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Conserved domains on  [gi|295442798|ref|NP_588527|]
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transcription factor TFIID complex subunit Taf13 [Schizosaccharomyces pombe]

Protein Classification

TATA binding protein associated factor 13( domain architecture ID 7054)

TATA binding protein (TBP) associated factor 13 (TAF13) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TAF13 interacts with TAF11 and makes a histone-like heterodimer similar to H3/H4-like proteins. The dimer may be structurally and functionally similar to the spt3 protein within the SAGA histone acetyltransferase complex.

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HFD_SF super family cl45933
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 10-97 8.77e-46

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.


The actual alignment was detected with superfamily member COG5248:

Pssm-ID: 480273  Cd Length: 126  Bit Score: 143.95  E-value: 8.77e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295442798  10 PPTRRQHLFTKDLKSLMYAFGDDVNPAPDSINVLEEIVVDYINEMCLEAARIAGNRNKVKVDDFKFALRDDPKKLGRVEE 89
Cdd:COG5248    3 REARRVNLFMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQVRNKTKTEDFKFALRRDPKKLGRVEE 82


                 ....*...
gi 295442798  90 LLVLQKMI 97
Cdd:COG5248   83 LLITNEEI 90
 
Name Accession Description Interval E-value
TAF19 COG5248
Transcription initiation factor TFIID, subunit TAF13 [Transcription];
10-97 8.77e-46

Transcription initiation factor TFIID, subunit TAF13 [Transcription];


Pssm-ID: 227573  Cd Length: 126  Bit Score: 143.95  E-value: 8.77e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295442798  10 PPTRRQHLFTKDLKSLMYAFGDDVNPAPDSINVLEEIVVDYINEMCLEAARIAGNRNKVKVDDFKFALRDDPKKLGRVEE 89
Cdd:COG5248    3 REARRVNLFMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQVRNKTKTEDFKFALRRDPKKLGRVEE 82


                 ....*...
gi 295442798  90 LLVLQKMI 97
Cdd:COG5248   83 LLITNEEI 90
HFD_TAF13 cd07978
histone-fold domain found in transcription initiation factor TFIID subunit 13 (TAF13) and ...
 17-91 3.83e-30

histone-fold domain found in transcription initiation factor TFIID subunit 13 (TAF13) and similar proteins; TAF13, also called TATA Binding Protein (TBP) associated factor 13, transcription initiation factor TFIID 18 kDa subunit, TAF(II)18, TAFII-18, or TAFII18, is a component of the DNA-binding general RNA polymerase II transcription factor IID (TFIID) complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors. TAF13 interacts with TBP, and more strongly with TAF10 and TAF11.


Pssm-ID: 467023  Cd Length: 77  Bit Score: 102.54  E-value: 3.83e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 295442798  17 LFTKDLKSLMYAFGDDVNPAPDSINVLEEIVVDYINEMCLEAARIAGNRN--KVKVDDFKFALRDDPKKLGRVEELL 91
Cdd:cd07978    1 LFTKEIRQMMYGFGDVRNPLPETVDLLEEIVIEYITDLLHKAMEVAKLRGskKISVEDILFLLRKDPKKLARVKELL 77
TFIID-18kDa pfam02269
Transcription initiation factor IID, 18kD subunit; This family includes the Spt3 yeast ...
 16-101 6.88e-23

Transcription initiation factor IID, 18kD subunit; This family includes the Spt3 yeast transcription factors and the 18kD subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold


Pssm-ID: 190265  Cd Length: 93  Bit Score: 84.79  E-value: 6.88e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295442798   16 HLFTKDLKSLMYAFGDDVNPAPDSINVLEEIVVDYINEMCLEAARIAGNR--NKVKVDDFKFALRDDPKKLGRVEELLVL 93
Cdd:pfam02269   1 HLFRKELQSMMYGFGDVQDPLQETVQLLEDLVRGQLIELLQQAMKTAQLRgsRKITLEDIKFLIRKDPKKLNRLKDLLSM 80


                  ....*...
gi 295442798   94 QKMIADTR 101
Cdd:pfam02269  81 NELLKKAR 88
 
Name Accession Description Interval E-value
TAF19 COG5248
Transcription initiation factor TFIID, subunit TAF13 [Transcription];
10-97 8.77e-46

Transcription initiation factor TFIID, subunit TAF13 [Transcription];


