Reviewed, UniProtKB/Swiss-Prot P16104 (H2AX_HUMAN)

Names and origin

Protein names

Recommended name:
    Histone H2A.x
      Short name=H2a/x

Gene names

Name:	H2AFX
Synonyms:	H2AX

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	143 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	Variant histone H2A which replaces conventional H2A in a subset of 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. Required for checkpoint-mediated arrest of cell cycle progression in response to low doses of ionizing radiation and for efficient repair of DNA double strand breaks (DSBs) specifically when modified by C-terminal phosphorylation. Ref.7 Ref.10 Ref.13 Ref.16
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. Interacts with numerous proteins required for DNA damage signaling and repair when phosphorylated on Ser-140. These include MDC1, TP53BP1, BRCA1 and the MRN complex, composed of MRE11A, RAD50, and NBN. Interaction with the MRN complex is mediated at least in part by NBN. Also interacts with DHX9/NDHII when phosphorylated on Ser-140. Ref.10 Ref.13 Ref.16 Ref.18
Subcellular location	Nucleus. Ref.7 Ref.10 Ref.13 Ref.16 Ref.18 Ref.6 Ref.9 Ref.11 Ref.12 Ref.15
Developmental stage	Synthesized in G1 as well as in S-phase.
Domain	The [ST]-Q motif constitutes a recognition sequence for kinases from the PI3/PI4-kinase family.
Post-translational modification	Phosphorylated on Ser-140 (to form gamma-H2AFX or H2AX139ph) in response to DNA double strand breaks (DSBs) generated by exogenous genotoxic agents and by stalled replication forks, and may also occur during meiotic recombination events and immunoglobulin class switching in lymphocytes. Phosphorylation can extend up to several thousand nucleosomes from the actual site of the DSB and may mark the surrounding chromatin for recruitment of proteins required for DNA damage signaling and repair. Widespread phosphorylation may also serve to amplify the damage signal or aid repair of persistent lesions. Phosphorylation of Ser-140 (H2AX139ph) in response to ionizing radiation is mediated by both ATM and PRKDC while defects in DNA replication induce Ser-140 phosphorylation (H2AX139ph) subsequent to activation of ATR and PRKDC. Dephosphorylation of Ser-140 by PP2A is required for DNA DSB repair. In meiosis, Ser-140 phosphorylation (H2AX139ph) may occur at synaptonemal complexes during leptotene as an ATM-dependent response to the formation of programmed DSBs by SPO11. Ser-140 phosphorylation (H2AX139ph) may subsequently occurs at unsynapsed regions of both autosomes and the XY bivalent during zygotene, downstream of ATR and BRCA1 activation. Ser-140 phosphorylation (H2AX139ph) may also be required for transcriptional repression of unsynapsed chromatin and meiotic sex chromosome inactivation (MSCI), whereby the X and Y chromosomes condense in pachytene to form the heterochromatic XY-body. During immunoglobulin class switch recombination in lymphocytes, Ser-140 phosphorylation (H2AX139ph) may occur at sites of DNA-recombination subsequent to activation of the activation-induced cytidine deaminase AICDA. Phosphorylation at Tyr-143 (H2AXY142ph) by BAZ1B/WSTF determines the relative recruitment of either DNA repair or pro-apoptotic factors. Phosphorylation at Tyr-143 (H2AXY142ph) favors the recruitment of APBB1/FE65 and pro-apoptosis factors such as MAPK8/JNK1, triggering apoptosis. In contrast, dephosphorylation of Tyr-143 by EYA proteins (EYA1, EYA2, EYA3 or EYA4) favors the recruitment of MDC1-containing DNA repair complexes to the tail of phosphorylated Ser-140 (H2AX139ph). Monoubiquitination of Lys-120 (H2AXK119ub) by RING1 and RNF2/RING2 complex gives a specific tag for epigenetic transcriptional repression. 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. Monoubiquitination and ionizing radiation-induced 'Lys-63'-linked ubiquitination are distinct events.
Sequence similarities	Belongs to the histone H2A family.

