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Protein

Histone H2B-alpha

Gene

htb1

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Core component of nucleosome. Nucleosomes wrap and compact 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 histone code, and nucleosome remodeling.

GO - Molecular functioni

Complete GO annotation...

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2B-alpha
Alternative name(s):
H2B.1
Gene namesi
Name:htb1
ORF Names:SPCC622.09
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome III

Organism-specific databases

EuPathDBiFungiDB:SPCC622.09.
PomBaseiSPCC622.09. htb1.

Subcellular locationi

GO - Cellular componenti

  • nucleosome Source: UniProtKB-KW
  • nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi35 – 351E → K in HTB1-442; impairs growth at 36 degrees Celsius. 1 Publication
Mutagenesisi53 – 531G → D in HTB1-72; impairs growth at 36 degrees Celsius, leads to chromosome missegregetion, chromatin shrinkage, and diminished chromatin silencing. 1 Publication
Mutagenesisi103 – 1031P → L in HTB1-223; impairs growth at 36 degrees Celsius, leads to chromosome missegregetion, chromatin shrinkage, histone H2B deubiquitination and diminished chromatin silencing. 1 Publication
Mutagenesisi120 – 1201K → R: Impairs ubiquitination. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 126125Histone H2B-alphaPRO_0000071937Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei6 – 61N6-acetyllysine; alternateBy similarity
Cross-linki6 – 6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternateBy similarity
Modified residuei7 – 71N6-acetyllysine; alternateBy similarity
Cross-linki7 – 7Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternateBy similarity
Modified residuei10 – 101PhosphoserineBy similarity
Modified residuei11 – 111N6-acetyllysineBy similarity
Cross-linki120 – 120Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

Post-translational modificationi

Monoubiquitinated by the rhp6/ubc2-bre1 complex to form H2BK123ub1. H2BK123ub1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for H3K4me and H3K79me formation. H2BK123ub1 also modulates the formation of double-strand breaks during meiosis and is a prerequisite for DNA-damage checkpoint activation (By similarity).By similarity
Phosphorylated by shk1 to form H2BS10ph during progression through meiotic prophase. May be correlated with chromosome condensation (By similarity).By similarity
Acetylation of N-terminal lysines and particularly formation of H2BK11ac has a positive effect on transcription.By similarity
Sumoylation to form H2BK6su or H2BK7su occurs preferentially near the telomeres and represses gene transcription.By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP04913.
PRIDEiP04913.

PTM databases

SwissPalmiP04913.

Interactioni

Subunit structurei

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. Interacts with rik1.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
rik1Q104262EBI-1112091,EBI-1111936

Protein-protein interaction databases

BioGridi276085. 25 interactions.
IntActiP04913. 1 interaction.
MINTiMINT-4686769.

Structurei

3D structure databases

ProteinModelPortaliP04913.
SMRiP04913. Positions 4-124.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H2B family.Curated

Phylogenomic databases

HOGENOMiHOG000231213.
InParanoidiP04913.
KOiK11252.
OMAiMRILNSF.
OrthoDBiEOG7WHHPK.
PhylomeDBiP04913.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
IPR000558. Histone_H2B.
[Graphical view]
PANTHERiPTHR23428. PTHR23428. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00621. HISTONEH2B.
SMARTiSM00427. H2B. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00357. HISTONE_H2B. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P04913-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSAAEKKPAS KAPAGKAPRD TMKSADKKRG KNRKETYSSY IYKVLKQVHP
60 70 80 90 100
DTGISNQAMR ILNSFVNDIF ERIATEASKL AAYNKKSTIS SREIQTAVRL
110 120
ILPGELAKHA VTEGTKSVTK YSSSAQ
Length:126
Mass (Da):13,819
Last modified:January 23, 2007 - v3
Checksum:i64A02B9AFE7414E3
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti43 – 431K → R (PubMed:3018512).Curated
Sequence conflicti43 – 431K → R (PubMed:4092687).Curated
Sequence conflicti60 – 601R → P (PubMed:3018512).Curated
Sequence conflicti60 – 601R → P (PubMed:4092687).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M11494 Genomic DNA. Translation: AAA35312.1.
X05220 Genomic DNA. Translation: CAA28847.1.
CU329672 Genomic DNA. Translation: CAA21865.1.
PIRiA27399. HSZPB2.
RefSeqiNP_588181.1. NM_001023171.2.

Genome annotation databases

EnsemblFungiiSPCC622.09.1; SPCC622.09.1:pep; SPCC622.09.
GeneIDi2539523.
KEGGispo:SPCC622.09.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M11494 Genomic DNA. Translation: AAA35312.1.
X05220 Genomic DNA. Translation: CAA28847.1.
CU329672 Genomic DNA. Translation: CAA21865.1.
PIRiA27399. HSZPB2.
RefSeqiNP_588181.1. NM_001023171.2.

3D structure databases

ProteinModelPortaliP04913.
SMRiP04913. Positions 4-124.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi276085. 25 interactions.
IntActiP04913. 1 interaction.
MINTiMINT-4686769.

PTM databases

SwissPalmiP04913.

Proteomic databases

MaxQBiP04913.
PRIDEiP04913.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPCC622.09.1; SPCC622.09.1:pep; SPCC622.09.
GeneIDi2539523.
KEGGispo:SPCC622.09.

Organism-specific databases

EuPathDBiFungiDB:SPCC622.09.
PomBaseiSPCC622.09. htb1.

Phylogenomic databases

HOGENOMiHOG000231213.
InParanoidiP04913.
KOiK11252.
OMAiMRILNSF.
OrthoDBiEOG7WHHPK.
PhylomeDBiP04913.

Miscellaneous databases

PROiP04913.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
IPR000558. Histone_H2B.
[Graphical view]
PANTHERiPTHR23428. PTHR23428. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00621. HISTONEH2B.
SMARTiSM00427. H2B. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00357. HISTONE_H2B. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Organization, primary structure, and evolution of histone H2A and H2B genes of the fission yeast Schizosaccharomyces pombe."
    Choe J., Schuster T., Grunstein M.
    Mol. Cell. Biol. 5:3261-3269(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Histone gene organization of fission yeast: a common upstream sequence."
    Matsumoto S., Yanagida M.
    EMBO J. 4:3531-3538(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  4. "A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation."
    Horn P.J., Bastie J.-N., Peterson C.L.
    Genes Dev. 19:1705-1714(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: PARTIAL PROTEIN SEQUENCE, INTERACTION WITH RIK1.
  5. "Histone H2B mutations in inner region affect ubiquitination, centromere function, silencing and chromosome segregation."
    Maruyama T., Nakamura T., Hayashi T., Yanagida M.
    EMBO J. 25:2420-2431(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF GLU-35; GLY-53; PRO-103 AND LYS-120, UBIQUITINATION AT LYS-120.
  6. "ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe."
    Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S., Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S., Yoshida M.
    Nat. Biotechnol. 24:841-847(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiH2B1_SCHPO
AccessioniPrimary (citable) accession number: P04913
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 23, 2007
Last modified: June 8, 2016
This is version 135 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Caution

To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-6; H2BK6su = sumoylated Lys-6; H2BK7ac = acetylated Lys-7; H2BK7su = sumoylated Lys-7; H2BS10ph = phosphorylated Ser-10; H2BK11ac = acetylated Lys-11; H2BK123ub1 = monoubiquitinated Lys-120.Curated

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.