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Reviewed, UniProtKB/Swiss-Prot Q16695 (H31T_HUMAN)

Last modified January 19, 2010. Version 98. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | 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

Names and origin

Protein namesRecommended name:
    Histone H3.1t
      Short name=H3t
      Short name=H3/t
Alternative name(s):
    H3/g
Gene names
Name: HIST3H3
Synonyms: H3FT
OrganismHomo sapiens (Human) [Complete proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length136 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.

Tissue specificity

Expressed in testicular cells.

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 (H3K9ac) impairs methylation at Arg-9 (H3R8sme2). Acetylation on Lys-19 (H3K18ac) and Lys-24 (H3K24ac) favors methylation at Arg-18 (H3R17me) By similarity.

Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription By similarity.

Asymmetric dimethylation at Arg-18 (H3R17me2a) by CARM1 is linked to gene activation. Symmetric dimethylation at Arg-9 (H3R8sme2) by PRMT5 is linked to gene repression. Asymmetric dimethylation at Arg-3 (H3R2me2a) by PRMT6 is linked to gene repression and is mutually exclusive with H3 Lys-5 methylation (H3K4me2 and H3K4me3). H3R2me2a is present at the 3' of genes regardless of their transcription state and is enriched on inactive promoters, while it is absent on active promoters By similarity.

Methylation at Lys-5 (H3K4me), Lys-37 (H3K36me) and Lys-80 (H3K79me) are linked to gene activation. Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation of H3 and H4. Methylation at Lys-80 (H3K79me) is associated with DNA double-strand break (DSB) responses and is a specific target for TP53BP1. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are linked to gene repression. Methylation at Lys-10 (H3K9me) is a specific target for HP1 proteins (CBX1, CBX3 and CBX5) and prevents subsequent phosphorylation at Ser-11 (H3S10ph) and acetylation of H3 and H4. Methylation at Lys-5 (H3K4me) and Lys-80 (H3K79me) require preliminary monoubiquitination of H2B at 'Lys-120'. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are enriched in inactive X chromosome chromatin By similarity.

Phosphorylated at Thr-4 (H3T3ph) by GSG2/haspin during prophase and dephosphorylated during anaphase. At centromeres, specifically phosphorylated at Thr-12 (H3T11ph) from prophase to early anaphase. Phosphorylated at Ser-11 during the whole mitosis. Phosphorylation at Ser-11 (H3S10ph), which is linked to gene activation, prevents methylation at Lys-10 (H3K9me) but facilitates acetylation of H3 and H4. Phosphorylated at Ser-29 (H3S28ph) by MLTK isoform 1, RPS6KA5 or AURKB during mitosis or upon ultraviolet B irradiation By similarity. Ref.9

Phosphorylation at Ser-11 (H3S10ph) is crucial for chromosome condensation and cell-cycle progression during mitosis and meiosis. In addition phosphorylation at Ser-11 (H3S10ph) is important during interphase because it enables the transcription of genes following external stimulation, like stress or growth factors. Phosphorylation at Ser-11 (H3S10ph) is also an essential regulatory mechanism for neoplastic cell transformation. Phosphorylation at Ser-11 (H3S10ph) by AURKB/Aurora-B mediates the dissociation of HP1 proteins (CBX1, CBX3 and CBX5) from heterochromatin.

Ubiquitinated By similarity.

Sequence similarities

Belongs to the histone H3 family.

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

KDM1O603411EBI-358900,EBI-710124
KDM4AO751643EBI-358900,EBI-936709

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 136135Histone H3.1t
PRO_0000221248

Amino acid modifications

Modified residue31Asymmetric dimethylarginine; by PRMT6 By similarity
Modified residue41Phosphothreonine By similarity
Modified residue51N6-methylated lysine By similarity
Modified residue91Citrulline; alternate By similarity
Modified residue91Symmetric dimethylarginine; by PRMT5; alternate By similarity
Modified residue101N6-acetyllysine; alternate By similarity
Modified residue101N6-methylated lysine; alternate By similarity
Modified residue111Phosphoserine By similarity
Modified residue121Phosphothreonine By similarity
Modified residue151N6-acetyllysine By similarity
Modified residue181Asymmetric dimethylarginine; by CARM1; alternate By similarity
Modified residue181Citrulline; alternate By similarity
Modified residue191N6-acetyllysine; alternate By similarity
Modified residue191N6-methylated lysine; alternate By similarity
Modified residue241N6-acetyllysine Ref.10
Modified residue281N6-acetyllysine; alternate By similarity
Modified residue281N6-methylated lysine; alternate Ref.8
Modified residue291Phosphoserine Ref.9
Modified residue371N6-acetyllysine; alternate By similarity
Modified residue371N6-methylated lysine; alternate By similarity
Modified residue651N6-methylated lysine By similarity
Modified residue801N6-methylated lysine By similarity
Modified residue1231N6-methylated lysine By similarity

Secondary structure

... 136
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q16695-1 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 37375A2C3A377B2B

FASTA13615,508
        10         20         30         40         50         60 
MARTKQTARK STGGKAPRKQ LATKVARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE 

        70         80         90        100        110        120 
LLIRKLPFQR LMREIAQDFK TDLRFQSSAV MALQEACESY LVGLFEDTNL CVIHAKRVTI 

       130 
MPKDIQLARR IRGERA 

« Hide

References

« Hide 'large scale' references
[1]"A solitary human H3 histone gene on chromosome 1."
Albig W., Ebentheuer J., Klobeck H., Kunz J., Doenecke D.
Hum. Genet. 97:486-491(1996) [PubMed: 8834248] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"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].
[3]"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].
[4]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Testis.
[5]"The DNA sequence and biological annotation of human chromosome 1."
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. expand/collapse author list , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
Nature 441:315-321(2006) [PubMed: 16710414] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]"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.
[8]"Identifying and quantifying in vivo methylation sites by heavy methyl SILAC."
Ong S.E., Mittler G., Mann M.
Nat. Methods 1:119-126(2004) [PubMed: 15782174] [Abstract]
Cited for: METHYLATION [LARGE SCALE ANALYSIS] AT LYS-28, MASS SPECTROMETRY.
[9]"Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle."
Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M.
Mol. Cell 31:438-448(2008) [PubMed: 18691976] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-29, MASS SPECTROMETRY.
[10]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed: 19608861] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-19 AND LYS-24, MASS SPECTROMETRY.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z49861 Genomic DNA. Translation: CAA90020.1.
AF531308 Genomic DNA. Translation: AAN39284.1.
CR542013 mRNA. Translation: CAG46810.1.
AK312217 mRNA. Translation: BAG35150.1.
AL139288 Genomic DNA. Translation: CAI23333.1.
CH471098 Genomic DNA. Translation: EAW69877.1.
BC069079 mRNA. Translation: AAH69079.1.
BC101837 mRNA. Translation: AAI01838.1.
BC101839 mRNA. Translation: AAI01840.1.
IPIIPI00216402.
PIRS57473.
RefSeqNP_003484.1.
UniGeneHs.248171

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2V1DX-ray3.10C2-22[»]
SMRQ16695. Positions 2-136.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-922N.
IntActQ16695. 5 interactions.
STRINGQ16695.

PTM databases

PhosphoSiteQ16695.

Proteomic databases

PRIDEQ16695.

Genome annotation databases

EnsemblENST00000366696; ENSP00000355657; ENSG00000168148; Homo sapiens. [Genome view]
GeneID8290.
KEGGhsa:8290.
UCSCuc001hsx.1. human.

Organism-specific databases

CTD8290.
GeneCardsGC01M226679.
H-InvDBHIX0028778.
HGNCHGNC:4778. HIST3H3.
HPACAB001386.
CAB003812.
MIM602820. gene.
PharmGKBPA29153.
GenAtlasSearch...

Phylogenomic databases

eggNOGprNOG06375.
HOGENOMHBG715487.
HOVERGENQ16695.
InParanoidQ16695.
OMATDLRFQT.
OrthoDBEOG92Z78C.
PhylomeDBQ16695.

Enzyme and pathway databases

ReactomeREACT_7970. Telomere Maintenance.

Gene expression databases

ArrayExpressQ16695.
BgeeQ16695.
CleanExHS_HIST3H3.
GenevestigatorQ16695.
GermOnlineENSG00000168148. Homo sapiens.

Family and domain databases

InterProIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3.
[Graphical view]
Gene3DG3DSA:1.10.20.10. Histone-fold. 1 hit.
PANTHERPTHR11426. Histone_H3. 1 hit.
PfamPF00125. Histone. 1 hit.
[Graphical view]
PRINTSPR00622. HISTONEH3.
SMARTSM00428. H3. 1 hit.
[Graphical view]
PROSITEPS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. False negative.
[Graphical view]
ProtoNetSearch...

Other Resources

NextBio31067.
SOURCESearch...

Entry information

Entry nameH31T_HUMAN
AccessionPrimary (citable) accession number: Q16695
Secondary accession number(s): B2R5K3, Q6FGU4
Entry history
Integrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: January 23, 2007
Last modified: January 19, 2010
This is version 98 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHPI (Human Proteome Initiative)
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

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM

MIM cross-references

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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents