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Protein

Histone H2A.Z

Gene

HTZ1

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

Variant histone H2A which can replace H2A in some nucleosomes. 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. This variant is enriched at promoters, it may keep them in a repressed state until the appropriate activation signal is received. Near telomeres, it may counteract gene silencing caused by the spread of heterochromatin proteins. Required for the RNA polymerase II and SPT15/TBP recruitment to the target genes. Involved in chromosome stability.13 Publications

GO - Molecular functioni

  • chromatin binding Source: SGD
  • chromatin DNA binding Source: UniProtKB
  • identical protein binding Source: IntAct
  • RNA polymerase II core promoter proximal region sequence-specific DNA binding Source: UniProtKB

GO - Biological processi

  • chromatin remodeling Source: SGD
  • chromatin silencing at silent mating-type cassette Source: SGD
  • nuclear-transcribed mRNA catabolic process, non-stop decay Source: SGD
  • regulation of transcription from RNA polymerase II promoter Source: SGD
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Chromatin regulator

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33428-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2A.Z
Gene namesi
Name:HTZ1
Synonyms:H2AZ, HTA3
Ordered Locus Names:YOL012C
ORF Names:O2345
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOL012C.
SGDiS000005372. HTZ1.

Subcellular locationi

GO - Cellular componenti

  • nuclear chromatin Source: SGD
  • nuclear euchromatin Source: UniProtKB
  • nucleosome Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources1 Publication
Chaini2 – 134133Histone H2A.ZPRO_0000055340Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineCombined sources1 Publication
Modified residuei4 – 41N6-acetyllysine2 Publications
Modified residuei9 – 91N6-acetyllysine2 Publications
Modified residuei11 – 111N6-acetyllysine2 Publications
Modified residuei15 – 151N6-acetyllysine2 Publications

Post-translational modificationi

Acetylated by ESA1, a component of the NuA4 histone acetyltransferase (HAT) complex, and/or by GCN5, a component of the SAGA complex, to form H2A.ZK3Ac, H2A.ZK8Ac, H2A.ZK10Ac and H2A.ZK14Ac once deposited into chromatin. Acetylation is required for function at telomeres. H2A.ZK14Ac is acetylated at the promoters of active genes.2 Publications

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiQ12692.
PRIDEiQ12692.

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. H2A or its variant H2A.Z forms a heterodimer with H2B. H2A.Z associates with the VPS72/SWC2 subunit of the SWR1 chromatin remodeling complex. Interacts also with RBP1/DNA-directed RNA polymerase II largest subunit. Interacts with NAP1.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-8080,EBI-8080
BDF1P358174EBI-8080,EBI-3493
HHO1P535513EBI-8080,EBI-8064
MPS3P470693EBI-8080,EBI-25811
SWR1Q054718EBI-8080,EBI-22102

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi34392. 569 interactions.
DIPiDIP-1381N.
IntActiQ12692. 128 interactions.
MINTiMINT-387304.

Structurei

Secondary structure

1
134
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi25 – 295Combined sources
Helixi35 – 4410Combined sources
Helixi54 – 8128Combined sources
Beta strandi85 – 873Combined sources
Helixi89 – 979Combined sources
Helixi100 – 11213Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2FSBmodel-A104-134[»]
C/G1-134[»]
2JSSNMR-A23-119[»]
4M6BX-ray1.78A/D23-119[»]
ProteinModelPortaliQ12692.
SMRiQ12692. Positions 28-114.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ12692.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni98 – 10811Interaction with VPS72Add
BLAST

