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Protein

Histone H3

Gene

HHT1

more
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. Component of the UAF (upstream activation factor) complex which interacts with the upstream element of the RNA polymerase I promoter and forms a stable preinitiation complex. Together with SPT15/TBP, UAF seems to stimulate basal transcription to a fully activated level.

Miscellaneous

Present with 213000 molecules/cell in log phase SD medium.1 Publication

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: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me1 = monomethylated Lys-10; H3S10ph = phosphorylated Ser-11; H3K14ac = acetylated Lys-15; H3K14me2 = dimethylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me1 = monomethylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me1 = monomethylated Lys-24; H3K27ac = acetylated Lys-28; H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3K36ac = acetylated Lys-37; H3K36me1/2/3 = mono-, di- and trimethylated Lys-37; H3K56ac = acetylated Lys-57; H3K64ac = acetylated Lys-65; H3K79me1/2/3 = mono-, di- and trimethylated Lys-80.Curated

GO - Molecular functioni

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

GO - Biological processi

  • chromatin assembly or disassembly Source: SGD
  • global genome nucleotide-excision repair Source: SGD
  • nucleosome assembly Source: GO_Central
  • rRNA transcription Source: SGD
  • sexual sporulation resulting in formation of a cellular spore Source: SGD

Keywordsi

Molecular functionDNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-28997-MONOMER
YEAST:G3O-33068-MONOMER
ReactomeiR-SCE-1266695 Interleukin-7 signaling
R-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-3214841 PKMTs methylate histone lysines
R-SCE-3214842 HDMs demethylate histones
R-SCE-3214847 HATs acetylate histones
R-SCE-3214858 RMTs methylate histone arginines
R-SCE-3247509 Chromatin modifying enzymes
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-5689901 Metalloprotease DUBs
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 H3
Gene namesi
Name:HHT1
Ordered Locus Names:YBR010W
ORF Names:YBR0201
AND
Name:HHT2
Synonyms:SIN2
Ordered Locus Names:YNL031C
ORF Names:N2749
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componentsi: Chromosome II, Chromosome XIV

Organism-specific databases

SGDiS000000214 HHT1
S000004976 HHT2

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
Mutagenesisi11S → A: Impairs histone H3 phosphorylation and reduces transcription of some GCN5 regulated genes. 2 Publications1
Mutagenesisi53R → A, K or Q: Lethal. 1 Publication1
Mutagenesisi57K → A, Q or R: Increases sensitivity to genotoxic agents inducing DNA breaks during replication. 3 Publications1
Mutagenesisi80K → A, P or Q: Compromises telomeric silencing. 2 Publications1
Mutagenesisi119T → A or E: Lethal. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved2 Publications
ChainiPRO_00002213702 – 136Histone H3Add BLAST135

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei5N6,N6,N6-trimethyllysine; alternate11 Publications1
Modified residuei5N6,N6-dimethyllysine; alternate11 Publications1
Modified residuei5N6-methyllysine; alternate11 Publications1
Modified residuei10N6-acetyllysine; alternate5 Publications1
Modified residuei10N6-crotonyllysine; alternate1 Publication1
Modified residuei10N6-methyllysine; alternate1 Publication1
Modified residuei11Phosphoserine3 Publications1
Modified residuei15N6,N6-dimethyllysine; alternate1 Publication1
Modified residuei15N6-acetyllysine; alternate8 Publications1
Modified residuei15N6-butyryllysine; alternate2 Publications1
Modified residuei19N6-acetyllysine; alternate5 Publications1
Modified residuei19N6-butyryllysine; alternate1 Publication1
Modified residuei19N6-methyllysine; alternate1 Publication1
Modified residuei24N6-acetyllysine; alternate3 Publications1
Modified residuei24N6-butyryllysine; alternate1 Publication1
Modified residuei24N6-methyllysine; alternate1 Publication1
Modified residuei24N6-propionyllysine; alternate1 Publication1
Modified residuei28N6,N6,N6-trimethyllysine; alternate1 Publication1
Modified residuei28N6,N6-dimethyllysine; alternate1 Publication1
Modified residuei28N6-acetyllysine; alternate3 Publications1
Modified residuei28N6-butyryllysine; alternate1 Publication1
Modified residuei28N6-methyllysine; alternate1 Publication1
Modified residuei37N6,N6,N6-trimethyllysine; alternate7 Publications1
Modified residuei37N6,N6-dimethyllysine; alternate8 Publications1
Modified residuei37N6-acetyllysine; alternate3 Publications1
Modified residuei37N6-methyllysine; alternate8 Publications1
Modified residuei38N6-acetyllysine; alternate1 Publication1
Modified residuei38N6-methyllysine; alternate1 Publication1
Modified residuei57N6-acetyllysine6 Publications1
Modified residuei57N6-malonyllysine; alternate1 Publication1
Modified residuei57N6-propionyllysine; alternate1 Publication1
Modified residuei65N6-acetyllysine1 Publication1
Modified residuei80N6,N6,N6-trimethyllysine; alternate6 Publications1
Modified residuei80N6,N6-dimethyllysine; alternate6 Publications1
Modified residuei80N6-methyllysine; alternate6 Publications1
Modified residuei80N6-succinyllysine; alternate1 Publication1

