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Protein

Histone H2B.1

Gene

HTB1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -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.9 Publications

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-7; H2BK6su = sumoylated Lys-7; H2BK7ac = acetylated Lys-8; H2BK7su = sumoylated Lys-8; H2BS10ph = phosphorylated Ser-11; H2BK11ac = acetylated Lys-12; H2BK16ac = acetylated Lys-17; H2BK16su = sumoylated Lys-17; H2BK17su = sumoylated Lys-18; H2BK123ub1 = monoubiquitinated Lys-124.Curated

GO - Molecular functioni

  • DNA binding Source: SGD
  • protein heterodimerization activity Source: InterPro

GO - Biological processi

  • chromatin assembly or disassembly Source: SGD
  • negative regulation of transcription by RNA polymerase II Source: SGD
  • postreplication repair Source: SGD

Keywordsi

Molecular functionDNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29804-MONOMER
ReactomeiR-SCE-2299718 Condensation of Prophase Chromosomes
R-SCE-2559580 Oxidative Stress Induced Senescence
R-SCE-2559582 Senescence-Associated Secretory Phenotype (SASP)
R-SCE-3214815 HDACs deacetylate histones
R-SCE-3214847 HATs acetylate histones
R-SCE-427359 SIRT1 negatively regulates rRNA expression
R-SCE-5625886 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
R-SCE-5689880 Ub-specific processing proteases
R-SCE-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-SCE-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-SCE-9018519 Estrogen-dependent gene expression

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2B.1
Alternative name(s):
Suppressor of Ty protein 12
Gene namesi
Name:HTB1
Synonyms:H2B1, SPT12
Ordered Locus Names:YDR224C
ORF Names:YD9934.09C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDR224C
SGDiS000002632 HTB1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi7 – 8KK → AA: Reduces sumoylation. 1 Publication2
Mutagenesisi11S → A: Desensitizes cells to H(2)O(2) treatment. 1 Publication1
Mutagenesisi11S → E: Induces apoptotic-like features including chromatin condensation. 1 Publication1
Mutagenesisi17 – 18KK → AA: Reduces sumoylation. 1 Publication2
Mutagenesisi48V → F: Confers UV-radiation sensitivity; when associated with F-87 and S-88. 1 Publication1
Mutagenesisi87Y → F: Confers UV-radiation sensitivity; when associated with F-48 and S-88. 1 Publication1
Mutagenesisi88N → S: Confers UV-radiation sensitivity; when associated with F-48 and F-87. 1 Publication1
Mutagenesisi124K → R: Impairs ubiquitin conjugation, DNA double-strand brakes formation during meiosis and histone H3-K79 methylation. 5 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCurated
ChainiPRO_00000719382 – 131Histone H2B.1Add BLAST130

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei7N6-acetyllysine; alternate1 Publication1
Cross-linki7Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate
Modified residuei8N6-acetyllysine; alternate1 Publication1
Cross-linki8Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate
Modified residuei11Phosphoserine2 Publications1
Modified residuei12N6-acetyllysine2 Publications1
Modified residuei17N6-acetyllysine; alternate4 Publications1
Cross-linki17Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternateCurated
Modified residuei18N6-acetyllysine; alternate1 Publication1
Cross-linki18Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternateCurated
Modified residuei22N6-acetyllysine; alternate1 Publication1
Modified residuei22N6-butyryllysine; alternate1 Publication1
Modified residuei23N6-acetyllysine; alternate1 Publication1
Modified residuei23N6-methyllysine; alternate1 Publication1
Modified residuei35N6-succinyllysine1 Publication1
Modified residuei38N6,N6-dimethyllysine1 Publication1
Modified residuei47N6-succinyllysine1 Publication1
Cross-linki124Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)6 Publications

Post-translational modificationi

Monoubiquitinated by the RAD6/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. Deubiquitination is performed by UBP8 in presence of SGF11.
Phosphorylated by STE20 to form H2BS10ph during progression through meiotic prophase. May be correlated with chromosome condensation. H2BS10ph is also formed after H2O2 treatment, and is a step leading to apoptosis.2 Publications
Acetylated by GCN5, a component of the SAGA complex, to form H2BK11ac and H2BK16ac. H2BK16ac can also be formed by ESA1, a component of the NuA4 histone acetyltransferase (HAT) complex. Acetylation of N-terminal lysines and particularly formation of H2BK11acK16ac has a positive effect on transcription.4 Publications
Sumoylation to form H2BK6su or H2BK7su, and probably also H2BK16su or H2BK17su, occurs preferentially near the telomeres and represses gene transcription.2 Publications

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP02293
PaxDbiP02293
PRIDEiP02293

PTM databases

iPTMnetiP02293

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.

