Histone H2B 1/2/3/4/6 - Gallus gallus (Chicken)

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Reviewed, UniProtKB/Swiss-Prot P0C1H3 (H2B1_CHICK)

Last modified October 13, 2009. Version 33. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Histone H2B 1/2/3/4/6
Alternative name(s):
    H2B I
    H2B II
    H2B III
    H2B IV
    H2B VI

Gene names

Name:	H2B-I
AND
Name:	H2B-II
AND
Name:	H2B-III
AND
Name:	H2B-IV
AND
Name:	H2B-VI

Organism

Gallus gallus (Chicken)

Taxonomic identifier

9031 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Archosauria › Dinosauria › Saurischia › Theropoda › Coelurosauria › Aves › Neognathae › Galliformes › Phasianidae › Phasianinae › Gallus

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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.

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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.11 Has broad-spectrum antibacterial activity. May be important in the antimicrobial defenses of chick reproductive system during follicle development in the ovary and egg formation in the oviduct. Ref.11
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.
Post-translational modification	Monoubiquitination of Lys-121 by the BRE1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation By similarity. Phosphorylated on Ser-15 during apoptosis; which facilitates apoptotic chromatin condensation. Ref.9
Sequence similarities	Belongs to the histone H2B family.

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Ontologies

Keywords
Cellular component	Chromosomal protein Nucleosome core Nucleus
Ligand	DNA-binding
Molecular function	Antibiotic Antimicrobial
PTM	Acetylation Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	defense response to bacterium Inferred from electronic annotation. Source: UniProtKB-KW nucleosome assembly Inferred from electronic annotation. Source: InterPro
Cellular component	nucleosome Inferred from electronic annotation. Source: UniProtKB-KW nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
IPL1	P38991	1	EBI-368069,EBI-9319	From a different organism.

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.6 Ref.7

Chain

2 – 126

125

Histone H2B 1/2/3/4/6

PRO_0000071846

Amino acid modifications

Modified residue

N6-acetyllysine Ref.10

Modified residue

N6-acetyllysine Ref.10

Modified residue

Phosphoserine Ref.9

Modified residue

N6-acetyllysine Ref.10

Modified residue

N6-acetyllysine Ref.10

Cross-link

121

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

Experimental info

Sequence conflict

G → A in CAA28745. Ref.2

Sequence conflict

E → A in CAA28747. Ref.2

Sequence conflict

I → S AA sequence Ref.6

Sequence conflict

123

T → I in CAA28751. Ref.2

Secondary structure

126

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P0C1H3-1 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 908F039A02A3400D
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FASTA

126

13,922

        10         20         30         40         50         60 
MPEPAKSAPA PKKGSKKAVT KTQKKGDKKR KKSRKESYSI YVYKVLKQVH PDTGISSKAM 

