P02309 (H4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone H4

Gene names

Name:	HHF1
Ordered Locus Names:	YBR009C
ORF Names:	YBR0122
AND
Name:	HHF2
Ordered Locus Names:	YNL030W
ORF Names:	N2752

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	103 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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.

Ontologies

Keywords
Cellular component	Chromosome Nucleosome core Nucleus
Ligand	DNA-binding
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	chromatin assembly or disassembly Traceable author statement PubMed 2275823. Source: SGD histone H3-K79 methylation Inferred from mutant phenotype PubMed 18158898. Source: SGD nucleosome assembly Inferred from electronic annotation. Source: InterPro sexual sporulation resulting in formation of a cellular spore Inferred from mutant phenotype PubMed 20713519. Source: SGD
Cellular_component	nuclear nucleosome Traceable author statement PubMed 2275823. Source: SGD replication fork protection complex Inferred from direct assay PubMed 16531994. Source: SGD
Molecular_function	DNA binding Traceable author statement PubMed 2275823. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ASF1	P32447	4	EBI-8113,EBI-3003
FPR4	Q06205	5	EBI-8113,EBI-6956
HHT2	P61830	6	EBI-8113,EBI-8098
HIF1	Q12373	5	EBI-8113,EBI-31911
SET3	P36124	2	EBI-8113,EBI-16993
STH1	P32597	4	EBI-8113,EBI-18410

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed

Chain

2 – 103

102

Histone H4

PRO_0000158377

Regions

DNA binding

17 – 21

5

Amino acid modifications

Modified residue

6

1

N6-acetyllysine

Modified residue

9

1

N6-acetyllysine

Modified residue

17

1

N6-acetyllysine

Modified residue

48

1

Phosphoserine Ref.12

Modified residue

61

1

Phosphoserine Ref.12

Modified residue

65

1

Phosphoserine Ref.11

Experimental info

Sequence conflict

46

1

R → K AA sequence Ref.8

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

103

Helix Strand Turn

Details...

Beta strand

4 – 7

4

Beta strand

16 – 19

4

Helix

27 – 29

3

Helix

32 – 41

10

Turn

46 – 49

4

Helix

51 – 76

26

Beta strand

80 – 82

3

Helix

84 – 93

10

Beta strand

98 – 101

4

Sequences

	Sequence		Length	Mass (Da)
	P02309 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 69B7D1F89E62DE41	FASTA	103	11,368
	10 20 30 40 50 60 MSGRGKGGKG LGKGGAKRHR KILRDNIQGI TKPAIRRLAR RGGVKRISGL IYEEVRAVLK 70 80 90 100 SFLESVIRDS VTYTEHAKRK TVTSLDVVYA LKRQGRTLYG FGG

References

	« Hide 'large scale' referencesShow '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. , 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. , 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]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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. , 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.
[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, MASS SPECTROMETRY.
[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-48 AND SER-61, MASS SPECTROMETRY.
[13]	"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.
+	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.

PIR

HSBY4. A02647.

RefSeq

NP_009563.1. NM_001178357.1.
NP_014368.1. NM_001182869.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1E6I	X-ray	1.87	P	16-30	[»]
1ID3	X-ray	3.10	B/F	2-103	[»]
1SZC	X-ray	1.75	B	13-22	[»]
1SZD	X-ray	1.50	B	13-22	[»]
2E3K	X-ray	2.30	Q/R	2-16	[»]
2FSB	model	-	B/F	1-103	[»]
2H2H	X-ray	2.20	B	76-86	[»]
2L5A	NMR	-	A	42-103	[»]
2QQF	X-ray	2.00	B	13-23	[»]
2QQG	X-ray	2.05	B	13-23	[»]
3TO6	X-ray	2.10	B	12-23	[»]

ProteinModelPortal

P02309.

SMR

P02309. Positions 19-103.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-418N.

IntAct

P02309. 300 interactions.

MINT

MINT-613388.

STRING

4932.YBR009C.

Proteomic databases

PaxDb

P02309.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YBR009C; YBR009C; YBR009C.
YNL030W; YNL030W; YNL030W.

GeneID

852294.
855701.

KEGG

sce:YBR009C.
sce:YNL030W.

Organism-specific databases

SGD

S000000213. HHF1.
S000004975. HHF2.

Phylogenomic databases

eggNOG

COG2036.

GeneTree

ENSGT00690000101714.

HOGENOM

HOG000234654.

KO

K11254.

OMA

TAMDIVY.

OrthoDB

EOG476P8Z.

Gene expression databases

Genevestigator

P02309.

GermOnline

YBR009C. Saccharomyces cerevisiae.
YNL030W. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

1.10.20.10. 1 hit.

InterPro

IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR001951. Histone_H4.
IPR019809. Histone_H4_CS.
[Graphical view]

PANTHER

PTHR10484. PTHR10484. 1 hit.

Pfam

PF00125. Histone. 1 hit.
[Graphical view]

PRINTS

PR00623. HISTONEH4.

SMART

SM00417. H4. 1 hit.
[Graphical view]

SUPFAM

SSF47113. Histone-fold. 1 hit.

PROSITE

PS00047. HISTONE_H4. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P02309.

NextBio

970946.

Entry information

Entry name

H4_YEAST

Accession

Primary (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:	April 3, 2013
This is version 147 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program