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Q02874 (H2AY_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 113. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Core histone macro-H2A.1
Short name=Histone macroH2A1
Short name=mH2A1
Alternative name(s):
H2A.y
H2A/y
Gene names
Name:H2afy
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length371 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.5

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

Subcellular location

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

Tissue specificity

Isoform 1 is present only in liver and brain, whereas isoform 2 is present in brain, thymus, testis, liver and kidney (at protein level). Ref.3

Post-translational modification

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.

Sequence similarities

Contains 1 histone H2A domain.

Contains 1 Macro domain.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 2 (identifier: Q02874-1)

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.
Isoform 1 (identifier: Q02874-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 371371Core histone macro-H2A.1
PRO_0000055319

Regions

Domain2 – 117116Histone H2A
Domain183 – 369187Macro
Compositional bias118 – 16144Lys-rich

Amino acid modifications

Modified residue181N6-methyllysine By similarity
Modified residue1291Phosphothreonine By similarity
Modified residue1691Phosphoserine By similarity
Modified residue1721Phosphoserine By similarity
Cross-link116Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate By similarity
Cross-link117Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate By similarity

Natural variations

Alternative sequence197 – 22832NLIHS…LKDDL → QVVQADIASIDSDAVVHPTN ADFYIGGEV in isoform 1.
VSP_002057

Secondary structure

1 ...................... 371
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 2 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: 697D4EF813AAAC6D

FASTA37139,504
        10         20         30         40         50         60 
MSSRGGKKKS TKTSRSAKAG VIFPVGRMLR YIKKGHPKYR IGVGAPVYMA AVLEYLTAEI 

        70         80         90        100        110        120 
LELAGNAARD NKKGRVTPRH ILLAVANDEE LNQLLKGVTI ASGGVLPNIH PELLAKKRGS 

       130        140        150        160        170        180 
KGKLEAIITP PPAKKAKSPS QKKPVAKKTG GKKGARKSKK QGEVSKAASA DSTTEGAPTD 

       190        200        210        220        230        240 
GFTVLSTKSL FLGQKLNLIH SEISNLAGFE VEAIINPTNA DIDLKDDLGS TLEKKGGKEF 

       250        260        270        280        290        300 
VEAVLELRKK NGPLEVAGAA VSAGHGLPAK FVIHCNSPVW GADKCEELLE KTVKNCLALA 

       310        320        330        340        350        360 
DDRKLKSIAF PSIGSGRNGF PKQTAAQLIL KAISSYFVST MSSSIKTVYF VLFDSESIGI 

       370 
YVQEMAKLDA N

« Hide

Isoform 1 [UniParc].

Checksum: 59ACA1B086CF5C69
Show »

FASTA36839,040

References

« Hide 'large scale' references
[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]"Structural characterization of the histone variant macroH2A."
Chakravarthy S., Gundimella S.K., Caron C., Perche P.-Y., Pehrson J.R., Khochbin S., Luger K.
Mol. Cell. Biol. 25:7616-7624(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 181-371 (ISOFORM 1), FUNCTION.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		M99065 mRNA. Translation: AAA41561.2.
M99066 mRNA. Translation: AAA41560.1.
U79139 mRNA. Translation: AAB38330.1.
BC089093 mRNA. Translation: AAH89093.1.
IPIIPI00193500.
IPI00231507.
PIRI59567.
I80811.
RefSeqNP_058878.1. NM_017182.2.
UniGeneRn.11098.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1YD9X-ray1.60A/B/C/D181-371[»]
ProteinModelPortalQ02874.
SMRQ02874. Positions 10-117, 180-368.
ModBaseSearch...

PTM databases

PhosphoSiteQ02874.

Proteomic databases

PaxDbQ02874.
PRIDEQ02874.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000015632; ENSRNOP00000015632; ENSRNOG00000011523.
ENSRNOT00000051702; ENSRNOP00000049143; ENSRNOG00000011523.
GeneID29384.
KEGGrno:29384.
UCSCRGD:621462. rat.

Organism-specific databases

CTD9555.
RGD621462. H2afy.

Phylogenomic databases

eggNOGCOG2110.
GeneTreeENSGT00690000101745.
HOGENOMHOG000234653.
HOVERGENHBG009342.
InParanoidQ02874.
KOK11251.
OrthoDBEOG4XH00N.

Gene expression databases

ArrayExpressQ02874.
GenevestigatorQ02874.
GermOnlineENSRNOG00000011523. Rattus norvegicus.

Family and domain databases

Gene3D1.10.20.10. 1 hit.
InterProIPR002589. A1pp.
IPR021171. Core_histone_macro-H2A.
IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR002119. Histone_H2A.
[Graphical view]
PfamPF00125. Histone. 1 hit.
PF01661. Macro. 1 hit.
[Graphical view]
PIRSFPIRSF037942. Core_histone_macro-H2A. 1 hit.
PRINTSPR00620. HISTONEH2A.
SMARTSM00506. A1pp. 1 hit.
SM00414. H2A. 1 hit.
[Graphical view]
SUPFAMSSF47113. Histone-fold. 1 hit.
PROSITEPS51154. MACRO. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ02874.
NextBio608979.

Entry information

Entry nameH2AY_RAT
AccessionPrimary (citable) accession number: Q02874
Secondary accession number(s): O09140, Q63325
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: January 23, 2007
Last modified: April 3, 2013
This is version 113 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents