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P04908 (H2A1B_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 150. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Histone H2A type 1-B/E
Alternative name(s):
Histone H2A.2
Histone H2A/a
Histone H2A/m
Gene names
Name:HIST1H2AB
Synonyms:H2AFM
AND
Name:HIST1H2AE
Synonyms:H2AFA
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length130 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.

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.

Subcellular location

Nucleus. Chromosome.

Post-translational modification

Deiminated on Arg-4 in granulocytes upon calcium entry.

Monoubiquitination of Lys-120 (H2AK119Ub) by RING1 and RNF2/RING2 complex gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. It is involved in the initiation of both imprinted and random X inactivation. Ubiquitinated H2A is enriched in inactive X chromosome chromatin. Ubiquitination of H2A functions downstream of methylation of 'Lys-27' of histone H3 (H3K27me). H2AK119Ub by RNF2/RING2 can also be induced by ultraviolet and may be involved in DNA repair. Following DNA double-strand breaks (DSBs), it is ubiquitinated through 'Lys-63' linkage of ubiquitin moieties by the E2 ligase UBE2N and the E3 ligases RNF8 and RNF168, leading to the recruitment of repair proteins to sites of DNA damage. Ubiquitination at Lys-14 and Lys-16 (H2AK13Ub and H2AK15Ub, respectively) in response to DNA damage is initiated by RNF168 that mediates monoubiquitination at these 2 sites, and 'Lys-63'-linked ubiquitin are then conjugated to monoubiquitin; RNF8 is able to extend 'Lys-63'-linked ubiquitin chains in vitro. H2AK119Ub and ionizing radiation-induced 'Lys-63'-linked ubiquitination (H2AK13Ub and H2AK15Ub) are distinct events. Ref.9 Ref.12 Ref.13 Ref.15 Ref.16 Ref.17 Ref.18 Ref.20 Ref.21

Phosphorylation on Ser-2 (H2AS1ph) is enhanced during mitosis. Phosphorylation on Ser-2 by RPS6KA5/MSK1 directly represses transcription. Acetylation of H3 inhibits Ser-2 phosphorylation by RPS6KA5/MSK1. Phosphorylation at Thr-121 (H2AT120ph) by VPRBP is present in the regulatory region of many tumor suppresor genes and down-regulates their transcription. Ref.10 Ref.11 Ref.14

Glutamine methylation at Gln-105 (H2AQ104me) by FBL is specifically dedicated to polymerase I. It is present at 35S ribosomal DNA locus and impairs binding of the FACT complex (Ref.23).

Symmetric dimethylation on Arg-4 by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage By similarity.

Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes. Ref.19

Sequence similarities

Belongs to the histone H2A family.

Mass spectrometry

Molecular mass is 14037.9 Da from positions 2 - 130. Determined by ESI. Monoisotopic with N-acetylserine. Ref.14

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed
Chain2 – 130129Histone H2A type 1-B/E
PRO_0000055237

Amino acid modifications

Modified residue21N-acetylserine Ref.10 Ref.11 Ref.14
Modified residue21Phosphoserine; by RPS6KA5 Ref.8 Ref.10
Modified residue41Citrulline; alternate
Modified residue41Symmetric dimethylarginine; by PRMT5; alternate By similarity
Modified residue61N6-acetyllysine By similarity
Modified residue371N6-crotonyllysine Ref.19
Modified residue1051N5-methylglutamine Ref.23
Modified residue1191N6-crotonyllysine Ref.19
Modified residue1201N6-crotonyllysine; alternate Ref.19
Modified residue1211Phosphothreonine; by VPRBP Ref.7 Ref.22
Modified residue1261N6-crotonyllysine Ref.19
Cross-link14Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.20 Ref.21
Cross-link16Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.20 Ref.21
Cross-link120Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate Ref.9 Ref.12 Ref.13

Experimental info

Mutagenesis21S → A: Blocks the inhibition of transcription by RPS6KA5/MSK1. Ref.8
Sequence conflict38 – 392GN → AH in CAA24951. Ref.1

Secondary structure

.................... 130
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P04908 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 9CFE6184B2CC89F5

FASTA13014,135
        10         20         30         40         50         60 
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT 

        70         80         90        100        110        120 
AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK 