Binary interactionsi

WithEntry#Exp.IntActNotes
STH1P325973EBI-8088,EBI-18410

GO - Molecular functioni

Protein-protein interaction databases

BioGridi32276, 415 interactors
ComplexPortaliCPX-1611 Nucleosome, variant HTA2-HTB1
CPX-1612 Nucleosome, variant HTA1-HTB1
CPX-1613 Nucleosome, variant HTZ1-HTB1
DIPiDIP-416N
ELMiP02293
IntActiP02293, 240 interactors
MINTiP02293
STRINGi4932.YDR224C

Structurei

Secondary structure

1131
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP02293
SMRiP02293
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP02293

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H2B family.Curated

Phylogenomic databases

GeneTreeiENSGT00760000118976
HOGENOMiHOG000231213
InParanoidiP02293
KOiK11252
OMAiDIFDRMA
OrthoDBiEOG092C5QTV

Family and domain databases

Gene3Di1.10.20.10, 1 hit
InterProiView protein in InterPro
IPR009072 Histone-fold
IPR007125 Histone_H2A/H2B/H3
IPR000558 Histone_H2B
PANTHERiPTHR23428 PTHR23428, 1 hit
PfamiView protein in Pfam
PF00125 Histone, 1 hit
PRINTSiPR00621 HISTONEH2B
SMARTiView protein in SMART
SM00427 H2B, 1 hit
SUPFAMiSSF47113 SSF47113, 1 hit
PROSITEiView protein in PROSITE
PS00357 HISTONE_H2B, 1 hit

Sequencei

Sequence statusi: Complete.

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

P02293-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSAKAEKKPA SKAPAEKKPA AKKTSTSTDG KKRSKARKET YSSYIYKVLK
60 70 80 90 100
QTHPDTGISQ KSMSILNSFV NDIFERIATE ASKLAAYNKK STISAREIQT
110 120 130
AVRLILPGEL AKHAVSEGTR AVTKYSSSTQ A
Length:131
Mass (Da):14,252
Last modified:January 23, 2007 - v2
Checksum:i9F5E9CFB341DB399
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J01327 Genomic DNA Translation: AAA88719.1
U13239 Genomic DNA Translation: AAC33141.1
Z48612 Genomic DNA Translation: CAA88504.1
AY557724 Genomic DNA Translation: AAS56050.1
M37743 mRNA Translation: AAA34694.2
BK006938 Genomic DNA Translation: DAA12066.1
PIRiA02621 HSBY22
RefSeqiNP_010510.3, NM_001180532.3

Genome annotation databases

EnsemblFungiiYDR224C; YDR224C; YDR224C
GeneIDi851810
KEGGisce:YDR224C

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J01327 Genomic DNA Translation: AAA88719.1
U13239 Genomic DNA Translation: AAC33141.1
Z48612 Genomic DNA Translation: CAA88504.1
AY557724 Genomic DNA Translation: AAS56050.1
M37743 mRNA Translation: AAA34694.2
BK006938 Genomic DNA Translation: DAA12066.1
PIRiA02621 HSBY22
RefSeqiNP_010510.3, NM_001180532.3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2JSSNMR-A37-131[»]
4KUDX-ray3.20D/H1-131[»]
4M6BX-ray1.78A/D37-131[»]
4WNNX-ray1.80B/D/F/H31-131[»]
5BT1X-ray2.62D1-131[»]
ProteinModelPortaliP02293
SMRiP02293
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32276, 415 interactors
ComplexPortaliCPX-1611 Nucleosome, variant HTA2-HTB1
CPX-1612 Nucleosome, variant HTA1-HTB1
CPX-1613 Nucleosome, variant HTZ1-HTB1
DIPiDIP-416N
ELMiP02293
IntActiP02293, 240 interactors
MINTiP02293
STRINGi4932.YDR224C

PTM databases

iPTMnetiP02293

Proteomic databases

MaxQBiP02293
PaxDbiP02293
PRIDEiP02293

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDR224C; YDR224C; YDR224C
GeneIDi851810
KEGGisce:YDR224C

Organism-specific databases

EuPathDBiFungiDB:YDR224C
SGDiS000002632 HTB1

Phylogenomic databases

GeneTreeiENSGT00760000118976
HOGENOMiHOG000231213
InParanoidiP02293
KOiK11252
OMAiDIFDRMA
OrthoDBiEOG092C5QTV

Enzyme and pathway databases

BioCyciYEAST:G3O-29804-MONOMER
ReactomeiR-SCE-2299718 Condensation of Prophase Chromosomes
R-SCE-2559580 Oxidative Stress Induced Senescence
R-SCE-2559582 Senescence-Associated Secretory Phenotype (SASP)
R-SCE-3214815 HDACs deacetylate histones
R-SCE-3214847 HATs acetylate histones
R-SCE-427359 SIRT1 negatively regulates rRNA expression
R-SCE-5625886 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
R-SCE-5689880 Ub-specific processing proteases
R-SCE-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-SCE-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-SCE-9018519 Estrogen-dependent gene expression

Miscellaneous databases

EvolutionaryTraceiP02293
PROiPR:P02293

Family and domain databases

Gene3Di1.10.20.10, 1 hit
InterProiView protein in InterPro
IPR009072 Histone-fold
IPR007125 Histone_H2A/H2B/H3
IPR000558 Histone_H2B
PANTHERiPTHR23428 PTHR23428, 1 hit
PfamiView protein in Pfam
PF00125 Histone, 1 hit
PRINTSiPR00621 HISTONEH2B
SMARTiView protein in SMART
SM00427 H2B, 1 hit
SUPFAMiSSF47113 SSF47113, 1 hit
PROSITEiView protein in PROSITE
PS00357 HISTONE_H2B, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiH2B1_YEAST
AccessioniPrimary (citable) accession number: P02293
Secondary accession number(s): D6VSK6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: October 10, 2018
This is version 191 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
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