Sequence similaritiesi

Belongs to the histone H2A family.Curated

Phylogenomic databases

GeneTreeiENSGT00710000106735.
HOGENOMiHOG000234652.
InParanoidiQ12692.
KOiK11251.
OMAiXFPVGRI.
OrthoDBiEOG7GN30N.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR002119. Histone_H2A.
IPR007125. Histone_H2A/H2B/H3.
IPR032454. Histone_H2A_C.
IPR032458. Histone_H2A_CS.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
PF16211. Histone_H2A_C. 1 hit.
[Graphical view]
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00046. HISTONE_H2A. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q12692-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGKAHGGKG KSGAKDSGSL RSQSSSARAG LQFPVGRIKR YLKRHATGRT
60 70 80 90 100
RVGSKAAIYL TAVLEYLTAE VLELAGNAAK DLKVKRITPR HLQLAIRGDD
110 120 130
ELDSLIRATI ASGGVLPHIN KALLLKVEKK GSKK
Length:134
Mass (Da):14,283
Last modified:January 23, 2007 - v3
Checksum:i1D8FCEE3C8A504E7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z74754 Genomic DNA. Translation: CAA99011.1.
AY558000 Genomic DNA. Translation: AAS56326.1.
BK006948 Genomic DNA. Translation: DAA10771.1.
PIRiS66694.
RefSeqiNP_014631.1. NM_001183266.1.

Genome annotation databases

EnsemblFungiiYOL012C; YOL012C; YOL012C.
GeneIDi854150.
KEGGisce:YOL012C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z74754 Genomic DNA. Translation: CAA99011.1.
AY558000 Genomic DNA. Translation: AAS56326.1.
BK006948 Genomic DNA. Translation: DAA10771.1.
PIRiS66694.
RefSeqiNP_014631.1. NM_001183266.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2FSBmodel-A104-134[»]
C/G1-134[»]
2JSSNMR-A23-119[»]
4M6BX-ray1.78A/D23-119[»]
ProteinModelPortaliQ12692.
SMRiQ12692. Positions 28-114.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34392. 569 interactions.
DIPiDIP-1381N.
IntActiQ12692. 128 interactions.
MINTiMINT-387304.

Proteomic databases

MaxQBiQ12692.
PRIDEiQ12692.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOL012C; YOL012C; YOL012C.
GeneIDi854150.
KEGGisce:YOL012C.

Organism-specific databases

EuPathDBiFungiDB:YOL012C.
SGDiS000005372. HTZ1.

Phylogenomic databases

GeneTreeiENSGT00710000106735.
HOGENOMiHOG000234652.
InParanoidiQ12692.
KOiK11251.
OMAiXFPVGRI.
OrthoDBiEOG7GN30N.