Pssm-ID: 227573  Cd Length: 126  Bit Score: 143.95  E-value: 8.77e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295442798  10 PPTRRQHLFTKDLKSLMYAFGDDVNPAPDSINVLEEIVVDYINEMCLEAARIAGNRNKVKVDDFKFALRDDPKKLGRVEE 89
Cdd:COG5248    3 REARRVNLFMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQVRNKTKTEDFKFALRRDPKKLGRVEE 82


                 ....*...
gi 295442798  90 LLVLQKMI 97
Cdd:COG5248   83 LLITNEEI 90
HFD_TAF13 cd07978
histone-fold domain found in transcription initiation factor TFIID subunit 13 (TAF13) and ...
 17-91 3.83e-30

histone-fold domain found in transcription initiation factor TFIID subunit 13 (TAF13) and similar proteins; TAF13, also called TATA Binding Protein (TBP) associated factor 13, transcription initiation factor TFIID 18 kDa subunit, TAF(II)18, TAFII-18, or TAFII18, is a component of the DNA-binding general RNA polymerase II transcription factor IID (TFIID) complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors. TAF13 interacts with TBP, and more strongly with TAF10 and TAF11.


Pssm-ID: 467023  Cd Length: 77  Bit Score: 102.54  E-value: 3.83e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 295442798  17 LFTKDLKSLMYAFGDDVNPAPDSINVLEEIVVDYINEMCLEAARIAGNRN--KVKVDDFKFALRDDPKKLGRVEELL 91
Cdd:cd07978    1 LFTKEIRQMMYGFGDVRNPLPETVDLLEEIVIEYITDLLHKAMEVAKLRGskKISVEDILFLLRKDPKKLARVKELL 77
TFIID-18kDa pfam02269
Transcription initiation factor IID, 18kD subunit; This family includes the Spt3 yeast ...
 16-101 6.88e-23

Transcription initiation factor IID, 18kD subunit; This family includes the Spt3 yeast transcription factors and the 18kD subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold


Pssm-ID: 190265  Cd Length: 93  Bit Score: 84.79  E-value: 6.88e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295442798   16 HLFTKDLKSLMYAFGDDVNPAPDSINVLEEIVVDYINEMCLEAARIAGNR--NKVKVDDFKFALRDDPKKLGRVEELLVL 93
Cdd:pfam02269   1 HLFRKELQSMMYGFGDVQDPLQETVQLLEDLVRGQLIELLQQAMKTAQLRgsRKITLEDIKFLIRKDPKKLNRLKDLLSM 80


                  ....*...
gi 295442798   94 QKMIADTR 101
Cdd:pfam02269  81 NELLKKAR 88
HFD_SPT3 cd22926
histone-fold domain found in protein SPT3 and similar proteins; SPT3, also called suppressor ...
 18-94 1.13e-10

histone-fold domain found in protein SPT3 and similar proteins; SPT3, also called suppressor of Ty 3 homolog, or positive regulator of Ty transcription, is a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. SAGA (Spt-Ada-Gcn5-acetyltransferase) is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TATA binding protein (TBP) interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA (SAGA altered, SPT8 absent), an altered form of SAGA, may be involved in positive transcriptional regulation. Besides lacking SPT8, SALSA contains an SPT7 subunit that is truncated. SPT3 is required for recruitment of TATA-binding protein (TBP) to SAGA-dependent promoters. During SAGA-mediated transcriptional inhibition, SPT3 and SPT8 prevent binding of TBP to the TATA box. SLIK (SAGA-like) is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. SPT factors 3, 7 and 8 are required for the initiation of Ty transcription from the delta promoter. SPT3 regulates Ty1 as well as mating factor genes.


Pssm-ID: 467051  Cd Length: 81  Bit Score: 53.35  E-value: 1.13e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 295442798  18 FTKDLKSLMYAFGDDVNPAPDSINVLEEIVVDYINEMCLEAARIAGNRN--KVKVDDFKFALRDDPKKLGRVEELLVLQ 94
Cdd:cd22926    2 YRTEIQQMMFVLGDVRDPLPETVDLVEDIVRQQMILLLYQASELASSRGsrQITPEDVLFLLRHDKVKLNRLLTYLKWK 80
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 23-78 7.81e-05

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.


Pssm-ID: 467021  Cd Length: 63  Bit Score: 37.58  E-value: 7.81e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 295442798  23 KSLMYAFGDDvNPAPDSINVLEEIVVDYINEMCLEAARIA--GNRNKVKVDDFKFALR 78
Cdd:cd00076    7 ARILKSAGFD-SVSKSALELLSDLLERYLEELARAAKAYAelAGRTTPNAEDVELALE 63
 
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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