Ontologies

Keywords
Biological process	Cell cycle DNA damage DNA recombination DNA repair Meiosis
Cellular component	Chromosomal protein Nucleosome core Nucleus
Ligand	DNA-binding
PTM	Acetylation Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	3D-structure
Gene Ontology (GO)
Biological process	meiosis Inferred from electronic annotation. Source: UniProtKB-KW nucleosome assembly Ref.1 Non-traceable author statement. Source: UniProtKB positive regulation of DNA repair Ref.27 Non-traceable author statement. Source: UniProtKB response to ionizing radiation Ref.27 Non-traceable author statement. Source: UniProtKB
Cellular component	nucleoplasm Ref.7 Ref.10 Inferred from Experiment. Source: Reactome nucleosome Non-traceable author statement. Source: UniProtKB
Molecular function	enzyme binding Ref.27 Inferred from physical interaction. Source: UniProtKB histone binding Ref.27 Inferred from physical interaction. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
BRCA1	P38398	1	EBI-494830,EBI-349905
MDC1	Q14676	3	EBI-494830,EBI-495644
MRE11A	P49959	1	EBI-494830,EBI-396513
NBN	O60934	6	EBI-494830,EBI-494844
TP53BP1	Q12888	1	EBI-494830,EBI-396540

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed By similarity
	Chain	2 – 143	142	Histone H2A.x		PRO_0000055242
Regions
	Motif	140 – 141	2	[ST]-Q motif
Amino acid modifications
	Modified residue	2	1	N-acetylserine By similarity
	Modified residue	2	1	Phosphoserine By similarity
	Modified residue	121	1	Phosphothreonine Ref.19
	Modified residue	140	1	Phosphoserine; by ATM, ATR and PRKDC Ref.7 Ref.10 Ref.13 Ref.18 Ref.6 Ref.9 Ref.11 Ref.12 Ref.15 Ref.5 Ref.8 Ref.14 Ref.17 Ref.23
	Modified residue	143	1	Phosphotyrosine; by WSTF
	Cross-link	120		Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity
Experimental info
	Mutagenesis	141	1	Q → N: Reduced phosphorylation of S-140 in response to DNA damage. Ref.5
	Mutagenesis	143	1	Y → F: Displays a reduced apoptotic response. S-140 phosphorylation is reduced.
	Sequence conflict	78	1	R → L in CAG33360. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P16104-1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: D4683775C2E6C3A9	FASTA	143	15,145
	10 20 30 40 50 60 MSGRGKTGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGHY AERVGAGAPV YLAAVLEYLT 70 80 90 100 110 120 AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLGG VTIAQGGVLP NIQAVLLPKK 130 140 TSATVGPKAP SGGKKATQAS QEY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"H2A.X. a histone isoprotein with a conserved C-terminal sequence, is encoded by a novel mRNA with both DNA replication type and polyA 3' processing signals." Mannironi C., Bonner W.M., Hatch C.L. Nucleic Acids Res. 17:9113-9126(1989) [PubMed: 2587254] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)." Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B. Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]	NIEHS SNPs program Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Lung and Placenta.
[5]	"DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139." Rogakou E.P., Pilch D.R., Orr A.H., Ivanova V.S., Bonner W.M. J. Biol. Chem. 273:5858-5868(1998) [PubMed: 9488723] [Abstract] Cited for: PHOSPHORYLATION AT SER-140, MUTAGENESIS OF GLN-141.
[6]	"Megabase chromatin domains involved in DNA double-strand breaks in vivo." Rogakou E.P., Boon C., Redon C., Bonner W.M. J. Cell Biol. 146:905-916(1999) [PubMed: 10477747] [Abstract] Cited for: SUBCELLULAR LOCATION, PHOSPHORYLATION AT SER-140.
[7]	"A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage." Paull T.T., Rogakou E.P., Yamazaki V., Kirchgessner C.U., Gellert M., Bonner W.M. Curr. Biol. 10:886-895(2000) [PubMed: 10959836] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, PHOSPHORYLATION AT SER-140.
[8]	"Initiation of DNA fragmentation during apoptosis induces phosphorylation of H2AX histone at serine 139." Rogakou E.P., Nieves-Neira W., Boon C., Pommier Y., Bonner W.M. J. Biol. Chem. 275:9390-9395(2000) [PubMed: 10734083] [Abstract] Cited for: PHOSPHORYLATION AT SER-140.
[9]	"Histone H2AX is phosphorylated in an ATR-dependent manner in response to replicational stress." Ward I.M., Chen J. J. Biol. Chem. 276:47759-47762(2001) [PubMed: 11673449] [Abstract] Cited for: SUBCELLULAR LOCATION, PHOSPHORYLATION AT SER-140.
[10]	"NBS1 localizes to gamma-H2AX foci through interaction with the FHA/BRCT domain." Kobayashi J., Tauchi H., Sakamoto S., Nakamura A., Morishima K., Matsuura S., Kobayashi T., Tamai K., Tanimoto K., Komatsu K. Curr. Biol. 12:1846-1851(2002) [PubMed: 12419185] [Abstract] Cited for: FUNCTION, INTERACTION WITH NBN AND BRCA1, SUBCELLULAR LOCATION, PHOSPHORYLATION AT SER-140.
