Q93079 (H2B1H_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone H2B type 1-H

Alternative name(s):
Histone H2B.j
Short name=H2B/j

Gene names

Name:	HIST1H2BH
Synonyms:	H2BFJ

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Dipnotetrapodomorpha › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Boreoeutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	126 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. Chromosome.
Post-translational modification	Monoubiquitination at Lys-35 (H2BK34Ub) by the MSL1/MSL2 dimer is required for histone H3 'Lys-4' (H3K4me) and 'Lys-79' (H3K79me) methylation and transcription activation at specific gene loci, such as HOXA9 and MEIS1 loci. Similarly, monoubiquitination at Lys-121 (H2BK120Ub) by the RNF20/40 complex gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation. It also functions cooperatively with the FACT dimer to stimulate elongation by RNA polymerase II. H2BK120Ub also acts as a regulator of mRNA splicing: deubiquitination by USP49 is required for efficient cotranscriptional splicing of a large set of exons. Phosphorylation at Ser-37 (H2BS36ph) by AMPK in response to stress promotes transcription By similarity. Phosphorylated on Ser-15 (H2BS14ph) by STK4/MST1 during apoptosis; which facilitates apoptotic chromatin condensation. Also phosphorylated on Ser-15 in response to DNA double strand breaks (DSBs), and in correlation with somatic hypermutation and immunoglobulin class-switch recombination. Ref.7 GlcNAcylation at Ser-113 promotes monoubiquitination of Lys-121. It fluctuates in response to extracellular glucose, and associates with transcribed genes 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.12
Sequence similarities	Belongs to the histone H2B family.

Ontologies

Keywords
Cellular component	Chromosome Nucleosome core Nucleus
Ligand	DNA-binding
PTM	Acetylation Glycoprotein Isopeptide bond Methylation Phosphoprotein Ubl conjugation
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	chromatin organization Traceable author statement. Source: Reactome nucleosome assembly Non-traceable author statement Ref.1. Source: UniProtKB
Cellular_component	extracellular vesicular exosome Inferred from direct assay PubMed 20458337. Source: UniProt nucleoplasm Traceable author statement. Source: Reactome nucleosome Non-traceable author statement Ref.1. Source: UniProtKB nucleus Inferred from direct assay PubMed 21630459. Source: UniProt
Molecular_function	DNA binding Non-traceable author statement Ref.1. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed By similarity
	Chain	2 – 126	125	Histone H2B type 1-H		PRO_0000071833
Amino acid modifications
	Modified residue	2	1	N-acetylproline By similarity
	Modified residue	6	1	N6-acetyllysine; alternate Ref.6 Ref.9
	Modified residue	6	1	N6-crotonyllysine; alternate Ref.12
	Modified residue	12	1	N6-acetyllysine; alternate Ref.6
	Modified residue	12	1	N6-crotonyllysine; alternate Ref.12
	Modified residue	13	1	N6-acetyllysine; alternate Ref.6 Ref.9
	Modified residue	13	1	N6-crotonyllysine; alternate Ref.12
	Modified residue	15	1	Phosphoserine; by STK4/MST1 Ref.7
	Modified residue	16	1	N6-acetyllysine; alternate Ref.6 Ref.9
	Modified residue	16	1	N6-crotonyllysine; alternate Ref.12
	Modified residue	17	1	N6-acetyllysine; alternate Ref.6
	Modified residue	17	1	N6-crotonyllysine; alternate Ref.12
	Modified residue	21	1	N6-acetyllysine; alternate Ref.6 Ref.9
	Modified residue	21	1	N6-crotonyllysine; alternate Ref.12
	Modified residue	24	1	N6-acetyllysine; alternate By similarity
	Modified residue	24	1	N6-crotonyllysine; alternate Ref.12
	Modified residue	35	1	N6-crotonyllysine; alternate Ref.12
	Modified residue	37	1	Phosphoserine; by AMPK By similarity
	Modified residue	47	1	N6-methyllysine Ref.6
	Modified residue	58	1	N6,N6-dimethyllysine Ref.6
	Modified residue	80	1	Dimethylated arginine By similarity
	Modified residue	86	1	N6,N6,N6-trimethyllysine; alternate By similarity
	Modified residue	86	1	N6-acetyllysine; alternate By similarity
	Modified residue	87	1	Omega-N-methylarginine By similarity
	Modified residue	93	1	Omega-N-methylarginine By similarity
	Modified residue	109	1	N6-methyllysine Ref.6
	Modified residue	116	1	Phosphothreonine By similarity
	Modified residue	117	1	N6-methylated lysine By similarity
	Glycosylation	113	1	O-linked (GlcNAc) By similarity
	Cross-link	35		Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate Ref.13
	Cross-link	121		Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.6 Ref.8 Ref.10

Sequences

	Sequence		Length	Mass (Da)
	Q93079 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: FAE0F79FF4BF703D	FASTA	126	13,892
	10 20 30 40 50 60 MPDPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM 70 80 90 100 110 120 GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Thalamus.
[4]	"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. , 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].
[5]	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].
[6]	"Quantitative proteomic analysis of post-translational modifications of human histones." Beck H.C., Nielsen E.C., Matthiesen R., Jensen L.H., Sehested M., Finn P., Grauslund M., Hansen A.M., Jensen O.N. Mol. Cell. Proteomics 5:1314-1325(2006) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 7-24, ACETYLATION AT LYS-6; LYS-12; LYS-13; LYS-16; LYS-17 AND LYS-21, METHYLATION AT LYS-47; LYS-58 AND LYS-109, UBIQUITINATION AT LYS-121, IDENTIFICATION BY MASS SPECTROMETRY.
[7]	"Apoptotic phosphorylation of histone H2B is mediated by mammalian sterile twenty kinase." Cheung W.L., Ajiro K., Samejima K., Kloc M., Cheung P., Mizzen C.A., Beeser A., Etkin L.D., Chernoff J., Earnshaw W.C., Allis C.D. Cell 113:507-517(2003) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION AT SER-15.
[8]	"Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation." Zhu B., Zheng Y., Pham A.-D., Mandal S.S., Erdjument-Bromage H., Tempst P., Reinberg D. Mol. Cell 20:601-611(2005) [PubMed] [Europe PMC] [Abstract] Cited for: UBIQUITINATION AT LYS-121.
[9]	"Inhibition of core histones acetylation by carcinogenic nickel(II)." Golebiowski F., Kasprzak K.S. Mol. Cell. Biochem. 279:133-139(2005) [PubMed] [Europe PMC] [Abstract] Cited for: ACETYLATION AT LYS-6; LYS-13; LYS-16 AND LYS-21.
[10]	"Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II." Pavri R., Zhu B., Li G., Trojer P., Mandal S., Shilatifard A., Reinberg D. Cell 125:703-717(2006) [PubMed] [Europe PMC] [Abstract] Cited for: UBIQUITINATION AT LYS-121.
[11]	"Gene-specific characterization of human histone H2B by electron capture dissociation." Siuti N., Roth M.J., Mizzen C.A., Kelleher N.L., Pesavento J.J. J. Proteome Res. 5:233-239(2006) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY.
[12]	"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-6; LYS-12; LYS-13; LYS-16; LYS-17; LYS-21; LYS-24 AND LYS-35.
[13]	"The RING finger protein MSL2 in the MOF complex is an E3 ubiquitin ligase for H2B K34 and is involved in crosstalk with H3 K4 and K79 methylation." Wu L., Zee B.M., Wang Y., Garcia B.A., Dou Y. Mol. Cell 43:132-144(2011) [PubMed] [Europe PMC] [Abstract] Cited for: UBIQUITINATION AT LYS-35.
[14]	"USP49 deubiquitinates histone H2B and regulates cotranscriptional pre-mRNA splicing." Zhang Z., Jones A., Joo H.Y., Zhou D., Cao Y., Chen S., Erdjument-Bromage H., Renfrow M., He H., Tempst P., Townes T.M., Giles K.E., Ma L., Wang H. Genes Dev. 27:1581-1595(2013) [PubMed] [Europe PMC] [Abstract] Cited for: UBIQUITINATION, DEUBIQUITINATION BY USP49.

Cross-references

Sequence databases
EMBL GenBank DDBJ	Z80781 Genomic DNA. Translation: CAB02543.1. AF531291 Genomic DNA. Translation: AAN06691.1. AK312052 mRNA. Translation: BAG34988.1. AL031777 Genomic DNA. Translation: CAB39185.1. CH471087 Genomic DNA. Translation: EAW55552.1. BC096116 mRNA. Translation: AAH96116.1. BC096117 mRNA. Translation: AAH96117.1. BC096118 mRNA. Translation: AAH96118.1. BC096119 mRNA. Translation: AAH96119.1.
CCDS	CCDS4601.1.
RefSeq	NP_003515.1. NM_003524.2.
UniGene	Hs.247815.
3D structure databases
ProteinModelPortal	Q93079.
SMR	Q93079. Positions 5-126.
ModBase	Search...
MobiDB	Search...
Protein-protein interaction databases
BioGrid	113941. 10 interactions.
IntAct	Q93079. 8 interactions.
MINT	MINT-4829860.
STRING	9606.ENSP00000348706.
PTM databases
PhosphoSite	Q93079.
Polymorphism databases
DMDM	7387739.
Proteomic databases
MaxQB	Q93079.
PaxDb	Q93079.
PRIDE	Q93079.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000356350; ENSP00000348706; ENSG00000197459.
GeneID	8345.
KEGG	hsa:8345.
UCSC	uc003nhh.3. human.
Organism-specific databases
CTD	8345.
GeneCards	GC06P026251.
HGNC	HGNC:4755. HIST1H2BH.
MIM	602806. gene.
neXtProt	NX_Q93079.
PharmGKB	PA29130.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG315146.
HOGENOM	HOG000231213.
HOVERGEN	HBG007774.
InParanoid	Q93079.
KO	K11252.
OMA	TSAKTIY.
OrthoDB	EOG72VH8J.
PhylomeDB	Q93079.
TreeFam	TF300212.
Enzyme and pathway databases
Reactome	REACT_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
Bgee	Q93079.
CleanEx	HS_HIST1H2BH.
Genevestigator	Q93079.
Family and domain databases
Gene3D	1.10.20.10. 1 hit.
InterPro	IPR009072. Histone-fold. IPR007125. Histone_core_D. IPR000558. Histone_H2B. [Graphical view]
PANTHER	PTHR23428. PTHR23428. 1 hit.
Pfam	PF00125. Histone. 1 hit. [Graphical view]
PRINTS	PR00621. HISTONEH2B.
SMART	SM00427. H2B. 1 hit. [Graphical view]
SUPFAM	SSF47113. SSF47113. 1 hit.
PROSITE	PS00357. HISTONE_H2B. 1 hit. [Graphical view]
ProtoNet	Search...
Other
ChiTaRS	HIST1H2BH. human.
GeneWiki	HIST1H2BH.
GenomeRNAi	8345.
NextBio	31252.
PRO	Q93079.
SOURCE	Search...

Entry information

Entry name

H2B1H_HUMAN

Accession

Primary (citable) accession number: Q93079
Secondary accession number(s): B2R541, Q4VB74

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	January 23, 2007
Last modified:	July 9, 2014
This is version 134 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

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.