Post-translational modificationi

Phosphorylated by IPL1 to form H3S10ph in a cell cycle-dependent manner during mitosis and meiosis. H3S10ph is also formed by SNF1, promotes subsequent H3K14ac formation by GCN5, and is required for transcriptional activation through TBP recruitment to the promoters. Dephosphorylation is performed by GLC7.3 Publications
Mono-, di- and trimethylated by the COMPASS complex to form H3K4me1/2/3. H3K4me activates gene expression by regulating transcription elongation and plays a role in telomere length maintenance. H3K4me enrichment correlates with transcription levels, and occurs in a 5' to 3' gradient with H3K4me3 enrichment at the 5'-end of genes, shifting to H3K4me2 and then H3K4me1. Methylated by SET2 to form H3K36me. H3K36me represses gene expression. Methylated by DOT1 to form H3K79me. H3K79me is required for association of SIR proteins with telomeric regions and for telomeric silencing. The COMPASS-mediated formation of H3K4me2/3 and the DOT1-mediated formation of H3K79me require H2BK123ub1.20 Publications
Acetylation of histone H3 leads to transcriptional activation. H3K14ac formation by GCN5, a component of the SAGA complex, is promoted by H3S10ph. Further acetylated by GCN5 to form H3K9ac, H3K18ac, H3K23ac, H3K27ac and H3K36ac. H3K14ac can also be formed by ESA1, a component of the NuA4 histone acetyltransferase (HAT) complex. H3K56ac formation occurs predominantly in newly synthesized H3 molecules during G1, S and G2/M of the cell cycle and may be involved in DNA repair.13 Publications
Crotonylation (Kcr) marks active promoters and enhancers and confers resistance to transcriptional repressors.1 Publication

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

MaxQBiP61830
PaxDbiP61830
PRIDEiP61830

PTM databases

CarbonylDBiP61830
iPTMnetiP61830

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. Histone H3 is a component of the UAF (upstream activation factor) complex, which consists of UAF30, RRN5, RRN9, RRN10, and histones H3 and H4.1 Publication

Binary interactionsi

Show more details

GO - Molecular functioni

Protein-protein interaction databases

BioGridi32711, 815 interactors
35796, 687 interactors
DIPiDIP-417N
IntActiP61830, 152 interactors
MINTiP61830
STRINGi4932.YNL031C

