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Reviewed, UniProtKB/Swiss-Prot P68431 (H31_HUMAN)

Last modified November 4, 2008. Version 57. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    Histone H3.1
Alternative name(s):
    H3/a
    H3/b
    H3/c
    H3/d
    H3/f
    H3/h
    H3/i
    H3/j
    H3/k
    H3/l
Gene names
Name: HIST1H3A
Synonyms: H3FA
AND
Name: HIST1H3B
Synonyms: H3FL
AND
Name: HIST1H3C
Synonyms: H3FC
AND
Name: HIST1H3D
Synonyms: H3FB
AND
Name: HIST1H3E
Synonyms: H3FD
AND
Name: HIST1H3F
Synonyms: H3FI
AND
Name: HIST1H3G
Synonyms: H3FH
AND
Name: HIST1H3H
Synonyms: H3FK
AND
Name: HIST1H3I
Synonyms: H3FF
AND
Name: HIST1H3J
Synonyms: H3FJ
OrganismHomo sapiens (Human)
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

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Protein attributes

Sequence length136 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level.

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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.

Developmental stage

Expressed during S phase, then expression strongly decreases as cell division slows down during the process of differentiation.

Post-translational modification

Acetylation is generally linked to gene activation. Acetylation on Lys-10 impairs methylation at Arg-9. Acetylation on Lys-19 and Lys-24 favors methylation at Arg-18.

Citrullination at Arg-9 and/or Arg-18 by PADI4 impairs methylation and represses transcription.

Asymmetric dimethylation at Arg-18 by CARM1 is linked to gene activation. Symmetric dimethylation at Arg-9 by PRMT5 is linked to gene repression.

Methylation at Lys-5, Lys-37 and Lys-80 are linked to gene activation. Methylation at Lys-5 facilitates subsequent acetylation of H3 and H4. Methylation at Lys-80 is associated with DNA double-strand break (DSB) responses and is a specific target for TP53BP1. Methylation at Lys-10 and Lys-28 are linked to gene repression. Methylation at Lys-10 is a specific target for HP1 proteins (CBX1, CBX3 and CBX5) and prevents subsequent phosphorylation at Ser-11 and acetylation of H3 and H4. Methylation at Lys-5 and Lys-80 require preliminary monoubiquitination of H2B at 'Lys-120'. Methylation at Lys-10 and Lys-28 are enriched in inactive X chromosome chromatin.

Phosphorylated at Thr-4 by GSG2/haspin during prophase and dephosphorylated during anaphase. At centromeres, specifically phosphorylated at Thr-12 from prophase to early anaphase, probably by DAPK3 By similarity. Phosphorylation at 'Ser-11' by AURKB is crucial for chromosome condensation and cell-cycle progression during mitosis and meiosis. In addition phosphorylation at 'Ser-11' by RPS6KA4 and RPS6KA5 is important during interphase because it enables the transcription of genes following external stimulation, like mitogens, stress, growth factors or UV irradiation and result in the activation of genes, such as c-fos and c-jun. Phosphorylation at Ser-11, which is linked to gene activation, prevents methylation at Lys-10 but facilitates acetylation of H3 and H4. Phosphorylation at Ser-11 by AURKB mediates the dissociation of HP1 proteins (CBX1, CBX3 and CBX5) from heterochromatin. Phosphorylation at 'Ser-11' is also an essential regulatory mechanism for neoplastic cell transformation. Phosphorylated at Ser-29 by MLTK isoform 1, RPS6KA5 or AURKB during mitosis or upon ultraviolet B irradiation.

Ubiquitinated by the CUL4-DDB-RBX1 complex in response to ultraviolet irradiation. This may weaken the interaction between histones and DNA and facilitate DNA accessibility to repair proteins.

Miscellaneous

This histone is only present in mammals and is enriched in acetylation of Lys-15 and dimethylation of Lys-10.

Sequence similarities

Belongs to the histone H3 family.

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Binary interactions

With

Entry

#Exp.

IntAct

Notes

ASF1BQ9NVP21EBI-79722,EBI-1055650
CBX1P839161EBI-79722,EBI-78129
Cbx2P306581EBI-79722,EBI-360174From a different organism.
Cbx3P231981EBI-79722,EBI-78162From a different organism.
Cbx5Q616861EBI-79722,EBI-307973From a different organism.
IPL1P389912EBI-79722,EBI-9319From a different organism.
Pax5Q026501EBI-79722,EBI-296260From a different organism.
SETD7Q8WTS64EBI-79722,EBI-1268586
Setdb1O889741EBI-79722,EBI-79658From a different organism.
SUV39H1O434631EBI-79722,EBI-349968
Suv39h1O548641EBI-79722,EBI-302230From a different organism.

