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P02294 (H2B2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 146. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Histone H2B.2
Gene names
Name:HTB2
Synonyms:H2B2
Ordered Locus Names:YBL002W
ORF Names:YBL0104
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length131 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. Ref.9 Ref.16 Ref.19 Ref.20 Ref.21 Ref.22 Ref.25

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. Interacts with NAP1. Ref.26 Ref.28

Subcellular location

Nucleus. Chromosome.

Post-translational modification

Monoubiquitinated by the RAD6/UBC2-BRE1 complex to form H2BK123ub1. H2BK123ub1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for H3K4me and H3K79me formation. H2BK123ub1 also modulates the formation of double-strand breaks during meiosis and is a prerequisite for DNA-damage checkpoint activation. Deubiquitination is performed by UBP8 in presence of SGF11.

Phosphorylated by STE20 to form H2BS10ph during progression through meiotic prophase. May be correlated with chromosome condensation. H2BS10ph is also formed after H2O2 treatment, and is a step leading to apoptosis. Ref.20 Ref.21

Acetylated by GCN5, a component of the SAGA complex, to form H2BK11ac and H2BK16ac. H2BK16ac can also be formed by ESA1, a component of the NuA4 histone acetyltransferase (HAT) complex. Acetylation of N-terminal lysines and particularly formation of H2BK11acK16ac has a positive effect on transcription. Ref.7 Ref.8 Ref.15 Ref.25

Sumoylation to form H2BK6su or H2BK7su, and probably also H2BK16su or H2BK17su, occurs preferentially near the telomeres and represses gene transcription. Ref.25

Miscellaneous

Present with 443000 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the histone H2B family.

Caution

To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK6su = sumoylated Lys-7; H2BK7ac = acetylated Lys-8; H2BK7su = sumoylated Lys-8; H2BS10ph = phosphorylated Ser-11; H2BK11ac = acetylated Lys-12; H2BK16ac = acetylated Lys-17; H2BK16su = sumoylated Lys-17; H2BK17su = sumoylated Lys-18; H2BK123ub1 = monoubiquitinated Lys-124.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Probable
Chain2 – 131130Histone H2B.2
PRO_0000071939

Amino acid modifications

Modified residue71N6-acetyllysine; alternate Ref.25
Modified residue81N6-acetyllysine; alternate Ref.25
Modified residue111Phosphoserine Ref.20 Ref.21
Modified residue121N6-acetyllysine Ref.8 Ref.15
Modified residue171N6-acetyllysine; alternate Ref.8 Ref.15 Ref.25
Cross-link7Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate Ref.25
Cross-link8Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate Ref.25
Cross-link17Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate Probable
Cross-link18Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Probable
Cross-link124Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.11 Ref.12 Ref.14 Ref.17 Ref.19

Experimental info

Mutagenesis7 – 82KK → AA: Reduces sumoylation. Ref.25
Mutagenesis111S → A: Desensitizes cells to H(2)O(2) treatment. Ref.20 Ref.25
Mutagenesis111S → E: Induces apoptotic-like features including chromatin condensation. Ref.20 Ref.25
Mutagenesis17 – 182KK → AA: Reduces sumoylation. Ref.25
Mutagenesis1241K → R: Impairs ubiquitin conjugation, DNA double-strand breaks formation during meiosis and histone H3-K79 methylation. Ref.9 Ref.17 Ref.19 Ref.25

Secondary structure

............ 131
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P02294 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 3DCC26FF124D71E8

FASTA13114,237
        10         20         30         40         50         60 
MSSAAEKKPA SKAPAEKKPA AKKTSTSVDG KKRSKVRKET YSSYIYKVLK QTHPDTGISQ 

        70         80         90        100        110        120 
KSMSILNSFV NDIFERIATE ASKLAAYNKK STISAREIQT AVRLILPGEL AKHAVSEGTR 