Enzyme and pathway databases

BioCyciYEAST:G3O-33428-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ12692.
PROiQ12692.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR002119. Histone_H2A.
IPR007125. Histone_H2A/H2B/H3.
IPR032454. Histone_H2A_C.
IPR032458. Histone_H2A_CS.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
PF16211. Histone_H2A_C. 1 hit.
[Graphical view]
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00046. HISTONE_H2A. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
    Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
    , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
    Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. "Acetylation of H2AZ Lys 14 is associated with genome-wide gene activity in yeast."
    Millar C.B., Xu F., Zhang K., Grunstein M.
    Genes Dev. 20:711-722(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-21, ACETYLATION AT SER-2; LYS-4; LYS-9; LYS-11 AND LYS-15, IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION.
  5. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  6. "A likely histone H2A.F/Z variant in Saccharomyces cerevisiae."
    Jackson J.D., Falciano V.T., Gorovsky M.A.
    Trends Biochem. Sci. 21:466-467(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: SIMILARITY TO VARIANT H2A, GENE NAME.
  7. "Histone H2A.Z regulates transcription and is partially redundant with nucleosome remodeling complexes."
    Santisteban M.S., Kalashnikova T., Smith M.M.
    Cell 103:411-422(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "A histone variant, Htz1p, and a Sir1p-like protein, Esc2p, mediate silencing at HMR."
    Dhillon N., Kamakaka R.T.
    Mol. Cell 6:769-780(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "Histone H2A.Z has a conserved function that is distinct from that of the major H2A sequence variants."
    Jackson J.D., Gorovsky M.A.
    Nucleic Acids Res. 28:3811-3816(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. "H2A.Z is required for global chromatin integrity and for recruitment of RNA polymerase II under specific conditions."
    Adam M., Robert F., Larochelle M., Gaudreau L.
    Mol. Cell. Biol. 21:6270-6279(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RPB1.
  11. "Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin."
    Meneghini M.D., Wu M., Madhani H.D.
    Cell 112:725-736(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  12. Cited for: FUNCTION OF THE SWR1 COMPLEX, IDENTIFICATION IN THE SWR1 COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  13. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  14. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  15. "A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin."
    Kobor M.S., Venkatasubrahmanyam S., Meneghini M.D., Gin J.W., Jennings J.L., Link A.J., Madhani H.D., Rine J.
    PLoS Biol. 2:587-599(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION IN THE SWR1 COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  16. "Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4."
    Krogan N.J., Baetz K., Keogh M.-C., Datta N., Sawa C., Kwok T.C.Y., Thompson N.J., Davey M.G., Pootoolal J., Hughes T.R., Emili A., Buratowski S., Hieter P., Greenblatt J.F.
    Proc. Natl. Acad. Sci. U.S.A. 101:13513-13518(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  17. "ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex."
    Mizuguchi G., Shen X., Landry J., Wu W.-H., Sen S., Wu C.
    Science 303:343-348(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE SWR1 COMPLEX, FUNCTION OF THE SWR1 COMPLEX, INTERACTION WITH HISTONE H2B, IDENTIFICATION BY MASS SPECTROMETRY.
  18. "Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin."
    Raisner R.M., Hartley P.D., Meneghini M.D., Bao M.Z., Liu C.L., Schreiber S.L., Rando O.J., Madhani H.D.
    Cell 123:233-248(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  19. "Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange."
    Wu W.-H., Alami S., Luk E., Wu C.-H., Sen S., Mizuguchi G., Wei D., Wu C.
    Nat. Struct. Mol. Biol. 12:1064-1071(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH VPS72.
  20. "Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling."
    Li B., Pattenden S.G., Lee D., Gutierrez J., Chen J., Seidel C., Gerton J., Workman J.L.
    Proc. Natl. Acad. Sci. U.S.A. 102:18385-18390(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  21. "Telomeric heterochromatin boundaries require NuA4-dependent acetylation of histone variant H2A.Z in Saccharomyces cerevisiae."
    Babiarz J.E., Halley J.E., Rine J.
    Genes Dev. 20:700-710(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION AT LYS-4; LYS-9; LYS-11 AND LYS-15, IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION.
  22. "Histone sumoylation is a negative regulator in Saccharomyces cerevisiae and shows dynamic interplay with positive-acting histone modifications."
    Nathan D., Ingvarsdottir K., Sterner D.E., Bylebyl G.R., Dokmanovic M., Dorsey J.A., Whelan K.A., Krsmanovic M., Lane W.S., Meluh P.B., Johnson E.S., Berger S.L.
    Genes Dev. 20:966-976(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: LACK OF SUMOYLATION.
  23. "Phosphorylation by casein kinase 2 regulates Nap1 localization and function."
    Calvert M.E.K., Keck K.M., Ptak C., Shabanowitz J., Hunt D.F., Pemberton L.F.
    Mol. Cell. Biol. 28:1313-1325(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH NAP1, IDENTIFICATION BY MASS SPECTROMETRY.

Entry informationi

Entry nameiH2AZ_YEAST
AccessioniPrimary (citable) accession number: Q12692
Secondary accession number(s): D6W255
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 23, 2007
Last modified: June 8, 2016
This is version 154 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2840 molecules/cell in log phase SD medium.1 Publication
In contrast to H2A1 and H2A2, appears to be weakly or not sumoylated.

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: H2A.ZK3ac = acetylated Lys-4; H2A.ZK8ac = acetylated Lys-9; H2A.ZK10ac = acetylated Lys-11; H2A.ZK14ac = acetylated Lys-15.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 XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: 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.