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed
Chain2 – 136135Histone H3.1
PRO_0000221245

Amino acid modifications

Modified residue41Phosphothreonine
Modified residue51N6-acetyllysine; alternate
Modified residue51N6-methyllysine; alternate
Modified residue91Citrulline; alternate
Modified residue91Symmetric dimethylarginine; by PRMT5; alternate By similarity
Modified residue101N6,N6,N6-trimethyllysine; alternate
Modified residue101N6,N6-dimethyllysine; alternate
Modified residue101N6-acetyllysine; alternate
Modified residue101N6-methyllysine; alternate
Modified residue111Phosphoserine
Modified residue121Phosphothreonine
Modified residue151N6-acetyllysine
Modified residue181Asymmetric dimethylarginine; by CARM1; alternate
Modified residue181Citrulline; alternate
Modified residue191N6-acetyllysine; alternate
Modified residue191N6-methyllysine; alternate
Modified residue241N6-acetyllysine; alternate
Modified residue241N6-methyllysine; alternate
Modified residue281N6,N6,N6-trimethyllysine; alternate
Modified residue281N6,N6-dimethyllysine; alternate
Modified residue281N6-acetyllysine; alternate
Modified residue281N6-methyllysine; alternate
Modified residue291Phosphoserine
Modified residue371N6,N6,N6-trimethyllysine; alternate
Modified residue371N6,N6-dimethyllysine; alternate
Modified residue371N6-acetyllysine; alternate
Modified residue371N6-methyllysine; alternate
Modified residue381N6-methyllysine
Modified residue571N6,N6,N6-trimethyllysine; alternate
Modified residue571N6-acetyllysine; alternate
Modified residue571N6-methyllysine; alternate
Modified residue651N6-methyllysine
Modified residue801N6,N6,N6-trimethyllysine; alternate By similarity
Modified residue801N6,N6-dimethyllysine; alternate
Modified residue801N6-acetyllysine; alternate
Modified residue801N6-methyllysine; alternate
Modified residue1231N6-methyllysine

Experimental info

Sequence conflict701R → C in AAH67493. Ref.12
Sequence conflict1001Y → T in CAB02546. Ref.7
Sequence conflict1221P → L in AAH66884. Ref.12
Sequence conflict1351Missing Ref.2

Secondary structure

1 ............. 136
Helix Strand Turn

Details...

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Sequences

Sequence LengthMass (Da)Tools
P68431-1 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 9B89008EA50A0EF6

FASTA13615,404
        10         20         30         40         50         60 
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE 

        70         80         90        100        110        120 
LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEACEAY LVGLFEDTNL CAIHAKRVTI 