Structurei

Secondary structure

1136
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 8Combined sources3
Helixi46 – 55Combined sources10
Helixi66 – 77Combined sources12
Helixi87 – 114Combined sources28
Beta strandi118 – 120Combined sources3
Helixi124 – 131Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ID3X-ray3.10A/E2-136[»]
1M1DX-ray2.20B/D2-21[»]
1PEGX-ray2.59P/Q2-16[»]
1PU9X-ray2.30B6-24[»]
1PUAX-ray2.30B6-24[»]
1QSNX-ray2.20B10-20[»]
2CNXX-ray2.10P2-6[»]
2H2GX-ray1.63B114-124[»]
2IDCX-ray2.20A119-135[»]
2JMJNMR-P2-10[»]
2RNWNMR-B2-16[»]
2RNXNMR-B32-43[»]
2RSNNMR-B2-18[»]
3MP1X-ray2.60P2-6[»]
3MP6X-ray1.48P2-5[»]
3Q33X-ray2.80D2-15[»]
4JJNX-ray3.09A/E2-136[»]
4KUDX-ray3.20A/E1-136[»]
4PSXX-ray2.51P/Y2-16[»]
5D7EX-ray1.90C6-12[»]
5IOKX-ray2.22C6-12[»]
ProteinModelPortaliP61830
SMRiP61830
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP61830

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H3 family.Curated

Phylogenomic databases

GeneTreeiENSGT00760000118967
InParanoidiP61830
KOiK11253
OMAiKRIEPEY
OrthoDBiEOG092C5B6S

Family and domain databases

Gene3Di1.10.20.10, 1 hit
InterProiView protein in InterPro
IPR009072 Histone-fold
IPR007125 Histone_H2A/H2B/H3
IPR000164 Histone_H3/CENP-A
PANTHERiPTHR11426 PTHR11426, 1 hit
PfamiView protein in Pfam
PF00125 Histone, 1 hit
PRINTSiPR00622 HISTONEH3
SMARTiView protein in SMART
SM00428 H3, 1 hit
SUPFAMiSSF47113 SSF47113, 1 hit
PROSITEiView protein in PROSITE
PS00322 HISTONE_H3_1, 1 hit
PS00959 HISTONE_H3_2, 1 hit

Sequencei

Sequence statusi: Complete.

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

P61830-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARTKQTARK STGGKAPRKQ LASKAARKSA PSTGGVKKPH RYKPGTVALR
60 70 80 90 100
EIRRFQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAI GALQESVEAY
110 120 130
LVSLFEDTNL AAIHAKRVTI QKKDIKLARR LRGERS
Length:136
Mass (Da):15,356
Last modified:January 23, 2007 - v2
Checksum:iA6115FEB480AC67A
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti124D → E AA sequence (PubMed:7035169).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X00724 Genomic DNA Translation: CAA25310.1
X00725 Genomic DNA Translation: CAA25312.1
Z35879 Genomic DNA Translation: CAA84948.1
Z71306 Genomic DNA Translation: CAA95893.1
Z71307 Genomic DNA Translation: CAA95894.1
AY558343 Genomic DNA Translation: AAS56669.1
AY692987 Genomic DNA Translation: AAT93006.1
AY554000 Genomic DNA Translation: AAS64341.1
AY554001 Genomic DNA Translation: AAS64342.1
AY554002 Genomic DNA Translation: AAS64343.1
AY554003 Genomic DNA Translation: AAS64344.1
AY554004 Genomic DNA Translation: AAS64345.1
AY554005 Genomic DNA Translation: AAS64346.1
AY554006 Genomic DNA Translation: AAS64347.1
AY554007 Genomic DNA Translation: AAS64348.1
AY554008 Genomic DNA Translation: AAS64349.1
BK006936 Genomic DNA Translation: DAA07131.1
BK006947 Genomic DNA Translation: DAA10514.1
PIRiS45265 HSBY3
RefSeqiNP_009564.1, NM_001178358.1
NP_014367.1, NM_001182870.1

Genome annotation databases

EnsemblFungiiYBR010W; YBR010W; YBR010W
YNL031C; YNL031C; YNL031C
GeneIDi852295
855700
KEGGisce:YBR010W
sce:YNL031C

Similar proteinsi

Entry informationi

Entry nameiH3_YEAST
AccessioniPrimary (citable) accession number: P61830
Secondary accession number(s): D6VQ11
, E9PAG1, P02303, P13996, Q6B1U3, Q6Q7G9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: May 23, 2018
This is version 155 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

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