       130 
TESHHKAKGK 

« Hide

References

« Hide 'large scale' references
[1]"The primary structure and expression of four cloned human histone genes."
Zhong R., Roeder R.G., Heintz N.
Nucleic Acids Res. 11:7409-7425(1983) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HIST1H2AB).
[2]"Isolation and characterization of two human H1 histone genes within clusters of core histone genes."
Albig W., Kardalinou E., Drabent B., Zimmer A., Doenecke D.
Genomics 10:940-948(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HIST1H2AE).
[3]"The human histone gene cluster at the D6S105 locus."
Albig W., Doenecke D.
Hum. Genet. 101:284-294(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HIST1H2AE).
[4]"The human and mouse replication-dependent histone genes."
Marzluff W.F., Gongidi P., Woods K.R., Jin J., Maltais L.J.
Genomics 80:487-498(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HIST1H2AB AND HIST1H2AE).
[5]"The DNA sequence and analysis of human chromosome 6."
Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D. expand/collapse author list , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]"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] (HIST1H2AE).
Tissue: Liver.
[7]"Nucleosomal histone kinase-1 phosphorylates H2A Thr 119 during mitosis in the early Drosophila embryo."
Aihara H., Nakagawa T., Yasui K., Ohta T., Hirose S., Dhomae N., Takio K., Kaneko M., Takeshima Y., Muramatsu M., Ito T.
Genes Dev. 18:877-888(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION AT THR-121.
[8]"Phosphorylation of histone H2A inhibits transcription on chromatin templates."
Zhang Y., Griffin K., Mondal N., Parvin J.D.
J. Biol. Chem. 279:21866-21872(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION AT SER-2, MUTAGENESIS OF SER-2.
[9]"Role of histone H2A ubiquitination in Polycomb silencing."
Wang H., Wang L., Erdjument-Bromage H., Vidal M., Tempst P., Jones R.S., Zhang Y.
Nature 431:873-878(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION AT LYS-120.
[10]"Global regulation of post-translational modifications on core histones."
Galasinski S.C., Louie D.F., Gloor K.K., Resing K.A., Ahn N.G.
J. Biol. Chem. 277:2579-2588(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, PHOSPHORYLATION AT SER-2, ACETYLATION AT SER-2.
[11]"Deimination of histone H2A and H4 at arginine 3 in HL-60 granulocytes."
Hagiwara T., Hidaka Y., Yamada M.
Biochemistry 44:5827-5834(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION AT SER-2, CITRULLINATION AT ARG-4, IDENTIFICATION BY MASS SPECTROMETRY.
[12]"Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing."
Cao R., Tsukada Y., Zhang Y.
Mol. Cell 20:845-854(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION AT LYS-120.
[13]"DNA damage triggers nucleotide excision repair-dependent monoubiquitylation of histone H2A."
Bergink S., Salomons F.A., Hoogstraten D., Groothuis T.A.M., de Waard H., Wu J., Yuan L., Citterio E., Houtsmuller A.B., Neefjes J., Hoeijmakers J.H.J., Vermeulen W., Dantuma N.P.
Genes Dev. 20:1343-1352(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION AT LYS-120.
[14]"Precise characterization of human histones in the H2A gene family by top down mass spectrometry."
Boyne M.T. II, Pesavento J.J., Mizzen C.A., Kelleher N.L.
J. Proteome Res. 5:248-253(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: MASS SPECTROMETRY, ACETYLATION AT SER-2.
[15]"RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins."
Mailand N., Bekker-Jensen S., Faustrup H., Melander F., Bartek J., Lukas C., Lukas J.
Cell 131:887-900(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION.
[16]"RNF8 transduces the DNA-damage signal via histone ubiquitylation and checkpoint protein assembly."
Huen M.S.Y., Grant R., Manke I., Minn K., Yu X., Yaffe M.B., Chen J.
Cell 131:901-914(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION.
[17]"The RIDDLE syndrome protein mediates a ubiquitin-dependent signaling cascade at sites of DNA damage."
Stewart G.S., Panier S., Townsend K., Al-Hakim A.K., Kolas N.K., Miller E.S., Nakada S., Ylanko J., Olivarius S., Mendez M., Oldreive C., Wildenhain J., Tagliaferro A., Pelletier L., Taubenheim N., Durandy A., Byrd P.J., Stankovic T., Taylor A.M.R., Durocher D.
Cell 136:420-434(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION.
[18]"RNF168 binds and amplifies ubiquitin conjugates on damaged chromosomes to allow accumulation of repair proteins."
Doil C., Mailand N., Bekker-Jensen S., Menard P., Larsen D.H., Pepperkok R., Ellenberg J., Panier S., Durocher D., Bartek J., Lukas J., Lukas C.
Cell 136:435-446(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION.
[19]"Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification."
Tan M., Luo H., Lee S., Jin F., Yang J.S., Montellier E., Buchou T., Cheng Z., Rousseaux S., Rajagopal N., Lu Z., Ye Z., Zhu Q., Wysocka J., Ye Y., Khochbin S., Ren B., Zhao Y.
Cell 146:1016-1028(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: CROTONYLATION AT LYS-37; LYS-119; LYS-120 AND LYS-126.
[20]"RNF168 ubiquitinates K13-15 on H2A/H2AX to drive DNA Damage signaling."
Mattiroli F., Vissers J.H., van Dijk W.J., Ikpa P., Citterio E., Vermeulen W., Marteijn J.A., Sixma T.K.
Cell 150:1182-1195(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION AT LYS-14 AND LYS-16 BY RNF168.
[21]"A novel ubiquitin mark at the N-terminal tail of histone H2As targeted by RNF168 ubiquitin ligase."
Gatti M., Pinato S., Maspero E., Soffientini P., Polo S., Penengo L.
Cell Cycle 11:2538-2544(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION AT LYS-14 AND LYS-16 BY RNF168.
[22]"VprBP has intrinsic kinase activity targeting histone H2A and represses gene transcription."
Kim K., Kim J.M., Kim J.S., Choi J., Lee Y.S., Neamati N., Song J.S., Heo K., An W.
Mol. Cell 52:459-467(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION AT THR-121.
[23]"Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification."
Tessarz P., Santos-Rosa H., Robson S.C., Sylvestersen K.B., Nelson C.J., Nielsen M.L., Kouzarides T.
Nature 505:564-568(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: METHYLATION AT GLN-105.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X00089 Genomic DNA. Translation: CAA24951.1.
M60752 Genomic DNA. Translation: AAA63191.1.
Z83741 Genomic DNA. Translation: CAB06036.1.
AY131983 Genomic DNA. Translation: AAN59964.1.
AY131986 Genomic DNA. Translation: AAN59967.1.
AL031777 Genomic DNA. Translation: CAB39192.1.
BC093836 mRNA. Translation: AAH93836.1.
BC093862 mRNA. Translation: AAH93862.1.
CCDSCCDS4574.1.
CCDS4595.1.
PIRHSHUA5. B26318.
G40335.
RefSeqNP_003504.2. NM_003513.2.
NP_066390.1. NM_021052.2.
UniGeneHs.121017.
Hs.248174.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2CV5X-ray2.50C/G1-130[»]
3A6NX-ray2.70C/G1-130[»]
3AFAX-ray2.50C/G1-130[»]
3AN2X-ray3.60C/G1-130[»]
3AV1X-ray2.50C/G1-130[»]
3AV2X-ray2.80C/G1-130[»]
3AYWX-ray2.90C/G1-130[»]
3AZEX-ray3.00C/G1-130[»]
3AZFX-ray2.70C/G1-130[»]
3AZGX-ray2.40C/G1-130[»]
3AZHX-ray3.49C/G1-130[»]
3AZIX-ray2.70C/G1-130[»]
3AZJX-ray2.89C/G1-130[»]
3AZKX-ray3.20C/G1-130[»]
3AZLX-ray2.70C/G1-130[»]
3AZMX-ray2.89C/G1-130[»]
3AZNX-ray3.00C/G1-130[»]
3W96X-ray3.00C/G11-130[»]
3W97X-ray3.20C/G1-130[»]
3W98X-ray3.42C/G1-130[»]
3W99X-ray3.00C/G1-130[»]
3WKJX-ray2.80C/G1-130[»]
ProteinModelPortalP04908.
SMRP04908. Positions 12-119.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid109266. 16 interactions.
113931. 30 interactions.
DIPDIP-44197N.
IntActP04908. 26 interactions.
MINTMINT-1139478.
STRING9606.ENSP00000259791.

