P02293 (H2B1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone H2B.1

Alternative name(s):
Suppressor of Ty protein 12

Gene names

Name:	HTB1
Synonyms:	H2B1, SPT12
Ordered Locus Names:	YDR224C
ORF Names:	YD9934.09C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

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.10 Ref.11 Ref.16 Ref.19 Ref.20 Ref.21 Ref.22 Ref.23 Ref.26
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	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. Sumoylation to form H2BK6su or H2BK7su, and probably also H2BK16su or H2BK17su, occurs preferentially near the telomeres and represses gene transcription. Ref.26
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.

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	chromatin assembly or disassembly Inferred from direct assay PubMed 8017102PubMed 9256430. Source: SGD negative regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype PubMed 17526727. Source: SGD nucleosome assembly Inferred from electronic annotation. Source: InterPro postreplication repair Inferred from genetic interaction Ref.10. Source: SGD
Cellular_component	nuclear nucleosome Inferred from direct assay PubMed 9256430. Source: SGD replication fork protection complex Inferred from direct assay PubMed 16531994. Source: SGD
Molecular_function	DNA binding Inferred from direct assay PubMed 8017102. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
STH1	P32597	3	EBI-8088,EBI-18410
SWR1	Q05471	2	EBI-8088,EBI-22102

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.1

PRO_0000071938

Amino acid modifications

Modified residue

7

1

N6-acetyllysine; alternate Ref.26

Modified residue

8

1

N6-acetyllysine; alternate Ref.26

Modified residue

11

1

Phosphoserine Ref.20 Ref.21

Modified residue

12

1

N6-acetyllysine Ref.9 Ref.15

Modified residue

17

1

N6-acetyllysine; alternate Ref.9 Ref.15 Ref.26

Cross-link

7

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate Ref.26

Cross-link

8

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate Ref.26

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.8 Ref.13 Ref.14 Ref.17 Ref.19 Ref.27

Experimental info

Mutagenesis

7 – 8

2

KK → AA: Reduces sumoylation. Ref.26

Mutagenesis

11

1

S → A: Desensitizes cells to H(2)O(2) treatment. Ref.20 Ref.26

Mutagenesis

11

1

S → E: Induces apoptotic-like features including chromatin condensation. Ref.20 Ref.26

Mutagenesis

17 – 18

2

KK → AA: Reduces sumoylation. Ref.26

Mutagenesis

48

1

V → F: Confers UV-radiation sensitivity; when associated with F-87 and S-88. Ref.10 Ref.26

Mutagenesis

87

1

Y → F: Confers UV-radiation sensitivity; when associated with F-48 and S-88. Ref.10 Ref.26

Mutagenesis

88

1

N → S: Confers UV-radiation sensitivity; when associated with F-48 and F-87. Ref.10 Ref.26

Mutagenesis

124

1

K → R: Impairs ubiquitin conjugation, DNA double-strand brakes formation during meiosis and histone H3-K79 methylation. Ref.8 Ref.11 Ref.17 Ref.19 Ref.22 Ref.26

Secondary structure

1

.

.

.

.

.

.

.

.

.

131

Helix Strand Turn

Details...

Helix

42 – 52

11

Helix

60 – 86

27

Helix

95 – 105

11

Helix

109 – 128

20

Sequences

	Sequence		Length	Mass (Da)
	P02293 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 9F5E9CFB341DB399	FASTA	131	14,252
	10 20 30 40 50 60 MSAKAEKKPA SKAPAEKKPA AKKTSTSTDG KKRSKARKET 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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Insertion site specificity of the transposon Tn3." Davies C.J., Hutchison C.A. III Nucleic Acids Res. 23:507-514(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[6]	"Coding and noncoding sequences at the 3' end of yeast histone H2B mRNA confer cell cycle regulation." Xu H., Johnson L., Grunstein M. Mol. Cell. Biol. 10:2687-2694(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 115-131.
[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]	"Rad6-dependent ubiquitination of histone H2B in yeast." Robzyk K., Recht J., Osley M.A. Science 287:501-504(2000) [PubMed] [Europe PMC] [Abstract] Cited for: UBIQUITINATION AT LYS-124, MUTAGENESIS OF LYS-124.
[9]	"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.
[10]	"A role for histone H2B during repair of UV-induced DNA damage in Saccharomyces cerevisiae." Martini E.M.D., Keeney S., Osley M.A. Genetics 160:1375-1387(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF VAL-48; TYR-87 AND ASN-88.
[11]	"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.
[12]	"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.
[13]	"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.
[14]	"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.
[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], MASS SPECTROMETRY.
[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]	"The DNA damage checkpoint response requires histone H2B ubiquitination by Rad6-Bre1 and H3 methylation by Dot1." Giannattasio M., Lazzaro F., Plevani P., Muzi-Falconi M. J. Biol. Chem. 280:9879-9886(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF LYS-124.
[23]	"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.
[24]	"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.
[25]	"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.
[26]	"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: 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.
[27]	"A tandem affinity tag for two-step purification under fully denaturing conditions: application in ubiquitin profiling and protein complex identification combined with in vivocross-linking." Tagwerker C., Flick K., Cui M., Guerrero C., Dou Y., Auer B., Baldi P., Huang L., Kaiser P. Mol. Cell. Proteomics 5:737-748(2006) [PubMed] [Europe PMC] [Abstract] Cited for: UBIQUITINATION AT LYS-124.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J01327 Genomic DNA. Translation: AAA88719.1.
U13239 Genomic DNA. Translation: AAC33141.1.
Z48612 Genomic DNA. Translation: CAA88504.1.
AY557724 Genomic DNA. Translation: AAS56050.1.
M37743 mRNA. Translation: AAA34694.2.
BK006938 Genomic DNA. Translation: DAA12066.1.

PIR

HSBY22. A02621.

RefSeq

NP_010510.3. NM_001180532.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2JSS	NMR	-	A	37-131	[»]

ProteinModelPortal

P02293.

SMR

P02293. Positions 10-131.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-416N.

IntAct

P02293. 235 interactions.

MINT

MINT-564492.

STRING

4932.YDR224C.

Proteomic databases

PRIDE

P02293.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDR224C; YDR224C; YDR224C.

GeneID

851810.

KEGG

sce:YDR224C.
sce:YDR228C.

Organism-specific databases

SGD

S000002632. HTB1.

Phylogenomic databases

GeneTree

ENSGT00680000099513.

HOGENOM

HOG000231213.

KO

K11252.
K14400.

OMA

CSAMPEP.

OrthoDB

EOG4MKRS0.

Gene expression databases

Genevestigator

P02293.

GermOnline

YDR224C. Saccharomyces cerevisiae.

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. Histone-fold. 1 hit.

PROSITE

PS00357. HISTONE_H2B. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P02293.

NextBio

969662.

Entry information

Entry name

H2B1_YEAST

Accession

Primary (citable) accession number: P02293
Secondary accession number(s): D6VSK6

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 135 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program