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Protein

Histone H3

Gene

HHT1

more
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's 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. 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.

GO - Molecular functioni

  • DNA binding Source: SGD

GO - Biological processi

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

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-28997-MONOMER.
YEAST:G3O-33068-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-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-427359. SIRT1 negatively regulates rRNA 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

GO - Cellular componenti

  • CENP-A containing nucleosome Source: SGD
  • nuclear nucleosome Source: SGD
  • replication fork protection complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi11 – 111S → A: Impairs histone H3 phosphorylation and reduces transcription of some GCN5 regulated genes. 2 Publications
Mutagenesisi53 – 531R → A, K or Q: Lethal. 1 Publication
Mutagenesisi57 – 571K → A, Q or R: Increases sensitivity to genotoxic agents inducing DNA breaks during replication. 3 Publications
Mutagenesisi80 – 801K → A, P or Q: Compromises telomeric silencing. 2 Publications
Mutagenesisi119 – 1191T → A or E: Lethal. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved2 Publications
Chaini2 – 136135Histone H3PRO_0000221370Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei5 – 51N6,N6,N6-trimethyllysine; alternate11 Publications
Modified residuei5 – 51N6,N6-dimethyllysine; alternate11 Publications
Modified residuei5 – 51N6-methyllysine; alternate11 Publications
Modified residuei10 – 101N6-acetyllysine; alternate4 Publications
Modified residuei10 – 101N6-methyllysine; alternate1 Publication
Modified residuei11 – 111Phosphoserine3 Publications
Modified residuei15 – 151N6,N6-dimethyllysine; alternate1 Publication
Modified residuei15 – 151N6-acetyllysine; alternate7 Publications
Modified residuei19 – 191N6-acetyllysine; alternate4 Publications
Modified residuei19 – 191N6-methyllysine; alternate1 Publication
Modified residuei24 – 241N6-acetyllysine; alternate2 Publications
Modified residuei24 – 241N6-methyllysine; alternate1 Publication
Modified residuei28 – 281N6,N6,N6-trimethyllysine; alternate1 Publication
Modified residuei28 – 281N6,N6-dimethyllysine; alternate1 Publication
Modified residuei28 – 281N6-acetyllysine; alternate2 Publications
Modified residuei28 – 281N6-methyllysine; alternate1 Publication
Modified residuei37 – 371N6,N6,N6-trimethyllysine; alternate7 Publications
Modified residuei37 – 371N6,N6-dimethyllysine; alternate7 Publications
Modified residuei37 – 371N6-acetyllysine; alternate2 Publications
Modified residuei37 – 371N6-methyllysine; alternate7 Publications
Modified residuei57 – 571N6-acetyllysine5 Publications
Modified residuei65 – 651N6-acetyllysine1 Publication
Modified residuei80 – 801N6,N6,N6-trimethyllysine; alternate6 Publications
Modified residuei80 – 801N6,N6-dimethyllysine; alternate6 Publications
Modified residuei80 – 801N6-methyllysine; alternate6 Publications

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

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

MaxQBiP61830.

PTM databases

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

WithEntry#Exp.IntActNotes
ASF1P324474EBI-8098,EBI-3003
BDF1P358172EBI-8098,EBI-3493
FPR4Q062055EBI-8098,EBI-6956
HHF2P023097EBI-8098,EBI-8113
HOS2P530962EBI-8098,EBI-8475
SET3P361242EBI-8098,EBI-16993
STH1P325974EBI-8098,EBI-18410
YNG1Q084655EBI-8098,EBI-31890

Protein-protein interaction databases

BioGridi32711. 724 interactions.
35796. 650 interactions.
DIPiDIP-417N.
IntActiP61830. 146 interactions.
MINTiMINT-702778.

Structurei

Secondary structure

1
136
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 83Combined sources
Beta strandi11 – 133Combined sources
Helixi46 – 5510Combined sources
Helixi66 – 7712Combined sources
Helixi87 – 11428Combined sources
Beta strandi118 – 1203Combined sources
Helixi124 – 1318Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ID3X-ray3.10A/E2-136[»]
1M1DX-ray2.20B/D2-21[»]
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[»]
ProteinModelPortaliP61830.
SMRiP61830. Positions 2-136.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP61830.

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H3 family.Curated

Phylogenomic databases

GeneTreeiENSGT00760000118967.
InParanoidiP61830.
KOiK11253.
OMAiTEFANEM.
OrthoDBiEOG092C5B6S.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
IPR000164. Histone_H3/CENP-A.
[Graphical view]
PANTHERiPTHR11426. PTHR11426. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00622. HISTONEH3.
SMARTiSM00428. H3. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view]

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti124 – 1241D → E AA sequence (PubMed:7035169).Curated

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.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ID3X-ray3.10A/E2-136[»]
1M1DX-ray2.20B/D2-21[»]
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[»]
ProteinModelPortaliP61830.
SMRiP61830. Positions 2-136.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32711. 724 interactions.
35796. 650 interactions.
DIPiDIP-417N.
IntActiP61830. 146 interactions.
MINTiMINT-702778.

PTM databases

iPTMnetiP61830.

Proteomic databases

MaxQBiP61830.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

SGDiS000000214. HHT1.
S000004976. HHT2.

Phylogenomic databases

GeneTreeiENSGT00760000118967.
InParanoidiP61830.
KOiK11253.
OMAiTEFANEM.
OrthoDBiEOG092C5B6S.

Enzyme and pathway databases

BioCyciYEAST:G3O-28997-MONOMER.
YEAST:G3O-33068-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-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-427359. SIRT1 negatively regulates rRNA Expression.

Miscellaneous databases

EvolutionaryTraceiP61830.
PROiP61830.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
IPR000164. Histone_H3/CENP-A.
[Graphical view]
PANTHERiPTHR11426. PTHR11426. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00622. HISTONEH3.
SMARTiSM00428. H3. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiH3_YEAST
AccessioniPrimary (citable) accession number: P61830
Secondary accession number(s): D6VQ11
, E9PAG1, P02303, P13996, Q6B1U3, Q6Q7G9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 138 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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

Keywords - Technical termi

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

Documents

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

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.