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Protein

Core histone macro-H2A.1

Gene

H2afy

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Variant histone H2A which replaces conventional H2A in a subset of nucleosomes where it represses transcription. 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. Involved in stable X chromosome inactivation. Inhibits the binding of transcription factors and interferes with the activity of remodeling SWI/SNF complexes. Inhibits histone acetylation by EP300 and recruits class I HDACs, which induces a hypoacetylated state of chromatin. In addition, isoform 1, but not isoform 2, binds ADP-ribose and O-acetyl-ADP-ribose, and may be involved in ADP-ribose-mediated chromatin modulation.1 Publication

GO - Molecular functioni

  1. chromatin DNA binding Source: Ensembl
  2. double-stranded methylated DNA binding Source: Ensembl
  3. protein serine/threonine kinase inhibitor activity Source: Ensembl
  4. rDNA binding Source: Ensembl
  5. transcription regulatory region DNA binding Source: Ensembl

GO - Biological processi

  1. chromatin modification Source: UniProtKB-KW
  2. dosage compensation Source: Ensembl
  3. establishment of protein localization to chromatin Source: Ensembl
  4. negative regulation of cell cycle G2/M phase transition Source: Ensembl
  5. negative regulation of gene expression, epigenetic Source: Ensembl
  6. negative regulation of histone phosphorylation Source: Ensembl
  7. negative regulation of transcription from RNA polymerase II promoter Source: Ensembl
  8. negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter Source: Ensembl
  9. nucleosome assembly Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Core histone macro-H2A.1
Short name:
Histone macroH2A1
Short name:
mH2A1
Alternative name(s):
H2A.y
H2A/y
Gene namesi
Name:H2afy
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494 Componenti: Chromosome 17

Organism-specific databases

RGDi621462. H2afy.

Subcellular locationi

  1. Nucleus By similarity
  2. Chromosome By similarity

  3. Note: Enriched in inactive X chromosome chromatin and in senescence-associated heterochromatin.By similarity

GO - Cellular componenti

  1. Barr body Source: Ensembl
  2. chromatin Source: RGD
  3. condensed chromosome Source: Ensembl
  4. ESC/E(Z) complex Source: Ensembl
  5. extracellular vesicular exosome Source: Ensembl
  6. nuclear chromatin Source: Ensembl
  7. nucleolus Source: Ensembl
  8. nucleosome Source: RGD
  9. nucleus Source: RGD
  10. pericentric heterochromatin Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 371371Core histone macro-H2A.1PRO_0000055319Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei18 – 181N6-methyllysineBy similarity
Modified residuei116 – 1161N6-acetyllysine; alternateBy similarity
Cross-linki116 – 116Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternateBy similarity
Cross-linki117 – 117Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei123 – 1231N6-acetyllysineBy similarity
Modified residuei129 – 1291PhosphothreonineBy similarity
Modified residuei169 – 1691PhosphoserineBy similarity
Modified residuei172 – 1721PhosphoserineBy similarity

Post-translational modificationi

Monoubiquitinated at either Lys-116 or Lys-117. May also be polyubiquitinated. Ubiquitination is mediated by the CUL3/SPOP E3 complex and does not promote proteasomal degradation. Instead, it is required for enrichment in inactive X chromosome chromatin (By similarity).By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ02874.
PRIDEiQ02874.

PTM databases

PhosphoSiteiQ02874.

Expressioni

Tissue specificityi

Isoform 1 is present only in liver and brain, whereas isoform 2 is present in brain, thymus, testis, liver and kidney (at protein level).1 Publication

Gene expression databases

GenevestigatoriQ02874.

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. Interacts with SPOP. Part of a complex consisting of H2AFY, CUL3 and SPOP. Interacts with HDAC1 and HDAC2 (By similarity).By similarity

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000049143.

Structurei

Secondary structure

1
371
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi229 – 25123Combined sources
Beta strandi259 – 2635Combined sources
Beta strandi267 – 2759Combined sources
Helixi285 – 30218Combined sources
Beta strandi306 – 3105Combined sources
Beta strandi314 – 3163Combined sources
Helixi322 – 33716Combined sources
Beta strandi347 – 3515Combined sources
Helixi355 – 36511Combined sources
Turni366 – 3694Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YD9X-ray1.60A/B/C/D229-371[»]
ProteinModelPortaliQ02874.
SMRiQ02874. Positions 10-117, 180-368.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ02874.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 117116Histone H2AAdd
BLAST
Domaini183 – 369187MacroPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi118 – 16144Lys-richAdd
BLAST

