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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 217272833  37 DFRVQELPLARIKKIMKLDEDVK--------------------------------------RNDIAMAITKFDQFDFLID 78
Cdd:cd22908    2 DFKNHELPLARIKKIMKSDEDVKmisaeapvlfakacelfileltlrawihteenkrrtlqRSDIAAAITSSDMFDFLID 81

                 ...
gi 217272833  79 IVP 81
Cdd:cd22908   82 IVP 84

histone-fold domain found in nuclear transcription factor Y subunit gamma (NF-YC) and similar proteins; NF-YC, also called CAAT box DNA-binding protein subunit C, or nuclear transcription factor Y subunit C, or transactivator HSM-1/2, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y) which specifically recognizes a 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors. NF-Y is a heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding. The family also includes NF-YC homologs such as Aspergillus fumigatus CCAAT-binding complex (CBC) subunit HapE and Saccharomyces cerevisiae transcriptional activator Hap5. HapE is a component of CBC, which is composed of the histone-like subunits HapC and HapE as well as the DNA specificity conferring subunit HapB. In yeast, Hap5 is a component of the CCAT-binding factor (CBF or HAP complex II), which is a transcriptional activator and binds to the upstream activation site (UAS2) of the CYC1 gene and other genes involved in mitochondrial electron transport and activates their expression. It recognizes the sequence 5'-CCAAT-3'. Hap5 is essential for DNA-binding activity.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 217272833  37 DFRVQELPLARIKKIMKLDEDVK--------------------------------------RNDIAMAITKFDQFDFLID 78
Cdd:cd22908    2 DFKNHELPLARIKKIMKSDEDVKmisaeapvlfakacelfileltlrawihteenkrrtlqRSDIAAAITSSDMFDFLID 81

                 ...
gi 217272833  79 IVP 81
Cdd:cd22908   82 IVP 84

Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes archaebacterial histones and histone like transcription factors from eukaryotes.

                          10
                  ....*....|....*....
gi 217272833   42 ELPLARIKKIMKLDEDVKR 60
Cdd:pfam00808   2 ELPIARVKRIMKSDPDAGR 20

histone-fold domain found in nuclear transcription factor Y subunit gamma (NF-YC) and similar proteins; NF-YC, also called CAAT box DNA-binding protein subunit C, or nuclear transcription factor Y subunit C, or transactivator HSM-1/2, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y) which specifically recognizes a 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors. NF-Y is a heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding. The family also includes NF-YC homologs such as Aspergillus fumigatus CCAAT-binding complex (CBC) subunit HapE and Saccharomyces cerevisiae transcriptional activator Hap5. HapE is a component of CBC, which is composed of the histone-like subunits HapC and HapE as well as the DNA specificity conferring subunit HapB. In yeast, Hap5 is a component of the CCAT-binding factor (CBF or HAP complex II), which is a transcriptional activator and binds to the upstream activation site (UAS2) of the CYC1 gene and other genes involved in mitochondrial electron transport and activates their expression. It recognizes the sequence 5'-CCAAT-3'. Hap5 is essential for DNA-binding activity.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 217272833  37 DFRVQELPLARIKKIMKLDEDVK--------------------------------------RNDIAMAITKFDQFDFLID 78
Cdd:cd22908    2 DFKNHELPLARIKKIMKSDEDVKmisaeapvlfakacelfileltlrawihteenkrrtlqRSDIAAAITSSDMFDFLID 81

                 ...
gi 217272833  79 IVP 81
Cdd:cd22908   82 IVP 84

histone-fold domain found in DNA polymerase epsilon subunit 4 (POLE4) and similar proteins; POLE4, also called DNA polymerase II subunit 4, or DNA polymerase epsilon subunit p12, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex that consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. POLE4 forms a complex with POLE3. The POLE3-POLE4 is a histone chaperone that promotes tetrasome formation and DNA supercoiling in vitro. Interaction with POLE3 is a prerequisite for further binding with POLE and POLE2. In fungi, POLE4 has been named as DNA polymerase epsilon subunit C (DPB3, also known as DNA polymerase II subunit C). It is an accessory component of the DNA polymerase epsilon (DNA polymerase II) that participates in chromosomal DNA replication. DNA polymerase epsilon is a heterotetramer consisting of POL2, DPB2, DPB3 and DPB4. DPB3 is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. This subfamily also includes protein DLS1 (DPB3-like subunit of ISW2 complex 1). It functions as a component of the ISW2 complex, which at least consists of ISW2, ITC1, DLS1 and DPB4, and acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. The ISW2 complex is involved in coordinating transcriptional repression and in inheritance of telomeric silencing. It is involved in repression of MAT a-specific genes, INO1, and early meiotic genes during mitotic growth dependent upon transcription factor UME6 and in a parallel pathway to the RPD3-SIN3 histone deacetylase complex. DLS1 is partially required for the ISW2 complex chromatin remodeling activity and is not required for its interaction with chromatin.

                         10        20
                 ....*....|....*....|....*....
gi 217272833  43 LPLARIKKIMKLDEDVKR--NDIAMAITK 69
Cdd:cd22929    4 LPLSRVKRIMKLDPDVTLvsQEAVVAIAK 32

histone-fold domain found in Dr1-associated protein 1 (DRAP1) and similar proteins; DRAP1, also called Dr1-associated corepressor or negative cofactor 2-alpha (NC2-alpha), acts as a corepressor for Dr1 (down-regulator of transcription 1)-mediated repression of transcription. It forms a heterodimer with Dr1. The association of the Dr1/DRAP1 heterodimer with TBP results in a functional repression of both activated and basal transcription of class II genes. DRAP1 can bind to DNA on its own. It also binds TATA-binding protein-associated factor 172 (BTAF1).

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 217272833  44 PLARIKKIMKLDEDVKRndIAMA----ITKFDQFdFLIDIV 80
Cdd:cd22906    5 PAARIKKIMQSDEEVGK--VAAAvpvlISKALEL-FLEDLL 42

histone-fold domain found in chromatin accessibility complex protein 1 (CHRAC-1) and similar proteins; CHRAC-1, also called chromatin accessibility complex 15 kDa protein, or CHRAC-15, or DNA polymerase epsilon subunit p15, forms a complex with DNA polymerase epsilon subunit POLE3 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome remodeling activity of ISWI/SNF2H and ACF1. Together with POLE3, ACF1 and ISWI/SNF2H proteins, CHRAC-1 forms the ISWI chromatin-remodeling complex, CHRAC. This subfamily also includes Drosophila melanogaster chromatin accessibility complex 16kD protein (CHRAC-16), which is a histone-like protein that promotes nucleosome sliding of ATP-dependent nucleosome remodeling complexes. It is part of the CHRAC, composed of CHRAC-14, CHRAC-16, ACF and ISWI, which uses energy/ATP to increase the general accessibility of DNA in chromatin. It forms a heterodimer with CHRAC-14, binds DNA, and facilitates nucleosome sliding by ACF. It is required for oogenesis.

                         10        20
                 ....*....|....*....|....*....
gi 217272833  43 LPLARIKKIMKLDEDVK--RNDIAMAITK 69
Cdd:cd22924    1 LPLSRVRTIMKSSPDVSsiSQDAVFLITK 29