P02294 (H2B2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone H2B.2

Gene names

Name:	HTB2
Synonyms:	H2B2
Ordered Locus Names:	YBL002W
ORF Names:	YBL0104

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	131 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. Ref.8 Ref.15 Ref.18 Ref.19 Ref.20 Ref.21 Ref.24
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.19 Ref.20 Ref.25 Ref.27 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. Sumoylation to form H2BK6su or H2BK7su, and probably also H2BK16su or H2BK17su, occurs preferentially near the telomeres and represses gene transcription.
Miscellaneous	Present with 443000 molecules/cell in log phase SD medium. Ref.12
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 refering 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.

Ontologies

Keywords
Cellular component	Chromosome Nucleosome core Nucleus
Ligand	DNA-binding
PTM	Acetylation Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	nucleosome assembly Inferred from electronic annotation. Source: InterPro
Cellular component	nuclear nucleosome Traceable author statement. Source: SGD replication fork protection complex Inferred from direct assay. Source: SGD
Molecular function	DNA binding Traceable author statement. Source: SGD protein binding Inferred from physical interaction. 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 – 131

130

Histone H2B.2

PRO_0000071939

Amino acid modifications

Modified residue

7

1

N6-acetyllysine; alternate Ref.24

Modified residue

8

1

N6-acetyllysine; alternate Ref.24

Modified residue

11

1

Phosphoserine Ref.19 Ref.20

Modified residue

12

1

N6-acetyllysine Ref.7 Ref.14

Modified residue

17

1

N6-acetyllysine; alternate Ref.7 Ref.14 Ref.24

Modified residue

40

1

Phosphothreonine Ref.25

Modified residue

42

1

Phosphoserine Ref.27

Cross-link

7

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate Ref.24

Cross-link

8

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate Ref.24

Cross-link

17

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate Probable

Cross-link

18

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Probable

Cross-link

124

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.10 Ref.11 Ref.13 Ref.16 Ref.18

Experimental info

Mutagenesis

7 – 8

2

KK → AA: Reduces sumoylation. Ref.24

Mutagenesis

11

1

S → A: Desensitizes cells to H(2)O(2) treatment. Ref.19 Ref.24

Mutagenesis

11

1

S → E: Induces apoptotic-like features including chromatin condensation. Ref.19 Ref.24

Mutagenesis

17 – 18

2

KK → AA: Reduces sumoylation. Ref.24

Mutagenesis

124

1

K → R: Impairs ubiquitin conjugation, DNA double-strand breaks formation during meiosis and histone H3-K79 methylation. Ref.8 Ref.16 Ref.18 Ref.24

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

131

Helix Strand Turn

Details...

Helix

42 – 52

11

Helix

60 – 87

28

Beta strand

91 – 93

3

Helix

95 – 105

11

Helix

108 – 127

20

Sequences

	Sequence		Length	Mass (Da)
	P02294 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 3DCC26FF124D71E8	FASTA	131	14,237
	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

References

	« Hide 'large scale' referencesShow '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: 7006833] [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: 8091860] [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. , 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: 7813418] [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. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[6]	"Steady-state levels of histone acetylation in Saccharomyces cerevisiae." Waterborg J.H. J. Biol. Chem. 275:13007-13011(2000) [PubMed: 10777603] [Abstract] Cited for: ACETYLATION.
[7]	"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: 11545749] [Abstract] Cited for: ACETYLATION AT LYS-12 AND LYS-17.
[8]	"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: 12152067] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF LYS-124.
[9]	"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: 14563679] [Abstract] Cited for: UBIQUITINATION, DEUBIQUITINATION BY UBP8.
[10]	"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: 12535538] [Abstract] Cited for: UBIQUITINATION AT LYS-124.
[11]	"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: 12535539] [Abstract] Cited for: UBIQUITINATION AT LYS-124.
[12]	"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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[13]	"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: 14557538] [Abstract] Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-124, MASS SPECTROMETRY.
[14]	"Mapping global histone acetylation patterns to gene expression." Kurdistani S.K., Tavazoie S., Grunstein M. Cell 117:721-733(2004) [PubMed: 15186774] [Abstract] Cited for: ACETYLATION AT LYS-12 AND LYS-17.
[15]	"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: 14752010] [Abstract] Cited for: UBIQUITINATION BY UBC2, FUNCTION.
[16]	"Carbohydrates induce mono-ubiquitination of H2B in yeast." Dong L., Xu C.W. J. Biol. Chem. 279:1577-1580(2004) [PubMed: 14660635] [Abstract] Cited for: UBIQUITINATION AT LYS-124, MUTAGENESIS OF LYS-124.
[17]	"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: 15166219] [Abstract] Cited for: SUMOYLATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[18]	"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: 15280549] [Abstract] Cited for: FUNCTION, UBIQUITINATION AT LYS-124 BY THE UBC2-BRE1 COMPLEX, MUTAGENESIS OF LYS-124.
[19]	"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: 15652479] [Abstract] Cited for: PHOSPHORYLATION AT SER-11, MUTAGENESIS OF SER-11, FUNCTION.
[20]	"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: 15970663] [Abstract] Cited for: PHOSPHORYLATION AT SER-11, FUNCTION.
[21]	"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: 15632065] [Abstract] Cited for: UBIQUITINATION BY THE UBC2-BRE1 COMPLEX, FUNCTION.
[22]	"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: 15657441] [Abstract] Cited for: DEUBIQUITINATION BY THE UBP8-SGF11 COMPLEX.
[23]	"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: 15657442] [Abstract] Cited for: DEUBIQUITINATION BY THE UBP8-SGF11 COMPLEX.
[24]	"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: 16598039] [Abstract] Cited for: MASS SPECTROMETRY, 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.
[25]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed: 17287358] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-40, 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: 18086883] [Abstract] Cited for: INTERACTION WITH NAP1, MASS SPECTROMETRY.
[27]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-42, MASS SPECTROMETRY.
[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: 11566884] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF NUCLEOSOME CORE COMPLEX, SUBUNIT.
+	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.

PIR

HSBYB2. S44558.

RefSeq

NP_009553.1. NM_001178242.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ID3	X-ray	3.10	D/H	2-131	[»]
2FSB	model	-	D/H	1-131	[»]

ProteinModelPortal

P02294.

SMR

P02294. Positions 10-129.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-3897N.

IntAct

P02294. 98 interactions.

MINT

MINT-482371.

STRING

P02294.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YBL002W; YBL002W; YBL002W.

GeneID

852284.

KEGG

sce:YBL002W.

NMPDR

fig|4932.3.peg.248.

Organism-specific databases

SGD

S000000098. HTB2.

Phylogenomic databases

eggNOG

fuNOG10567.

GeneTree

EFGT00050000003769.

HOGENOM

HBG715487.

OMA

ISAKAMS.

OrthoDB

EOG4MKRS0.

Gene expression databases

ArrayExpress

P02294.

Genevestigator

P02294.

GermOnline

YBL002W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000558. Histone_H2B.
[Graphical view]

Gene3D

G3DSA:1.10.20.10. Histone-fold. 1 hit.

KO

K11252.

PANTHER

PTHR23428. Histone_H2B. 1 hit.

Pfam

PF00125. Histone. 1 hit.
[Graphical view]

PRINTS

PR00621. HISTONEH2B.

SMART

SM00427. H2B. 1 hit.
[Graphical view]

SUPFAM

SSF47113. Histone-fold. 1 hit.

PROSITE

PS00357. HISTONE_H2B. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

970916.

Entry information

Entry name

H2B2_YEAST

Accession

Primary (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:	December 14, 2011
This is version 125 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program