Sequence similaritiesi

Contains 1 histone H2A domain.Curated
Contains 1 Macro domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG2110.
GeneTreeiENSGT00760000119217.
HOGENOMiHOG000234653.
HOVERGENiHBG009342.
InParanoidiQ02874.
KOiK11251.
OMAiQVVQADI.
OrthoDBiEOG71G9VP.
PhylomeDBiQ02874.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR021171. Core_histone_macro-H2A.
IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR002119. Histone_H2A.
IPR002589. Macro_dom.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
PF01661. Macro. 1 hit.
[Graphical view]
PIRSFiPIRSF037942. Core_histone_macro-H2A. 1 hit.
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00506. A1pp. 1 hit.
SM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS51154. MACRO. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 2 (identifier: Q02874-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSSRGGKKKS TKTSRSAKAG VIFPVGRMLR YIKKGHPKYR IGVGAPVYMA
60 70 80 90 100
AVLEYLTAEI LELAGNAARD NKKGRVTPRH ILLAVANDEE LNQLLKGVTI
110 120 130 140 150
ASGGVLPNIH PELLAKKRGS KGKLEAIITP PPAKKAKSPS QKKPVAKKTG
160 170 180 190 200
GKKGARKSKK QGEVSKAASA DSTTEGAPTD GFTVLSTKSL FLGQKLNLIH
210 220 230 240 250
SEISNLAGFE VEAIINPTNA DIDLKDDLGS TLEKKGGKEF VEAVLELRKK
260 270 280 290 300
NGPLEVAGAA VSAGHGLPAK FVIHCNSPVW GADKCEELLE KTVKNCLALA
310 320 330 340 350
DDRKLKSIAF PSIGSGRNGF PKQTAAQLIL KAISSYFVST MSSSIKTVYF
360 370
VLFDSESIGI YVQEMAKLDA N
Length:371
Mass (Da):39,504
Last modified:January 23, 2007 - v4
Checksum:i697D4EF813AAAC6D
GO
Isoform 1 (identifier: Q02874-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     197-228: NLIHSEISNLAGFEVEAIINPTNADIDLKDDL → QVVQADIASIDSDAVVHPTNADFYIGGEV

Show »
Length:368
Mass (Da):39,040
Checksum:i59ACA1B086CF5C69
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei197 – 22832NLIHS…LKDDL → QVVQADIASIDSDAVVHPTN ADFYIGGEV in isoform 1. 1 PublicationVSP_002057Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M99065 mRNA. Translation: AAA41561.2.
M99066 mRNA. Translation: AAA41560.1.
U79139 mRNA. Translation: AAB38330.1.
BC089093 mRNA. Translation: AAH89093.1.
PIRiI59567.
I80811.
RefSeqiNP_058878.1. NM_017182.2. [Q02874-1]
XP_006253638.1. XM_006253576.2.
UniGeneiRn.11098.

Genome annotation databases

EnsembliENSRNOT00000051702; ENSRNOP00000049143; ENSRNOG00000011523. [Q02874-1]
GeneIDi29384.
KEGGirno:29384.
UCSCiRGD:621462. rat. [Q02874-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M99065 mRNA. Translation: AAA41561.2.
M99066 mRNA. Translation: AAA41560.1.
U79139 mRNA. Translation: AAB38330.1.
BC089093 mRNA. Translation: AAH89093.1.
PIRiI59567.
I80811.
RefSeqiNP_058878.1. NM_017182.2. [Q02874-1]
XP_006253638.1. XM_006253576.2.
UniGeneiRn.11098.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YD9X-ray1.60A/B/C/D229-371[»]
ProteinModelPortaliQ02874.
SMRiQ02874. Positions 10-117, 180-368.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000049143.

PTM databases

PhosphoSiteiQ02874.

Proteomic databases

PaxDbiQ02874.
PRIDEiQ02874.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000051702; ENSRNOP00000049143; ENSRNOG00000011523. [Q02874-1]
GeneIDi29384.
KEGGirno:29384.
UCSCiRGD:621462. rat. [Q02874-1]

Organism-specific databases

CTDi9555.
RGDi621462. H2afy.

Phylogenomic databases

eggNOGiCOG2110.
GeneTreeiENSGT00760000119217.
HOGENOMiHOG000234653.
HOVERGENiHBG009342.
InParanoidiQ02874.
KOiK11251.
OMAiQVVQADI.
OrthoDBiEOG71G9VP.
PhylomeDBiQ02874.

Miscellaneous databases

EvolutionaryTraceiQ02874.
NextBioi608979.
PROiQ02874.

Gene expression databases

GenevestigatoriQ02874.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR021171. Core_histone_macro-H2A.
IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR002119. Histone_H2A.
IPR002589. Macro_dom.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
PF01661. Macro. 1 hit.
[Graphical view]
PIRSFiPIRSF037942. Core_histone_macro-H2A. 1 hit.
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00506. A1pp. 1 hit.
SM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS51154. MACRO. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "MacroH2A, a core histone containing a large nonhistone region."
    Pehrson J.R., Fried V.A.
    Science 257:1398-1400(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), PARTIAL PROTEIN SEQUENCE.
    Tissue: Liver.
  2. Pehrson J.R.
    Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION (ISOFORM 1).
  3. "Developmental and tissue expression patterns of histone macroH2A1 subtypes."
    Pehrson J.R., Costanzi C., Dharia C.
    J. Cell. Biochem. 65:107-113(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), TISSUE SPECIFICITY.
    Tissue: Thymus.
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Strain: Brown Norway.
    Tissue: Kidney.
  5. Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 181-371 (ISOFORM 1), FUNCTION.

Entry informationi

Entry nameiH2AY_RAT
AccessioniPrimary (citable) accession number: Q02874
Secondary accession number(s): O09140, Q63325
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: January 23, 2007
Last modified: April 29, 2015
This is version 129 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

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

External Data

Dasty 3

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 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.