       130 
MPKDIQLARR IRGERA

« Hide

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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: 6647026] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HIST1H3B).
[2]"Enhancer-facilitated expression of prokaryotic and eukaryotic genes using human histone gene 5' regulatory sequences."
Marashi F., Helms S., Shiels A., Silverstein S., Greenspan D.S., Stein G., Stein J.
Biochem. Cell Biol. 64:277-289(1986) [PubMed: 3013246] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"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: 1916825] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (H3FD).
[4]"Association of a human H1 histone gene with an H2A pseudogene and genes encoding H2B.1 and H3.1 histones."
Kardalinou E., Eick S., Albig W., Doenecke D.
J. Cell. Biochem. 52:375-383(1993) [PubMed: 8227173] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[5]"Expression of human histone h1.1 and the nearby core histones."
Runge D., Eick S., Doenecke D.
Submitted (OCT-1994) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Tissue: Blood.
[6]"Characterization of the H1.5 gene completes the set of human H1 subtype genes."
Albig W., Meergans T., Doenecke D.
Gene 184:141-148(1997) [PubMed: 9031620] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HIST1H3I).
[7]"Human histone gene organization: nonregular arrangement within a large cluster."
Albig W., Kioschis P., Poustka A., Meergans K., Doenecke D.
Genomics 40:314-322(1997) [PubMed: 9119399] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HIST1H3D; HIST1H3F AND HIST1H3G).
[8]"The human histone gene cluster at the D6S105 locus."
Albig W., Doenecke D.
Hum. Genet. 101:284-294(1997) [PubMed: 9439656] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HIST1H3H AND HIST1H3J).
[9]"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: 12408966] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HIST1H3A; HIST1H3B; HIST1H3C; HIST1H3D; HIST1H3E; HIST1H3F; HIST1H3G; HIST1H3H; HIST1H3I; HIST1H3J).
[10]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Halleck A., Ebert L., Mkoundinya M., Schick M., Eisenstein S., Neubert P., Kstrang K., Schatten R., Shen B., Henze S., Mar W., Korn B., Zuo D., Hu Y., LaBaer J.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[11]"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: 14574404] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[12]"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: Blood, Kidney, Ovary, Spleen and Uterus.
[13]"Human spleen histone H3. Isolation and amino acid sequence."
Ohe Y., Iwai K.
J. Biochem. 90:1205-1211(1981) [PubMed: 7309716] [Abstract]
Cited for: PARTIAL PROTEIN SEQUENCE.
Tissue: Spleen.
[14]"Modifications of human histone H3 variants during mitosis."
Garcia B.A., Barber C.M., Hake S.B., Ptak C., Turner F.B., Busby S.A., Shabanowitz J., Moran R.G., Allis C.D., Hunt D.F.
Biochemistry 44:13202-13213(2005) [PubMed: 16185088] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-20, METHYLATION AT LYS-10; LYS-28 AND LYS-37, PHOSPHORYLATION AT THR-4; SER-11 AND SER-29, ACETYLATION AT LYS-10 AND LYS-15, MASS SPECTROMETRY.
[15]"Identification of a novel phosphorylation site on histone H3 coupled with mitotic chromosome condensation."
Goto H., Tomono Y., Ajiro K., Kosako H., Fujita M., Sakurai M., Okawa K., Iwamatsu A., Okigaki T., Takahashi T., Inagaki M.
J. Biol. Chem. 274:25543-25549(1999) [PubMed: 10464286] [Abstract]
Cited for: PROTEIN SEQUENCE OF 58-64; 117-120 AND 124-135, PHOSPHORYLATION AT SER-11 AND SER-29.
[16]"Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins."
Lachner M., O'Carroll D., Rea S., Mechtler K., Jenuwein T.
Nature 410:116-120(2001) [PubMed: 11242053] [Abstract]
Cited for: METHYLATION AT LYS-10.
[17]"Aurora-B phosphorylates Histone H3 at serine28 with regard to the mitotic chromosome condensation."
Goto H., Yasui Y., Nigg E.A., Inagaki M.
Genes Cells 7:11-17(2002) [PubMed: 11856369] [Abstract]
Cited for: PHOSPHORYLATION AT SER-11 AND SER-29.
[18]"Novel mitosis-specific phosphorylation of histone H3 at Thr11 mediated by Dlk/ZIP kinase."
Preuss U., Landsberg G., Scheidtmann K.H.
Nucleic Acids Res. 31:878-885(2003) [PubMed: 12560483] [Abstract]
Cited for: PHOSPHORYLATION AT SER-11 AND THR-12.
[19]"Ligand-dependent activation of the farnesoid X-receptor directs arginine methylation of histone H3 by CARM1."
Ananthanarayanan M., Li S., Balasubramaniyan N., Suchy F.J., Walsh M.J.
J. Biol. Chem. 279:54348-54357(2004) [PubMed: 15471871] [Abstract]
Cited for: METHYLATION AT ARG-18.
[20]"Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks."
Huyen Y., Zgheib O., Ditullio R.A. Jr., Gorgoulis V.G., Zacharatos P., Petty T.J., Sheston E.A., Mellert H.S., Stavridi E.S., Halazonetis T.D.
Nature 432:406-411(2004) [PubMed: 15525939] [Abstract]
Cited for: METHYLATION AT LYS-80.
[21]"Human PAD4 regulates histone arginine methylation levels via demethylimination."
Wang Y., Wysocka J., Sayegh J., Lee Y.-H., Perlin J.R., Leonelli L., Sonbuchner L.S., McDonald C.H., Cook R.G., Dou Y., Roeder R.G., Clarke S., Stallcup M.R., Allis C.D., Coonrod S.A.
Science 306:279-283(2004) [