*....|....*....|
gi 30682510   102 DLADKIATELQDCFFPGAEL 121
Cdd:pfam10537  82 DLVDDVYEEFKDRFFPGEEV 101
WSD pfam15613
Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined ...
 603-667 8.96e-27

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: 103.38  E-value: 8.96e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30682510   603 IRTNPLGKDRDYNRYWWF-RSNGRIFVENSDSEEWGYYTAKEELDALMGSLNRKGERELSLYTQLE 667
Cdd:pfam15613   1 IRSLPLGRDRRYNRYWWFdPGTGRLFVESPSDGEWGVYSSKEQLDALIASLNPRGVRESALKEALE 66
DDT pfam02791
DDT domain; The DDT domain is named after (DNA binding homeobox and Different Transcription ...
 298-355 8.38e-18

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: 77.55  E-value: 8.38e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 30682510   298 DCVGDLLMVWDFCTSFGRQLHLWRFSLEDFENAVCHKESNLVLIMEVHASLFRFLINE 355
Cdd:pfam02791   1 EAFGDLLMVWEFLNSFGEVLGLSPFTLDDFEEALLCTEEPSELLDEIHCALLKALVRD 58
DDT smart00571
domain in different transcription and chromosome remodeling factors;
297-358 9.17e-17

domain in different transcription and chromosome remodeling factors;


Pssm-ID: 214726  Cd Length: 63  Bit Score: 74.98  E-value: 9.17e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 30682510    297 MDCVGDLLMVWDFCTSFGRQLHLWRF--SLEDFENAVCHKESNlVLIMEVHASLFRFLINERGD 358
Cdd:smart00571   1 NEAFGDLLMVYEFLRSFGKVLGLSPFraTLEDFIAALKCRDQN-GLLTEVHVVLLRAILKDEGE 63
WHIM1 pfam15612
WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and ...
 399-435 6.78e-05

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, 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 conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.


Pssm-ID: 464774 [Multi-domain]  Cd Length: 46  Bit Score: 40.56  E-value: 6.78e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 30682510   399 TIKRGHYGLLDPNVKLKILRELVNHITETGMFKGEID 435
Cdd:pfam15612  10 TLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEIE 46
 
Name Accession Description Interval E-value
WAC_Acf1_DNA_bd pfam10537
ATP-utilizing chromatin assembly and remodelling N-terminal; ACF (for ATP-utilizing chromatin ...
 24-121 1.16e-34

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: 127.28  E-value: 1.16e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30682510    24 VYQVRLTNEIFRDYQLYLKRLNLYRNRVWTCKSTGKTSLSYEEALDSEKLAGKKVQT-LPRELVAPALRIIQFSTLS-LK 101
Cdd:pfam10537   2 VFVIPLTGEIFRDYEEYLERLDLYNQRIWSCEITGKSNLTYFEALESEEKARKKLEEkFPESLREPVLRLVQFSTRSrLD 81

                          90       100
                  ....*....|....*....|
gi 30682510   102 DLADKIATELQDCFFPGAEL 121
Cdd:pfam10537  82 DLVDDVYEEFKDRFFPGEEV 101
WSD pfam15613
Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined ...
 603-667 8.96e-27

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: 103.38  E-value: 8.96e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30682510   603 IRTNPLGKDRDYNRYWWF-RSNGRIFVENSDSEEWGYYTAKEELDALMGSLNRKGERELSLYTQLE 667
Cdd:pfam15613   1 IRSLPLGRDRRYNRYWWFdPGTGRLFVESPSDGEWGVYSSKEQLDALIASLNPRGVRESALKEALE 66
DDT pfam02791
DDT domain; The DDT domain is named after (DNA binding homeobox and Different Transcription ...
 298-355 8.38e-18

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: 77.55  E-value: 8.38e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 30682510   298 DCVGDLLMVWDFCTSFGRQLHLWRFSLEDFENAVCHKESNLVLIMEVHASLFRFLINE 355
Cdd:pfam02791   1 EAFGDLLMVWEFLNSFGEVLGLSPFTLDDFEEALLCTEEPSELLDEIHCALLKALVRD 58
DDT smart00571
domain in different transcription and chromosome remodeling factors;
297-358 9.17e-17

domain in different transcription and chromosome remodeling factors;


Pssm-ID: 214726  Cd Length: 63  Bit Score: 74.98  E-value: 9.17e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 30682510    297 MDCVGDLLMVWDFCTSFGRQLHLWRF--SLEDFENAVCHKESNlVLIMEVHASLFRFLINERGD 358
Cdd:smart00571   1 NEAFGDLLMVYEFLRSFGKVLGLSPFraTLEDFIAALKCRDQN-GLLTEVHVVLLRAILKDEGE 63
WHIM1 pfam15612
WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and ...
 399-435 6.78e-05

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, 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 conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.


Pssm-ID: 464774 [Multi-domain]  Cd Length: 46  Bit Score: 40.56  E-value: 6.78e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 30682510   399 TIKRGHYGLLDPNVKLKILRELVNHITETGMFKGEID 435
Cdd:pfam15612  10 TLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEIE 46
 
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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