Reviewed, UniProtKB/Swiss-Prot Q16695 (H31T_HUMAN)

Names and origin

Protein names

Recommended name:
    Histone H3.1t
      Short name=H3t
      Short name=H3/t
Alternative name(s):
    H3/g

Gene names

Name:	HIST3H3
Synonyms:	H3FT

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	136 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	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

Keywords
Cellular component	Chromosomal protein Nucleosome core Nucleus
Ligand	DNA-binding
PTM	Acetylation Citrullination Methylation Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	nucleosome assembly Non-traceable author statement. Source: UniProtKB
Cellular component	nucleoplasm Inferred from Experiment. Source: Reactome nucleosome Non-traceable author statement. Source: UniProtKB
Molecular function	DNA binding Non-traceable author statement. Source: UniProtKB protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
KDM1	O60341	1	EBI-358900,EBI-710124
KDM4A	O75164	3	EBI-358900,EBI-936709

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed By similarity

Chain

2 – 136

135

Histone H3.1t

PRO_0000221248

Amino acid modifications

Modified residue

3

1

Asymmetric dimethylarginine; by PRMT6 By similarity

Modified residue

4

1

Phosphothreonine By similarity

Modified residue

5

1

N6-methylated lysine By similarity

Modified residue

9

1

Citrulline; alternate By similarity

Modified residue

9

1

Symmetric dimethylarginine; by PRMT5; alternate By similarity

Modified residue

10

1

N6-acetyllysine; alternate By similarity

Modified residue

10

1

N6-methylated lysine; alternate By similarity

Modified residue

11

1

Phosphoserine By similarity

Modified residue

12

1

Phosphothreonine By similarity

Modified residue

15

1

N6-acetyllysine By similarity

Modified residue

18

1

Asymmetric dimethylarginine; by CARM1; alternate By similarity

Modified residue

18

1

Citrulline; alternate By similarity

Modified residue

19

1

N6-acetyllysine; alternate By similarity

Modified residue

19

1

N6-methylated lysine; alternate By similarity

Modified residue

24

1

N6-acetyllysine Ref.10

Modified residue

28

1

N6-acetyllysine; alternate By similarity

Modified residue

28

1

N6-methylated lysine; alternate Ref.8

Modified residue

29

1

Phosphoserine Ref.9

Modified residue

37

1

N6-acetyllysine; alternate By similarity

Modified residue

37

1

N6-methylated lysine; alternate By similarity

Modified residue

65

1

N6-methylated lysine By similarity

Modified residue

80

1

N6-methylated lysine By similarity

Modified residue

123

1

N6-methylated lysine By similarity

Secondary structure

1

.

.

.

136

Helix Strand Turn

Details...

Helix

3 – 5

3

Sequences

	Sequence		Length	Mass (Da)
	Q16695-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 37375A2C3A377B2B	FASTA	136	15,508
	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

References

	« Hide 'large scale' referencesShow '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. , 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. , 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. , 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.

IPI

IPI00216402.

PIR

S57473.

RefSeq

NP_003484.1.

UniGene

Hs.248171

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2V1D	X-ray	3.10	C	2-22	[»]

SMR

Q16695. Positions 2-136.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-922N.

IntAct

Q16695. 5 interactions.

STRING

Q16695.

PTM databases

PhosphoSite

Q16695.

Proteomic databases

PRIDE

Q16695.

Genome annotation databases

Ensembl

ENST00000366696; ENSP00000355657; ENSG00000168148; Homo sapiens. [Genome view]

GeneID

8290.

KEGG

hsa:8290.

UCSC

uc001hsx.1. human.

Organism-specific databases

CTD

8290.

GeneCards

GC01M226679.

H-InvDB

HIX0028778.

HGNC

HGNC:4778. HIST3H3.

HPA

CAB001386.
CAB003812.

MIM

602820. gene.

PharmGKB

PA29153.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG06375.

HOGENOM

HBG715487.

HOVERGEN

Q16695.

InParanoid

Q16695.

OMA

TDLRFQT.

OrthoDB

EOG92Z78C.

PhylomeDB

Q16695.

Enzyme and pathway databases

Reactome

REACT_7970. Telomere Maintenance.

Gene expression databases

ArrayExpress

Q16695.

Bgee

Q16695.

CleanEx

HS_HIST3H3.

Genevestigator

Q16695.

GermOnline

ENSG00000168148. Homo sapiens.

Family and domain databases

InterPro

IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3.
[Graphical view]

Gene3D

G3DSA:1.10.20.10. Histone-fold. 1 hit.

PANTHER

PTHR11426. Histone_H3. 1 hit.

Pfam

PF00125. Histone. 1 hit.
[Graphical view]

PRINTS

PR00622. HISTONEH3.

SMART

SM00428. H3. 1 hit.
[Graphical view]

PROSITE

PS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. False negative.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

31067.

SOURCE

Search...

Entry information

Entry name

H31T_HUMAN

Accession

Primary (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 status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

Disclaimer

Any 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.