       130 
AVTKYSSSTQ A 

« Hide

References

« Hide 'large scale' references
[1]"Histone H2B genes of yeast encode two different proteins."
Wallis J.W., Hereford L., Grunstein M.
Cell 22:799-805(1980) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Sequence around the centromere of Saccharomyces cerevisiae chromosome II: similarity of CEN2 to CEN4."
Wolfe K.H., Lohan A.J.E.
Yeast 10:S41-S46(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"Complete DNA sequence of yeast chromosome II."
Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. expand/collapse author list , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[6]"The histones of yeast. The isolation and partial structure of the core histones."
Brandt W.F., Patterson K., von Holt C.
Eur. J. Biochem. 110:67-76(1980) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 64-89, PROBABLE CLEAVAGE OF INITIATOR METHIONINE.
[7]"Steady-state levels of histone acetylation in Saccharomyces cerevisiae."
Waterborg J.H.
J. Biol. Chem. 275:13007-13011(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION.
[8]"Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin."
Suka N., Suka Y., Carmen A.A., Wu J., Grunstein M.
Mol. Cell 8:473-479(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION AT LYS-12 AND LYS-17.
[9]"Gene silencing: trans-histone regulatory pathway in chromatin."
Briggs S.D., Xiao T., Sun Z.-W., Caldwell J.A., Shabanowitz J., Hunt D.F., Allis C.D., Strahl B.D.
Nature 418:498-498(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF LYS-124.
[10]"Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8."
Henry K.W., Wyce A., Lo W.-S., Duggan L.J., Emre N.C.T., Kao C.-F., Pillus L., Shilatifard A., Osley M.A., Berger S.L.
Genes Dev. 17:2648-2663(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION, DEUBIQUITINATION BY UBP8.
[11]"A conserved RING finger protein required for histone H2B monoubiquitination and cell size control."
Hwang W.W., Venkatasubrahmanyam S., Ianculescu A.G., Tong A., Boone C., Madhani H.D.
Mol. Cell 11:261-266(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION AT LYS-124.
[12]"Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter."
Wood A., Krogan N.J., Dover J., Schneider J., Heidt J., Boateng M.A., Dean K., Golshani A., Zhang Y., Greenblatt J.F., Johnston M., Shilatifard A.
Mol. Cell 11:267-274(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION AT LYS-124.
[13]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[14]"A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery."
Hitchcock A.L., Auld K., Gygi S.P., Silver P.A.
Proc. Natl. Acad. Sci. U.S.A. 100:12735-12740(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-124.
[15]"Mapping global histone acetylation patterns to gene expression."
Kurdistani S.K., Tavazoie S., Grunstein M.
Cell 117:721-733(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION AT LYS-12 AND LYS-17.
[16]"Rad6 plays a role in transcriptional activation through ubiquitylation of histone H2B."
Kao C.-F., Hillyer C., Tsukuda T., Henry K.W., Berger S.L., Osley M.A.
Genes Dev. 18:184-195(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION BY UBC2, FUNCTION.
[17]"Carbohydrates induce mono-ubiquitination of H2B in yeast."
Dong L., Xu C.W.
J. Biol. Chem. 279:1577-1580(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION AT LYS-124, MUTAGENESIS OF LYS-124.
[18]"Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses."
Zhou W., Ryan J.J., Zhou H.
J. Biol. Chem. 279:32262-32268(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: SUMOYLATION [LARGE SCALE ANALYSIS].
[19]"Rad6-Bre1-mediated histone H2B ubiquitylation modulates the formation of double-strand breaks during meiosis."
Yamashita K., Shinohara M., Shinohara A.
Proc. Natl. Acad. Sci. U.S.A. 101:11380-11385(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, UBIQUITINATION AT LYS-124 BY THE UBC2-BRE1 COMPLEX, MUTAGENESIS OF LYS-124.
[20]"Sterile 20 kinase phosphorylates histone H2B at serine 10 during hydrogen peroxide-induced apoptosis in S. cerevisiae."
Ahn S.-H., Cheung W.L., Hsu J.-Y., Diaz R.L., Smith M.M., Allis C.D.
