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Protein

Histone H4

Gene

HHF1

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.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi17 – 215

GO - Molecular functioni

  • DNA binding Source: SGD

GO - Biological processi

  • chromatin assembly or disassembly Source: SGD
  • histone H3-K79 methylation Source: SGD
  • nucleosome assembly Source: InterPro
  • sexual sporulation resulting in formation of a cellular spore Source: SGD
  • transfer RNA gene-mediated silencing Source: SGD
Complete GO annotation...

Keywords - Ligandi

DNA-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-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 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

GO - Cellular componenti

  • nuclear nucleosome Source: SGD
  • replication fork protection complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCurated
Chaini2 – 103102Histone H4PRO_0000158377Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei6 – 61N6-acetyllysine1 Publication
Modified residuei13 – 131N6-acetyllysine1 Publication
Modified residuei17 – 171N6-acetyllysine3 Publications
Modified residuei61 – 611PhosphoserineCombined sources
Modified residuei65 – 651PhosphoserineCombined sources
Modified residuei80 – 801N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP02309.

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

WithEntry#Exp.IntActNotes
ASF1P324475EBI-8113,EBI-3003
ESA1Q086495EBI-8113,EBI-6648
FPR4Q062055EBI-8113,EBI-6956
HHT2P618307EBI-8113,EBI-8098
HIF1Q123735EBI-8113,EBI-31911
KAT8Q9H7Z62EBI-8113,EBI-896414From a different organism.
SET3P361242EBI-8113,EBI-16993
STH1P325974EBI-8113,EBI-18410

Protein-protein interaction databases

BioGridi32710. 586 interactions.
35797. 429 interactions.
DIPiDIP-418N.
IntActiP02309. 293 interactions.
MINTiMINT-613388.

Structurei

Secondary structure

1
103
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 74Combined sources
Beta strandi16 – 194Combined sources
Helixi26 – 294Combined sources
Helixi32 – 409Combined sources
Turni41 – 433Combined sources
Turni46 – 494Combined sources
Helixi51 – 7626Combined sources
Beta strandi80 – 823Combined sources
Helixi84 – 9310Combined sources
Beta strandi97 – 1015Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP02309.
SMRiP02309. Positions 13-103.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP02309.

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H4 family.Curated

Phylogenomic databases

GeneTreeiENSGT00760000119019.
HOGENOMiHOG000234654.
InParanoidiP02309.
KOiK11254.
OMAiVARQNAN.
OrthoDBiEOG092C5WME.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR001951. Histone_H4.
IPR019809. Histone_H4_CS.
[Graphical view]
PRINTSiPR00623. HISTONEH4.
SMARTiSM00417. H4. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00047. HISTONE_H4. 1 hit.
[Graphical view]

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti46 – 461R → K AA sequence (PubMed:7002547).Curated

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.

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
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[»]
ProteinModelPortaliP02309.
SMRiP02309. Positions 13-103.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32710. 586 interactions.
35797. 429 interactions.
DIPiDIP-418N.
IntActiP02309. 293 interactions.
MINTiMINT-613388.

PTM databases

iPTMnetiP02309.

Proteomic databases

MaxQBiP02309.

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.
OMAiVARQNAN.
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-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

EvolutionaryTraceiP02309.
PROiP02309.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR001951. Histone_H4.
IPR019809. Histone_H4_CS.
[Graphical view]
PRINTSiPR00623. HISTONEH4.
SMARTiSM00417. H4. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00047. HISTONE_H4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiH4_YEAST
AccessioniPrimary (citable) accession number: P02309
Secondary accession number(s): D6VQ10
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 177 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 524000 molecules/cell in log phase SD medium.1 Publication

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.