histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4, assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223150 151 YRRYVYKVMKQVHPDLGITSKAMTVVNMFMGDMFERIAQEAARLSDYTKRRTLSSREIEAAVRLVLPGELSRHAVAEGSK 230
Cdd:cd22910   9 FSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSEGTK 88

                ....*
gi 15223150 231 AVSNF 235
Cdd:cd22910  89 AVTKY 93

histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4, assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223150 151 YRRYVYKVMKQVHPDLGITSKAMTVVNMFMGDMFERIAQEAARLSDYTKRRTLSSREIEAAVRLVLPGELSRHAVAEGSK 230
Cdd:cd22910   9 FSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSEGTK 88

                ....*
gi 15223150 231 AVSNF 235
Cdd:cd22910  89 AVTKY 93

Histone H2B;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223150    149 DEYRRYVYKVMKQVHPDLGITSKAMTVVNMFMGDMFERIAQEAARLSDYTKRRTLSSREIEAAVRLVLPGELSRHAVAEG 228
Cdd:smart00427   9 ETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSEG 88

                   ....*....
gi 15223150    229 SKAVSNFVG 237
Cdd:smart00427  89 TKAVTKASS 97

ribonuclease E; Reviewed

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223150    24 VTVTEEGDPCVITETANDQETQDLTFSIPVGENVTTVEIPVEVPDERSLPVGENVTTVKIPVDD----RDESSPQPPETP 99
Cdd:PRK10811  909 VVVVETTHPEVIAAPVTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVVVAEpevvAQPAAPVVAEVA 988

                          90       100
                  ....*....|....*....|....*
gi 15223150   100 VEVRDEPSPQPPETPASKSEGTLKK 124
Cdd:PRK10811  989 AEVETVTAVEPEVAPAQVPEATVEH 1013

histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4, assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223150 151 YRRYVYKVMKQVHPDLGITSKAMTVVNMFMGDMFERIAQEAARLSDYTKRRTLSSREIEAAVRLVLPGELSRHAVAEGSK 230
Cdd:cd22910   9 FSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSEGTK 88

                ....*
gi 15223150 231 AVSNF 235
Cdd:cd22910  89 AVTKY 93

Histone H2B;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223150    149 DEYRRYVYKVMKQVHPDLGITSKAMTVVNMFMGDMFERIAQEAARLSDYTKRRTLSSREIEAAVRLVLPGELSRHAVAEG 228
Cdd:smart00427   9 ETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSEG 88

                   ....*....
gi 15223150    229 SKAVSNFVG 237
Cdd:smart00427  89 TKAVTKASS 97

Core histone H2A/H2B/H3/H4;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223150    87 DRDESSPQPPETPVEVrdepspqPPETPASKSEGTLKKTDKVEKKQENKKKKKKKKRDDLAGDEYRRYVYKVMKQVHP-- 164
Cdd:pfam00125   1 MARNKNKANPRRGGTA-------PEKKISQKSSSSSKKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQst 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 15223150   165 --DLGITSKAMTVVNMFMGDMFERIAQEAARLSDYTKRRTLSSREIEAAVRLV 215
Cdd:pfam00125  74 ktDLRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126

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
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223150 155 VYKVMKqVHPDLGITSKAMTVVNMFMGDMF-ERIAQEAARLSDYTKRRTLSSREIEAAVR 213
Cdd:cd22929   9 VKRIMK-LDPDVTLVSQEAVVAIAKATELFiQLLAKEAYSVAQQSKRKTLQLKDIDAAIK 67

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 15223150 152 RRYVYKVMKQVHPDlGITSKAMTVVNMFMGDMFERIAQEAARLSDYTKRRTLSSREIEAAVR 213
Cdd:cd00076   3 RSAVARILKSAGFD-SVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63