Cell 120:25-36(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION AT SER-11, MUTAGENESIS OF SER-11, FUNCTION.
[21]"H2B (Ser10) phosphorylation is induced during apoptosis and meiosis in S. cerevisiae."
Ahn S.-H., Henderson K.A., Keeney S., Allis C.D.
Cell Cycle 4:780-783(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION AT SER-11, FUNCTION.
[22]"Histone H2B ubiquitylation is associated with elongating RNA polymerase II."
Xiao T., Kao C.-F., Krogan N.J., Sun Z.-W., Greenblatt J.F., Osley M.A., Strahl B.D.
Mol. Cell. Biol. 25:637-651(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION BY THE UBC2-BRE1 COMPLEX, FUNCTION.
[23]"H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex."
Ingvarsdottir K., Krogan N.J., Emre N.C.T., Wyce A., Thompson N.J., Emili A., Hughes T.R., Greenblatt J.F., Berger S.L.
Mol. Cell. Biol. 25:1162-1172(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: DEUBIQUITINATION BY THE UBP8-SGF11 COMPLEX.
[24]"The deubiquitylation activity of Ubp8 is dependent upon Sgf11 and its association with the SAGA complex."
Lee K.K., Florens L., Swanson S.K., Washburn M.P., Workman J.L.
Mol. Cell. Biol. 25:1173-1182(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: DEUBIQUITINATION BY THE UBP8-SGF11 COMPLEX.
[25]"Histone sumoylation is a negative regulator in Saccharomyces cerevisiae and shows dynamic interplay with positive-acting histone modifications."
Nathan D., Ingvarsdottir K., Sterner D.E., Bylebyl G.R., Dokmanovic M., Dorsey J.A., Whelan K.A., Krsmanovic M., Lane W.S., Meluh P.B., Johnson E.S., Berger S.L.
Genes Dev. 20:966-976(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: SUMOYLATION AT LYS-7; LYS-8; LYS-17 AND LYS-18, ACETYLATION AT LYS-7; LYS-8 AND LYS-17, MUTAGENESIS OF 7-LYS-LYS-8 AND 17-LYS-LYS-18, FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY.
[26]"Phosphorylation by casein kinase 2 regulates Nap1 localization and function."
Calvert M.E.K., Keck K.M., Ptak C., Shabanowitz J., Hunt D.F., Pemberton L.F.
Mol. Cell. Biol. 28:1313-1325(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH NAP1, IDENTIFICATION BY MASS SPECTROMETRY.
[27]"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].
[28]"Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions."
White C.L., Suto R.K., Luger K.
EMBO J. 20:5207-5218(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF NUCLEOSOME CORE COMPLEX, SUBUNIT.
[29]"The path of DNA in the kinetochore."
Bloom K.S., Sharma S., Dokholyan N.V.
Curr. Biol. 16:R276-R278(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: 3D-STRUCTURE MODELING.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
V01308 Genomic DNA. Translation: CAA24615.1.
Z26494 Genomic DNA. Translation: CAA81268.1.
Z35763 Genomic DNA. Translation: CAA84817.1.
AY693063 Genomic DNA. Translation: AAT93082.1.
BK006936 Genomic DNA. Translation: DAA07120.1.
PIRHSBYB2. S44558.
RefSeqNP_009553.1. NM_001178242.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1ID3X-ray3.10D/H2-131[»]
2FSBmodel-D/H1-131[»]
4JJNX-ray3.09D/H2-131[»]
ProteinModelPortalP02294.
SMRP02294. Positions 10-129.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32700. 202 interactions.
DIPDIP-3897N.
IntActP02294. 80 interactions.
MINTMINT-482371.
STRING4932.YBL002W.

Proteomic databases

PaxDbP02294.
PRIDEP02294.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYBL002W; YBL002W; YBL002W.
GeneID852284.
KEGGsce:YBL002W.

Organism-specific databases

SGDS000000098. HTB2.

Phylogenomic databases

eggNOGNOG289161.
GeneTreeENSGT00730000110319.
HOGENOMHOG000231213.
KOK11252.
OMARINKKFT.
OrthoDBEOG7WHHPK.

Enzyme and pathway databases

BioCycYEAST:G3O-28908-MONOMER.

Gene expression databases

GenevestigatorP02294.

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

EvolutionaryTraceP02294.
NextBio970916.

Entry information

Entry nameH2B2_YEAST
AccessionPrimary (citable) accession number: P02294
Secondary accession number(s): D6VQ00
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 146 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome II

Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references