[11]	"Accumulation of checkpoint protein 53BP1 at DNA breaks involves its binding to phosphorylated histone H2AX." Ward I.M., Minn K., Jorda K.G., Chen J. J. Biol. Chem. 278:19579-19582(2003) [PubMed: 12697768] [Abstract] Cited for: SUBCELLULAR LOCATION, PHOSPHORYLATION AT SER-140.
[12]	"Phosphorylation of histone H2AX and activation of Mre11, Rad50, and Nbs1 in response to replication-dependent DNA double-strand breaks induced by mammalian DNA topoisomerase I cleavage complexes." Furuta T., Takemura H., Liao Z.-Y., Aune G.J., Redon C., Sedelnikova O.A., Pilch D.R., Rogakou E.P., Celeste A., Chen H.T., Nussenzweig A., Aladjem M.I., Bonner W.M., Pommier Y. J. Biol. Chem. 278:20303-20312(2003) [PubMed: 12660252] [Abstract] Cited for: SUBCELLULAR LOCATION, PHOSPHORYLATION AT SER-140.
[13]	"MDC1 is a mediator of the mammalian DNA damage checkpoint." Stewart G.S., Wang B., Bignell C.R., Taylor A.M.R., Elledge S.J. Nature 421:961-966(2003) [PubMed: 12607005] [Abstract] Cited for: FUNCTION, INTERACTION WITH MDC1 AND TP53BP1, SUBCELLULAR LOCATION, PHOSPHORYLATION AT SER-140.
[14]	"DNA-PK is activated by nucleosomes and phosphorylates H2AX within the nucleosomes in an acetylation-dependent manner." Park E.-J., Chan D.W., Park J.-H., Oettinger M.A., Kwon J. Nucleic Acids Res. 31:6819-6827(2003) [PubMed: 14627815] [Abstract] Cited for: PHOSPHORYLATION AT SER-140.
[15]	"ATM and DNA-PK function redundantly to phosphorylate H2AX after exposure to ionizing radiation." Stiff T., O'Driscoll M., Rief N., Iwabuchi K., Loebrich M., Jeggo P.A. Cancer Res. 64:2390-2396(2004) [PubMed: 15059890] [Abstract] Cited for: SUBCELLULAR LOCATION, PHOSPHORYLATION AT SER-140.
[16]	"Mdc1 couples DNA double-strand break recognition by Nbs1 with its H2AX-dependent chromatin retention." Lukas C., Melander F., Stucki M., Falck J., Bekker-Jensen S., Goldberg M., Lerenthal Y., Jackson S.P., Bartek J., Lukas J. EMBO J. 23:2674-2683(2004) [PubMed: 15201865] [Abstract] Cited for: FUNCTION, INTERACTION WITH MDC1 AND NBN, SUBCELLULAR LOCATION.
[17]	"Doxorubicin activates ATM-dependent phosphorylation of multiple downstream targets in part through the generation of reactive oxygen species." Kurz E.U., Douglas P., Lees-Miller S.P. J. Biol. Chem. 279:53272-53281(2004) [PubMed: 15489221] [Abstract] Cited for: PHOSPHORYLATION AT SER-140.
[18]	"Actinomycin D induces histone gamma-H2AX foci and complex formation of gamma-H2AX with Ku70 and nuclear DNA helicase II." Mischo H.E., Hemmerich P., Grosse F., Zhang S. J. Biol. Chem. 280:9586-9594(2005) [PubMed: 15613478] [Abstract] Cited for: INTERACTION WITH DHX9, SUBCELLULAR LOCATION, PHOSPHORYLATION AT SER-140.
[19]	"Global phosphoproteome of HT-29 human colon adenocarcinoma cells." Kim J.-E., Tannenbaum S.R., White F.M. J. Proteome Res. 4:1339-1346(2005) [PubMed: 16083285] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-121, MASS SPECTROMETRY.
[20]	"gamma-H2AX dephosphorylation by protein phosphatase 2A facilitates DNA double-strand break repair." Chowdhury D., Keogh M.-C., Ishii H., Peterson C.L., Buratowski S., Lieberman J. Mol. Cell 20:801-809(2005) [PubMed: 16310392] [Abstract] Cited for: DEPHOSPHORYLATION.
[21]	"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: 18001824] [Abstract] Cited for: UBIQUITINATION.
[22]	"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: 18001825] [Abstract] Cited for: UBIQUITINATION.
[23]	"ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage." Matsuoka S., Ballif B.A., Smogorzewska A., McDonald E.R. III, Hurov K.E., Luo J., Bakalarski C.E., Zhao Z., Solimini N., Lerenthal Y., Shiloh Y., Gygi S.P., Elledge S.J. Science 316:1160-1166(2007) [PubMed: 17525332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-140, MASS SPECTROMETRY.
[24]	"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: 19203578] [Abstract] Cited for: UBIQUITINATION.
[25]	"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: 19203579] [Abstract] Cited for: UBIQUITINATION.
[26]	"WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity." Xiao A., Li H., Shechter D., Ahn S.H., Fabrizio L.A., Erdjument-Bromage H., Ishibe-Murakami S., Wang B., Tempst P., Hofmann K., Patel D.J., Elledge S.J., Allis C.D. Nature 457:57-62(2009) [PubMed: 19092802] [Abstract] Cited for: PHOSPHORYLATION AT TYR-143, MUTAGENESIS OF TYR-143.
[27]	"Tyrosine dephosphorylation of H2AX modulates apoptosis and survival decisions." Cook P.J., Ju B.G., Telese F., Wang X., Glass C.K., Rosenfeld M.G. Nature 458:591-596(2009) [PubMed: 19234442] [Abstract] Cited for: PHOSPHORYLATION AT TYR-143, MUTAGENESIS OF TYR-143.
+	Additional computationally mapped references.

