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P02309 (H4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 159. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Histone H4
Gene names
Name:HHF1
Ordered Locus Names:YBR009C
ORF Names:YBR0122
AND
Name:HHF2
Ordered Locus Names:YNL030W
ORF Names:N2752
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length103 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Subunit structure

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. Ref.9

Subcellular location

Nucleus. Chromosome.

Miscellaneous

Present with 524000 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the histone H4 family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Probable
Chain2 – 103102Histone H4
PRO_0000158377

Regions

DNA binding17 – 215

Amino acid modifications

Modified residue61N6-acetyllysine Ref.19
Modified residue131N6-acetyllysine Ref.19
Modified residue171N6-acetyllysine Ref.14 Ref.16 Ref.20
Modified residue611Phosphoserine Ref.12 Ref.13
Modified residue651Phosphoserine Ref.11 Ref.13
Modified residue801N6-acetyllysine Ref.17

Experimental info

Sequence conflict461R → K AA sequence Ref.8

Secondary structure

................... 103
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P02309 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 69B7D1F89E62DE41

FASTA10311,368
        10         20         30         40         50         60 
MSGRGKGGKG LGKGGAKRHR KILRDNIQGI TKPAIRRLAR RGGVKRISGL IYEEVRAVLK 

        70         80         90        100 
SFLESVIRDS VTYTEHAKRK TVTSLDVVYA LKRQGRTLYG FGG 

« Hide

References

« Hide 'large scale' references
[1]"DNA sequences of yeast H3 and H4 histone genes from two non-allelic gene sets encode identical H3 and H4 proteins."
Smith M.M., Andresson O.S.
J. Mol. Biol. 169:663-690(1983) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]Lohan A.J.E., Wolfe K.H.
Submitted (AUG-1994) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The genes coding for histone H3 and H4 in Neurospora crassa are unique and contain intervening sequences."
Woudt L.P., Pastink A., Kempers-Veenstra A.E., Jansen A.E.M., Mager W.H., Planta R.J.
Nucleic Acids Res. 11:5347-5360(1983) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: Carlsbergensis.
[4]"Complete DNA sequence of yeast chromosome II."
Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. expand/collapse author list , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] (HHF1).
Strain: ATCC 204508 / S288c.
[5]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J. expand/collapse author list , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] (HHF2).
Strain: ATCC 204508 / S288c.
[6]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION (HHF1 AND HHF2).
Strain: ATCC 204508 / S288c.
[7]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[8]"The histones of yeast. The isolation and partial structure of the core histones."
Brandt W.F., Patterson K., von Holt C.
Eur. J. Biochem. 110:67-76(1980) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 25-48; 69-83 AND 86-100, PROBABLE CLEAVAGE OF INITIATOR METHIONINE.
[9]"Histones H3 and H4 are components of upstream activation factor required for the high-level transcription of yeast rDNA by RNA polymerase I."
Keener J., Dodd J.A., Lalo D., Nomura M.
Proc. Natl. Acad. Sci. U.S.A. 94:13458-13462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE UAF COMPLEX.
[10]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[11]"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-65, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"A multidimensional chromatography technology for in-depth phosphoproteome analysis."
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-61, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]"Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-61 AND SER-65, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]"The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p."
Owen D.J., Ornaghi P., Yang J.C., Lowe N., Evans P.R., Ballario P., Neuhaus D., Filetici P., Travers A.A.
EMBO J. 19:6141-6149(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.87 ANGSTROMS) OF 16-30, ACETYLATION AT LYS-17.
[15]"Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions."
White C.L., Suto R.K., Luger K.
EMBO J. 20:5207-5218(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF H4 IN NUCLEOSOME COMPLEX.
[16]"Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD(+)-dependent Sir2 histone/protein deacetylases."
Zhao K., Harshaw R., Chai X., Marmorstein R.
Proc. Natl. Acad. Sci. U.S.A. 101:8563-8568(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF 13-22, ACETYLATION AT LYS-17.
[17]"The structural basis of sirtuin substrate affinity."
Cosgrove M.S., Bever K., Avalos J.L., Muhammad S., Zhang X., Wolberger C.
Biochemistry 45:7511-7521(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 76-86, ACETYLATION AT LYS-80.
[18]"The path of DNA in the kinetochore."
Bloom K.S., Sharma S., Dokholyan N.V.
Curr. Biol. 16:R276-R278(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: 3D-STRUCTURE MODELING.
[19]"Structural basis for diacetylated histone H4 tail recognition by the second bromodomain of human BRD2."
Padmanabhan B., Umehara T., Nakano K., Jang M.K., Ozato K., Yokohama S.
Submitted (NOV-2006) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 2-16, ACETYLATION AT LYS-6 AND LYS-13.
[20]"Structural basis for nicotinamide inhibition and base exchange in Sir2 enzymes."
Sanders B.D., Zhao K., Slama J.T., Marmorstein R.
Mol. Cell 25:463-472(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 13-23, ACETYLATION AT LYS-17.
[21]"Structural basis for recognition of centromere histone variant CenH3 by the chaperone Scm3."
Zhou Z., Feng H., Zhou B.R., Ghirlando R., Hu K., Zwolak A., Miller Jenkins L.M., Xiao H., Tjandra N., Wu C., Bai Y.
Nature 472:234-237(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 42-103.
[22]"MYST protein acetyltransferase activity requires active site lysine autoacetylation."
Yuan H., Rossetto D., Mellert H., Dang W., Srinivasan M., Johnson J., Hodawadekar S., Ding E.C., Speicher K., Abshiru N., Perry R., Wu J., Yang C., Zheng Y.G., Speicher D.W., Thibault P., Verreault A., Johnson F.B. expand/collapse author list , Berger S.L., Sternglanz R., McMahon S.B., Cote J., Marmorstein R.
EMBO J. 31:58-70(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 12-23.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRHSBY4. A02647.
RefSeqNP_009563.1. NM_001178357.1.
NP_014368.1. NM_001182869.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalP02309.
SMRP02309. Positions 13-103.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32710. 586 interactions.
35797. 424 interactions.
DIPDIP-418N.
IntActP02309. 289 interactions.
MINTMINT-613388.
STRING4932.YBR009C.

Proteomic databases

MaxQBP02309.
PaxDbP02309.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYBR009C; YBR009C; YBR009C.
YNL030W; YNL030W; YNL030W.
GeneID852294.
855701.
KEGGsce:YBR009C.
sce:YNL030W.

Organism-specific databases

SGDS000000213. HHF1.
S000004975. HHF2.

Phylogenomic databases

eggNOGCOG2036.
GeneTreeENSGT00750000117310.
HOGENOMHOG000234654.
KOK11254.
OMAYEEVRVV.
OrthoDBEOG7HQNNQ.

Enzyme and pathway databases

BioCycYEAST:G3O-28996-MONOMER.
YEAST:G3O-33067-MONOMER.

Gene expression databases

GenevestigatorP02309.

Family and domain databases

Gene3D1.10.20.10. 1 hit.
InterProIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR001951. Histone_H4.
IPR019809. Histone_H4_CS.
[Graphical view]
PfamPF00125. Histone. 1 hit.
[Graphical view]
PRINTSPR00623. HISTONEH4.
SMARTSM00417. H4. 1 hit.
[Graphical view]
SUPFAMSSF47113. SSF47113. 1 hit.
PROSITEPS00047. HISTONE_H4. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP02309.
NextBio970946.
PROP02309.

Entry information

Entry nameH4_YEAST
AccessionPrimary (citable) accession number: P02309
Secondary accession number(s): D6VQ10
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 159 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome II

Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

Yeast chromosome XIV

Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references