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


KYTSSK

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References

[1]	"Complete nucleotide sequence of a chicken H2B histone gene." Grandy D.K., Engel J.D., Dodgson J.B. J. Biol. Chem. 257:8577-8580(1982) [PubMed: 7096326] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Structure and organization of the chicken H2B histone gene family." Grandy D.K., Dodgson J.B. Nucleic Acids Res. 15:1063-1080(1987) [PubMed: 3822819] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: White leghorn. Tissue: Blood.
[3]	"Nucleotide sequence of a member of the chicken H2B histone-encoding gene family." Nakayama T., Setoguchi Y. Gene 98:299-300(1991) [PubMed: 2016071] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"Organization of the chicken histone genes in a major gene cluster and generation of an almost complete set of the core histone protein sequences." Takami Y., Higashio M., Fukuoka T., Takechi S., Nakayama T. DNA Res. 3:95-99(1996) [PubMed: 8804862] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], NOMENCLATURE. Strain: White leghorn.
[5]	"Conservation of histone H2A/H2B intergene regions: a role for the H2B specific element in divergent transcription." Sturm R.A., Dalton S., Wells J.R.E. Nucleic Acids Res. 16:8571-8586(1988) [PubMed: 3267232] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[6]	"The complete amino-acid sequence of histone H2B from erythrocytes of the adult domestic fowl Gallus domesticus." van Helden P., Strickland W.N., Strickland M., von Holt C. Biochim. Biophys. Acta 703:17-20(1982) [PubMed: 7074112] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-126.
[7]	"Histone H2B variants from the erythrocytes of an amphibian, a reptile and a bird." van Helden P., Strickland W.N., Brandt W.F., von Holt C. Biochim. Biophys. Acta 533:278-281(1978) [PubMed: 638193] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-30 AND 62-90. Tissue: Erythrocyte.
[8]	"Ubiquitinated histone H2B is preferentially located in transcriptionally active chromatin." Nickel B.E., Allis C.D., Davie J.R. Biochemistry 28:958-963(1989) [PubMed: 2713375] [Abstract] Cited for: UBIQUITINATION.
[9]	"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: 12757711] [Abstract] Cited for: PHOSPHORYLATION AT SER-15.
[10]	"Acetylation of histone H2B mirrors that of H4 and H3 at the chicken beta-globin locus but not at housekeeping genes." Myers F.A., Chong W., Evans D.R., Thorne A.W., Crane-Robinson C. J. Biol. Chem. 278:36315-36322(2003) [PubMed: 12865423] [Abstract] Cited for: ACETYLATION AT LYS-6; LYS-13; LYS-16 AND LYS-21.
[11]	"Antimicrobial proteins in chicken reproductive system." Silphaduang U., Hincke M.T., Nys Y., Mine Y. Biochem. Biophys. Res. Commun. 340:648-655(2006) [PubMed: 16389069] [Abstract] Cited for: FUNCTION AS AN ANTIBIOTIC, MASS SPECTROMETRY.
[12]	"The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix." Arents G., Burlingame R.W., Wang B.-C., Love W.E., Moudrianakis E.N. Proc. Natl. Acad. Sci. U.S.A. 88:10148-10152(1991) [PubMed: 1946434] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS).
+	Additional computationally mapped references.

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Cross-references

Sequence databases

V00415 Genomic DNA. Translation: CAA23706.1.
X05094 Genomic DNA. Translation: CAA28745.1.
X05095 Genomic DNA. Translation: CAA28746.1.
X05096 Genomic DNA. Translation: CAA28747.1.
X05097 Genomic DNA. Translation: CAA28748.1.
X05098 Genomic DNA. Translation: CAA28749.1.
X05100 Genomic DNA. Translation: CAA28751.1.
X57263 Genomic DNA. Translation: CAA40537.1.
X07763 Genomic DNA. Translation: CAA30590.1.
X07766 Genomic DNA. Translation: CAA30596.1.

IPI

IPI00604087.

PIR

B26399.
HSCH22. S14510.

RefSeq

NP_001073188.1.
XP_001232871.1.
XP_001232985.1.
XP_001233227.1.
XP_001233337.1.

UniGene

Gga.35984
Gga.39540
Gga.39843
Gga.40427
Gga.44445

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2ARO	X-ray	2.10	B/F	1-126	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P0C1H3. 1 interaction.

Genome annotation databases

Ensembl

GeneID

417956.
769845.
769973.
770188.
770267.

KEGG

gga:417956.
gga:769845.
gga:769973.
gga:770188.
gga:770267.

Phylogenomic databases

HOVERGEN

P0C1H3.

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.

PANTHER

PTHR23428. Histone_H2B. 1 hit.

Pfam

PF00125. Histone. 1 hit.
[Graphical view]

PRINTS

PR00621. HISTONEH2B.

ProDom

PD000497. Histone_H2B. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00427. H2B. 1 hit.
[Graphical view]

PROSITE

PS00357. HISTONE_H2B. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

H2B1_CHICK

Accession

Primary (citable) accession number: P0C1H3
Secondary accession number(s): P02279, Q92067

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 11, 2006
Last sequence update:	January 23, 2007
Last modified:	October 13, 2009
This is version 33 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Genome annotation databases

Phylogenomic databases

Family and domain databases

Entry information

Relevant documents