Web resources

NIEHS-SNPs

Cross-references

Sequence databases

EMBLGenBankDDBJ

X14850 mRNA. Translation: CAA32968.1.
CR457079 mRNA. Translation: CAG33360.1.
DQ015918 Genomic DNA. Translation: AAY22178.1.
BC004915 mRNA. Translation: AAH04915.1.
BC011694 mRNA. Translation: AAH11694.1.
BC013416 mRNA. Translation: AAH13416.1.

IPI

IPI00219037.

PIR

S07631.

RefSeq

NP_002096.1.

UniGene

Hs.477879

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2D31	X-ray	3.20	C/F	78-86	[»]
2DYP	X-ray	2.50	C	78-86	[»]

SMR

P16104. Positions 2-123.

ModBase

Search...

Protein-protein interaction databases

IntAct

P16104. 13 interactions.

PTM databases

PhosphoSite

P16104.

Proteomic databases

PRIDE

P16104.

Genome annotation databases

Ensembl

ENSG00000188486. Homo sapiens. [Contig view]

GeneID

3014.

KEGG

hsa:3014.

Organism-specific databases

GeneCards

GC11M118469.

H-InvDB

HIX0017233.

HGNC

HGNC:4739. H2AFX.

HPA

CAB012264.

MIM

601772. gene.

PharmGKB

PA29116.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

P16104.

HOVERGEN

P16104.

OMA

P16104. SQASQEY.

Enzyme and pathway databases

Reactome

REACT_216. DNA Repair.
REACT_7970. Telomere Maintenance.

Gene expression databases

Bgee

P16104.

CleanEx

HS_H2AFX.

GermOnline

ENSG00000188486. Homo sapiens.

Family and domain databases

InterPro

IPR007125. Histone_core_D.
IPR002119. Histone_H2A.
[Graphical view]

PANTHER

PTHR23430. Histone_H2A. 1 hit.

Pfam

PF00125. Histone. 1 hit.
[Graphical view]

PRINTS

PR00620. HISTONEH2A.

ProDom

PD000522. Histone_H2A. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00414. H2A. 1 hit.
[Graphical view]

PROSITE

PS00046. HISTONE_H2A. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

11948.

SOURCE

Search...

Entry information

Entry name

H2AX_HUMAN

Accession

Primary (citable) accession number: P16104
Secondary accession number(s): Q4ZGJ7, Q6IAS5

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1990
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 101 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)