PTM databases

PhosphoSiteP04908.

Polymorphism databases

DMDM124028530.

Proteomic databases

MaxQBP04908.
PaxDbP04908.
PRIDEP04908.

Protocols and materials databases

DNASU3012.
8335.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000259791; ENSP00000259791; ENSG00000137259.
ENST00000303910; ENSP00000303373; ENSG00000168274.
GeneID3012.
8335.
KEGGhsa:3012.
hsa:8335.
UCSCuc003nft.1. human.

Organism-specific databases

CTD3012.
8335.
GeneCardsGC06M026033.
GC06P026255.
HGNCHGNC:4734. HIST1H2AB.
HGNC:4724. HIST1H2AE.
HPACAB011483.
CAB012242.
MIM602786. gene.
602795. gene.
neXtProtNX_P04908.
PharmGKBPA29111.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5262.
HOGENOMHOG000234652.
HOVERGENHBG009342.
InParanoidP04908.
KOK11251.
OMATKNAQSR.
OrthoDBEOG7M0NTR.
PhylomeDBP04908.
TreeFamTF300137.

Enzyme and pathway databases

ReactomeREACT_111102. Signal Transduction.
REACT_115566. Cell Cycle.
REACT_116125. Disease.
REACT_120956. Cellular responses to stress.
REACT_172623. Chromatin organization.
REACT_21300. Mitotic M-M/G1 phases.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpressP04908.
BgeeP04908.
CleanExHS_HIST1H2AB.
HS_HIST1H2AE.
GenevestigatorP04908.

Family and domain databases

Gene3D1.10.20.10. 1 hit.
InterProIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR002119. Histone_H2A.
[Graphical view]
PfamPF00125. Histone. 1 hit.
[Graphical view]
PRINTSPR00620. HISTONEH2A.
SMARTSM00414. H2A. 1 hit.
[Graphical view]
SUPFAMSSF47113. SSF47113. 1 hit.
PROSITEPS00046. HISTONE_H2A. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP04908.
GeneWikiHIST1H2AB.
HIST1H2AE.
NextBio11940.
PROP04908.
SOURCESearch...

Entry information

Entry nameH2A1B_HUMAN
AccessionPrimary (citable) accession number: P04908
Secondary accession number(s): P28001, Q76P63
Entry history
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 150 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 6

Human chromosome 6: entries, gene names and cross-references to MIM