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Protein

Histone H4

Gene

HHF1

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 524000 molecules/cell in log phase SD medium.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi17 – 215

GO - Molecular functioni

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

GO - Biological processi

Keywordsi

Molecular functionDNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-28996-MONOMER
YEAST:G3O-33067-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-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
R-SCE-4551638 SUMOylation of chromatin organization proteins
R-SCE-5625886 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
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 H4
Gene namesi
Name:HHF1
Ordered Locus Names:YBR009C
ORF Names:YBR0122
AND
Name:HHF2
Ordered Locus Names:YNL030W
ORF Names:N2752
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componentsi: Chromosome II, Chromosome XIV

Organism-specific databases

SGDiS000000213 HHF1
S000004975 HHF2

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCurated
ChainiPRO_00001583772 – 103Histone H4Add BLAST102

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei6N6-acetyllysine2 Publications1
Modified residuei9N6-acetyllysine; alternate2 Publications1
Modified residuei9N6-butyryllysine; alternate1 Publication1
Modified residuei13N6-acetyllysine; alternate2 Publications1
Modified residuei13N6-butyryllysine; alternate1 Publication1
Modified residuei17N6-acetyllysine4 Publications1
Modified residuei32N6-succinyllysine1 Publication1
Modified residuei56Omega-N-methylarginine1 Publication1
Modified residuei61PhosphoserineCombined sources1
Modified residuei65PhosphoserineCombined sources1
Modified residuei78N6-succinyllysine1 Publication1
Modified residuei80N6-acetyllysine1 Publication1

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

MaxQBiP02309
PaxDbiP02309
PRIDEiP02309

PTM databases

iPTMnetiP02309

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 H4 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

GO - Molecular functioni

Protein-protein interaction databases

BioGridi32710, 714 interactors
35797, 483 interactors
ComplexPortaliCPX-1101 RNA polymerase I upstream activating factor complex
CPX-1610 Nucleosome, variant HTA2-HTB2
CPX-1611 Nucleosome, variant HTA2-HTB1
CPX-1612 Nucleosome, variant HTA1-HTB1
CPX-1613 Nucleosome, variant HTZ1-HTB1
CPX-1614 Nucleosome, variant HTZ1-HTB2
CPX-2566 Nucleosome, variant HTA1-HTB2
DIPiDIP-418N
IntActiP02309, 311 interactors
MINTiP02309
STRINGi4932.YNL030W

Structurei

Secondary structure

1103
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP02309
SMRiP02309
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP02309

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H4 family.Curated

Phylogenomic databases

GeneTreeiENSGT00760000119019
HOGENOMiHOG000234654
InParanoidiP02309
KOiK11254
OMAiHINGITK
OrthoDBiEOG092C5WME

Family and domain databases

CDDicd00076 H4, 1 hit
Gene3Di1.10.20.10, 1 hit
InterProiView protein in InterPro
IPR035425 CENP-T/H4_C
IPR009072 Histone-fold
IPR001951 Histone_H4
IPR019809 Histone_H4_CS
PfamiView protein in Pfam
PF15511 CENP-T_C, 1 hit
PRINTSiPR00623 HISTONEH4
SMARTiView protein in SMART
SM00417 H4, 1 hit
SUPFAMiSSF47113 SSF47113, 1 hit
PROSITEiView protein in PROSITE
PS00047 HISTONE_H4, 1 hit

Sequencei

Sequence statusi: Complete.

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

P02309-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSGRGKGGKG LGKGGAKRHR KILRDNIQGI TKPAIRRLAR RGGVKRISGL
60 70 80 90 100
IYEEVRAVLK SFLESVIRDS VTYTEHAKRK TVTSLDVVYA LKRQGRTLYG

FGG
Length:103
Mass (Da):11,368
Last modified:January 23, 2007 - v2
Checksum:i69B7D1F89E62DE41
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti46R → K AA sequence (PubMed:7002547).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X00724 Genomic DNA Translation: CAA25311.1
X00725 Genomic DNA Translation: CAA25313.1
K03154 Genomic DNA Translation: AAA34660.1
Z35878 Genomic DNA Translation: CAA84947.1
Z71306 Genomic DNA Translation: CAA95892.1
AY692960 Genomic DNA Translation: AAT92979.1
BK006936 Genomic DNA Translation: DAA07130.1
BK006947 Genomic DNA Translation: DAA10515.1
PIRiA02647 HSBY4
RefSeqiNP_009563.1, NM_001178357.1
NP_014368.1, NM_001182869.1

Genome annotation databases

EnsemblFungiiYBR009C; YBR009C; YBR009C
YNL030W; YNL030W; YNL030W
GeneIDi852294
855701
KEGGisce:YBR009C
sce:YNL030W

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X00724 Genomic DNA Translation: CAA25311.1
X00725 Genomic DNA Translation: CAA25313.1
K03154 Genomic DNA Translation: AAA34660.1
Z35878 Genomic DNA Translation: CAA84947.1
Z71306 Genomic DNA Translation: CAA95892.1
AY692960 Genomic DNA Translation: AAT92979.1
BK006936 Genomic DNA Translation: DAA07130.1
BK006947 Genomic DNA Translation: DAA10515.1
PIRiA02647 HSBY4
RefSeqiNP_009563.1, NM_001178357.1
NP_014368.1, NM_001182869.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1E6IX-ray1.87P16-30[»]
1ID3X-ray3.10B/F2-103[»]
1Q1AX-ray1.50B13-22[»]
1SZCX-ray1.75B13-22[»]
1SZDX-ray1.50B13-22[»]
2DVQX-ray2.04P/Q2-16[»]
2DVRX-ray2.30P/Q2-16[»]
2E3KX-ray2.30Q/R2-16[»]
2FSBmodel-B/F1-103[»]
2H2HX-ray2.20B76-86[»]
2L5ANMR-A42-103[»]
2QQFX-ray2.00B13-23[»]
2QQGX-ray2.05B13-23[»]
3TO6X-ray2.10B12-23[»]
4JJNX-ray3.09B/F2-103[»]
4KUDX-ray3.20B/F1-103[»]
4PSXX-ray2.51C/F2-49[»]
4TWIX-ray1.79B9-21[»]
4TWJX-ray1.65B9-21[»]
5W0VX-ray2.82C/D2-35[»]
5ZBAX-ray3.50D1-103[»]
5ZBBX-ray3.60D1-103[»]
ProteinModelPortaliP02309
SMRiP02309
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32710, 714 interactors
35797, 483 interactors
ComplexPortaliCPX-1101 RNA polymerase I upstream activating factor complex
CPX-1610 Nucleosome, variant HTA2-HTB2
CPX-1611 Nucleosome, variant HTA2-HTB1
CPX-1612 Nucleosome, variant HTA1-HTB1
CPX-1613 Nucleosome, variant HTZ1-HTB1
CPX-1614 Nucleosome, variant HTZ1-HTB2
CPX-2566 Nucleosome, variant HTA1-HTB2
DIPiDIP-418N
IntActiP02309, 311 interactors
MINTiP02309
STRINGi4932.YNL030W

PTM databases

iPTMnetiP02309

Proteomic databases

MaxQBiP02309
PaxDbiP02309
PRIDEiP02309

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYBR009C; YBR009C; YBR009C
YNL030W; YNL030W; YNL030W
GeneIDi852294
855701
KEGGisce:YBR009C
sce:YNL030W

Organism-specific databases

SGDiS000000213 HHF1
S000004975 HHF2

Phylogenomic databases

GeneTreeiENSGT00760000119019
HOGENOMiHOG000234654
InParanoidiP02309
KOiK11254
OMAiHINGITK
OrthoDBiEOG092C5WME

Enzyme and pathway databases

BioCyciYEAST:G3O-28996-MONOMER
YEAST:G3O-33067-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-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
R-SCE-4551638 SUMOylation of chromatin organization proteins
R-SCE-5625886 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
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

EvolutionaryTraceiP02309
PROiPR:P02309

Family and domain databases

CDDicd00076 H4, 1 hit
Gene3Di1.10.20.10, 1 hit
InterProiView protein in InterPro
IPR035425 CENP-T/H4_C
IPR009072 Histone-fold
IPR001951 Histone_H4
IPR019809 Histone_H4_CS
PfamiView protein in Pfam
PF15511 CENP-T_C, 1 hit
PRINTSiPR00623 HISTONEH4
SMARTiView protein in SMART
SM00417 H4, 1 hit
SUPFAMiSSF47113 SSF47113, 1 hit
PROSITEiView protein in PROSITE
PS00047 HISTONE_H4, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiH4_YEAST
AccessioniPrimary (citable) accession number: P02309
Secondary accession number(s): D6VQ10
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: October 10, 2018
This is version 200 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 XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome II
    Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names
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Main funding by: National Institutes of Health

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