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Q5QNW6 (H2B2F_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 92. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Histone H2B type 2-F
Gene names
Name:HIST2H2BF
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length126 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. 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.4

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.10

Sequence similarities

Belongs to the histone H2B family.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q5QNW6-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q5QNW6-2)

The sequence of this isoform differs from the canonical sequence as follows:
     126-126: K → KLIGPILWK
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 126125Histone H2B type 2-F
PRO_0000244826

Amino acid modifications

Modified residue21N-acetylproline By similarity
Modified residue61N6-acetyllysine; alternate Ref.6
Modified residue61N6-crotonyllysine; alternate Ref.10
Modified residue121N6-acetyllysine; alternate By similarity
Modified residue121N6-crotonyllysine; alternate Ref.10
Modified residue131N6-acetyllysine; alternate Ref.6
Modified residue131N6-crotonyllysine; alternate Ref.10
Modified residue151Phosphoserine; by STK4/MST1 Ref.4
Modified residue161N6-acetyllysine; alternate Ref.6
Modified residue161N6-crotonyllysine; alternate Ref.10
Modified residue171N6-acetyllysine; alternate Ref.9
Modified residue171N6-crotonyllysine; alternate Ref.10
Modified residue211N6-acetyllysine; alternate Ref.6 Ref.9
Modified residue211N6-crotonyllysine; alternate Ref.10
Modified residue241N6-acetyllysine; alternate By similarity
Modified residue241N6-crotonyllysine; alternate Ref.10
Modified residue351N6-crotonyllysine; alternate Ref.10
Modified residue371Phosphoserine; by AMPK By similarity
Modified residue471N6-methyllysine By similarity
Modified residue581N6,N6-dimethyllysine By similarity
Modified residue801Dimethylated arginine By similarity
Modified residue861N6,N6,N6-trimethyllysine; alternate By similarity
Modified residue861N6-acetyllysine; alternate By similarity
Modified residue871Omega-N-methylarginine By similarity
Modified residue931Omega-N-methylarginine By similarity
Modified residue1091N6-methyllysine By similarity
Modified residue1161Phosphothreonine By similarity
Modified residue1171N6-methylated lysine By similarity
Glycosylation1131O-linked (GlcNAc) By similarity
Cross-link35Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate Ref.11
Cross-link121Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.5 Ref.7

Natural variations

Alternative sequence1261K → KLIGPILWK in isoform 2.
VSP_043431

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: E951DF3D7E97C106

FASTA12613,920
        10         20         30         40         50         60 
MPDPAKSAPA PKKGSKKAVT KVQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM 

        70         80         90        100        110        120 
GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT 


KYTSSK 

« Hide

Isoform 2 [UniParc].

Checksum: 6F656197FE8FD5E2
Show »

FASTA13414,841

References

« Hide 'large scale' references
[1]"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
Tissue: Amygdala and Tongue.
[2]"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Pancreas.
[4]"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.
[5]"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.
[6]"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.
[7]"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.
[8]"Characterization of histones H2A and H2B variants and their post-translational modifications by mass spectrometry."
Bonenfant D., Coulot M., Towbin H., Schindler P., van Oostrum J.
Mol. Cell. Proteomics 5:541-552(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[9]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-17 AND LYS-21, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"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.
[11]"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.
[12]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]"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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AK289664 mRNA. Translation: BAF82353.1.
AK296916 mRNA. Translation: BAG59471.1.
AL591493 Genomic DNA. Translation: CAI12558.1.
BC110793 mRNA. Translation: AAI10794.1.
CCDSCCDS30846.1. [Q5QNW6-1]
CCDS53359.1. [Q5QNW6-2]
RefSeqNP_001019770.1. NM_001024599.4. [Q5QNW6-1]
NP_001154806.1. NM_001161334.1. [Q5QNW6-2]
XP_006711400.1. XM_006711337.1. [Q5QNW6-1]
UniGeneHs.632451.

3D structure databases

ProteinModelPortalQ5QNW6.
SMRQ5QNW6. Positions 5-126.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid136811. 8 interactions.
IntActQ5QNW6. 7 interactions.
MINTMINT-3296686.
STRING9606.ENSP00000358164.

PTM databases

PhosphoSiteQ5QNW6.

Polymorphism databases

DMDM74743113.

Proteomic databases

PaxDbQ5QNW6.
PRIDEQ5QNW6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000369167; ENSP00000358164; ENSG00000203814. [Q5QNW6-1]
ENST00000545683; ENSP00000445831; ENSG00000203814. [Q5QNW6-2]
ENST00000578867; ENSP00000462132; ENSG00000263376. [Q5QNW6-2]
ENST00000583773; ENSP00000464073; ENSG00000263376. [Q5QNW6-1]
GeneID440689.
KEGGhsa:440689.
UCSCuc001esr.4. human. [Q5QNW6-1]
uc010pbj.2. human. [Q5QNW6-2]

Organism-specific databases

CTD440689.
GeneCardsGC01M149767.
HGNCHGNC:24700. HIST2H2BF.
HPACAB007814.
neXtProtNX_Q5QNW6.
PharmGKBPA145148722.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG289161.
HOGENOMHOG000231213.
HOVERGENHBG007774.
InParanoidQ5QNW6.
KOK11252.
PhylomeDBQ5QNW6.
TreeFamTF300212.

Enzyme and pathway databases

ReactomeREACT_172623. Chromatin organization.

Gene expression databases

BgeeQ5QNW6.
CleanExHS_HIST2H2BF.
GenevestigatorQ5QNW6.

Family and domain databases

Gene3D1.10.20.10. 1 hit.
InterProIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000558. Histone_H2B.
[Graphical view]
PANTHERPTHR23428. PTHR23428. 1 hit.
PfamPF00125. Histone. 1 hit.
[Graphical view]
PRINTSPR00621. HISTONEH2B.
SMARTSM00427. H2B. 1 hit.
[Graphical view]
SUPFAMSSF47113. SSF47113. 1 hit.
PROSITEPS00357. HISTONE_H2B. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSHIST2H2BF. human.
GeneWikiHIST2H2BF.
GenomeRNAi440689.
NextBio109448.
PROQ5QNW6.

Entry information

Entry nameH2B2F_HUMAN
AccessionPrimary (citable) accession number: Q5QNW6
Secondary accession number(s): A8K0U9, B4DLA9
Entry history
Integrated into UniProtKB/Swiss-Prot: July 11, 2006
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 92 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
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

SIMILARITY comments

Index of protein domains and families

Human chromosome 1

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