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        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 449452907  12 PEFPTGRVKKIMKLDKDIGKVNSEALFLVSCATELFLKLLAEKSAESAAEKKRKTVKLEHIRMAVKRHRSIsDFLLDSL 90
Cdd:cd22929    2 PKLPLSRVKRIMKLDPDVTLVSQEAVVAIAKATELFIQLLAKEAYSVAQQSKRKTLQLKDIDAAIKSDDRF-AFLEDVL 79

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        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 449452907  12 PEFPTGRVKKIMKLDKDIGKVNSEALFLVSCATELFLKLLAEKSAESAAEKKRKTVKLEHIRMAVKRHRSIsDFLLDSL 90
Cdd:cd22929    2 PKLPLSRVKRIMKLDPDVTLVSQEAVVAIAKATELFIQLLAKEAYSVAQQSKRKTLQLKDIDAAIKSDDRF-AFLEDVL 79

CCAAT-binding factor, subunit C [Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449452907  15 PTGRVKKIMKLDKDIGKVNSEALFLVSCATELFLKLLAEKSAESAAEKKRKTVKLEHIRMAVKRhRSISDFLLDSLPLPS 94
Cdd:COG5208  111 PLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKK-SEMFDFLIDIVPRNP 189

                 ....*...
gi 449452907  95 QPSDAPAK 102
Cdd:COG5208  190 FNHLVPSK 197

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        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 449452907  12 PEFPTGRVKKIMKLDKDIGKVNSEALFLVSCATELFLKLLAEKSAESAAEKKRKTVKLEHIRMAVKRHRSIsDFLLDSL 90
Cdd:cd22929    2 PKLPLSRVKRIMKLDPDVTLVSQEAVVAIAKATELFIQLLAKEAYSVAQQSKRKTLQLKDIDAAIKSDDRF-AFLEDVL 79

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        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 449452907  14 FPTGRVKKIMKLDKDIGKVNSEALFLVSCATELFLKLLAEKSAESAAEKKRKTVKLEHIRMAVKRHrSISDFL 86
Cdd:cd22906    4 FPAARIKKIMQSDEEVGKVAAAVPVLISKALELFLEDLLTKAAEVAKERNAKTITPSHLKQCVESE-EKFDFL 75

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 449452907  12 PEFPTGRVKKIMKLDKDIGKVNSEALFLVSCATELFLKLLAEKSAESAAEKKRKTVKLEHIRMAVKRHrSISDFLLDSLP 91
Cdd:cd22908    6 HELPLARIKKIMKSDEDVKMISAEAPVLFAKACELFILELTLRAWIHTEENKRRTLQRSDIAAAITSS-DMFDFLIDIVP 84

CCAAT-binding factor, subunit C [Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449452907  15 PTGRVKKIMKLDKDIGKVNSEALFLVSCATELFLKLLAEKSAESAAEKKRKTVKLEHIRMAVKRhRSISDFLLDSLPLPS 94
Cdd:COG5208  111 PLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKK-SEMFDFLIDIVPRNP 189

                 ....*...
gi 449452907  95 QPSDAPAK 102
Cdd:COG5208  190 FNHLVPSK 197

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 449452907  14 FPTGRVKKIMKLDKDIGkVNSEALFLVSCATELFLKLLAEKSAESAAEKKRKTVKLEHIRMAVK 77
Cdd:cd00076    1 LLRSAVARILKSAGFDS-VSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63

histone-fold domain found in centromere protein W (CENP-W) and similar proteins; CENP-W, also called cancer-up-regulated gene 2 protein (CUG2), is a component of the CENPA-NAC (nucleosome-associated) complex, which plays a central role in the assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENP-A into centromeres. CENP-W is also part of a nucleosome-associated complex that binds specifically to histone H3-containing nucleosomes at the centromere, as opposed to nucleosomes containing CENP-A. Moreover, CENP-W forms a heterodimer with CENP-T. This dimer co-assembles with CENP-S-CENP-X heterodimers at centromeres to form the tetrameric CENP-T-W-S-X complex, which is a subcomplex of the large constitutive centromere-associated network (CCAN, also known as the interphase centromere complex or ICEN). The heterotetrameric CENP-T-W-S-X complex binds and supercoils DNA and plays an important role in kinetochore assembly. CENP-W has a fundamental role in kinetochore assembly and function. It is one of the inner kinetochore proteins, with most further proteins binding downstream. It is required for normal chromosome organization and normal progress through mitosis.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 449452907  14 FPTGRVKKIMKLDKDIGKVNSEALFLVSCATELFLKLLAEKSAESAAEKKRKTVKLEHIRMAVKR 78
Cdd:cd13732    3 YPRSTLKKIIKKHLPGLRLAKNADILVYLDYLLFLQRLAEEARTEARESGSKTIKPEHVRKAAKK 67

Archaeal histone H3/H4 [Chromatin structure and dynamics];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 449452907  13 EFPTGRVKKIMKlDKDIGKVNSEALFLVSCATELFLKLLAEKSAESAAEKKRKTVKLEHIRMAVKR 78
Cdd:COG2036    1 ELPVAPVDRIIK-KAGAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65

histone-fold domain found in centromere protein X (CENP-X) and similar proteins; CENP-X, also called MHF2, FANCM-associated histone fold protein 2, FANCM-interacting histone fold protein 2, Fanconi anemia-associated polypeptide of 10 kDa, retinoic acid-inducible gene D9 protein homolog, or stimulated by retinoic acid gene 13 protein homolog, is a DNA-binding component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. CENP-X, together with CENP-S, forms the MHF heterodimer, which can further assemble to form tetrameric structures. CENP-X acts as a crucial cofactor for FANCM in both binding and ATP-dependent remodeling of DNA. It can stabilize FANCM. CENP-X also forms a discrete complex with FANCM and CENP-S, called FANCM-MHF. This interaction leads to synergistic activation of double-stranded DNA binding and strongly stimulates FANCM-mediated DNA remodeling. In complex with CENP-T, CENP-W and CENP-S (CENP-T-W-S-X heterotetramer), CENP-X is involved in the formation of a functional kinetochore outer plate, which is essential for kinetochore-microtubule attachment and faithful mitotic progression. As a component of the MHF and CENP-T-W-S-X complexes, CENP-X binds DNA and bends it to form a nucleosome-like structure. Its DNA-binding function is fulfilled in the presence of CENP-S. It does not bind DNA on its own.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 449452907  13 EFPTGRVKKIMKL---DKDIgKVNSEALFLVSCATELFLKLLAEKSAESAAEKKRKTVKLEHIrmavkrHRSISDFLLD 88
Cdd:cd22921    1 TFKPETIRRLLKLhfkDKKT-KINSDALKLSAELLRIFVVEAVARAARQAKAEGSNTVEVEHL------EKILPQLLLD 72