Histone H3.2 - Gallus gallus (Chicken)

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Reviewed, UniProtKB/Swiss-Prot P84229 (H32_CHICK)

Last modified September 22, 2009. Version 54. 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 H3.2
Alternative name(s):
Histone H3 class I

Gene names

Name:	H3-I
AND
Name:	H3-II
AND
Name:	H3-III
AND
Name:	H3-IV
AND
Name:	H3-V
AND
Name:	H3-VI
AND
Name:	H3-VII
AND
Name:	H3-VIII

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	136 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.
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.
Developmental stage	Expressed during S phase, then expression strongly decreases as cell division slows down during the process of differentiation.
Post-translational modification	Acetylation is generally linked to gene activation. Acetylation on Lys-19 (H3K18ac) and Lys-24 (H3K24ac) favors methylation at Arg-18 (H3R17me) By similarity. Asymmetric dimethylation at Arg-18 (H3R17me2a) is linked to gene activation Probable. Asymmetric dimethylation at Arg-3 (H3R2me2a) by PRMT6 is linked to gene repression and is mutually exclusive with H3 Lys-5 methylation (H3K4me2 and H3K4me3). H3R2me2a is present at the 3' of genes regardless of their transcription state and is enriched on inactive promoters, while it is absent on active promoters By similarity. Methylation at Lys-5 (H3K4me), Lys-37 (H3K36me) and Lys-80 (H3K79me) are linked to gene activation. Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation of H3 and H4. Methylation at Lys-80 (H3K79me) is associated with DNA double-strand break (DSB) responses and is a specific target for TP53BP1. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are linked to gene repression. Methylation at Lys-10 (H3K9me) is a specific target for HP1 proteins (CBX1, CBX3 and CBX5) and prevents subsequent phosphorylation at Ser-11 (H3S10ph) and acetylation of H3 and H4. Methylation at Lys-5 (H3K4me) and Lys-80 (H3K79me) require preliminary monoubiquitination of H2B at 'Lys-120' Probable. Phosphorylated at Thr-4 (H3T3ph) by GSG2/haspin during prophase and dephosphorylated during anaphase. At centromeres, specifically phosphorylated at Thr-12 (H3T11ph) from prophase to early anaphase, probably by DAPK3 By similarity. Phosphorylation at Ser-11 (H3S10ph) by AURKB is crucial for chromosome condensation and cell-cycle progression during mitosis and meiosis. In addition phosphorylation at Ser-11 (H3S10ph) by RPS6KA4 and RPS6KA5 is important during interphase because it enables the transcription of genes following external stimulation, like mitogens, stress, growth factors or UV irradiation and result in the activation of genes, such as c-fos and c-jun By similarity. Phosphorylation at Ser-11 (H3S10ph), which is linked to gene activation, prevents methylation at Lys-10 (H3K9me) but facilitates acetylation of H3 and H4. Phosphorylation at Ser-11 (H3S10ph) by AURKB mediates the dissociation of HP1 proteins (CBX1, CBX3 and CBX5) from heterochromatin By similarity.
Sequence similarities	Belongs to the histone H3 family.

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Ontologies

Keywords
Cellular component	Chromosomal protein Nucleosome core Nucleus
Ligand	DNA-binding
PTM	Acetylation Methylation Phosphoprotein
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	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-349995,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

Chain

2 – 136

135

Histone H3.2

PRO_0000221260

Amino acid modifications

Modified residue

Asymmetric dimethylarginine; by PRMT6 By similarity

Modified residue

Phosphothreonine By similarity

Modified residue

N6-methyllysine Ref.7

Modified residue

N6,N6,N6-trimethyllysine; alternate Ref.7

Modified residue

N6,N6-dimethyllysine; alternate Ref.7

Modified residue

N6-methyllysine; alternate Ref.7

Modified residue

Phosphoserine By similarity

Modified residue

N6,N6-dimethyllysine; alternate Ref.7

Modified residue

N6-acetyllysine; alternate Ref.7

Modified residue

Asymmetric dimethylarginine By similarity

Modified residue

N6-acetyllysine; alternate Ref.7

Modified residue

N6-methylated lysine; alternate By similarity

Modified residue

N6-acetyllysine Ref.7

Modified residue

N6-acetyllysine; alternate By similarity

Modified residue

N6-methylated lysine; alternate Ref.7

Modified residue

N6-acetyllysine; alternate By similarity

Modified residue

N6-methylated lysine; alternate Ref.7

Modified residue

N6-methylated lysine By similarity

Modified residue

N6,N6-dimethyllysine; alternate Ref.7

Modified residue

N6-methyllysine; alternate Ref.7

Modified residue

123

N6-methylated lysine By similarity

Secondary structure

136

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P84229-1 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 6FD8508EA50A0EEC
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FASTA

136

15,388

        10         20         30         40         50         60 
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE 

        70         80         90        100        110        120 
LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEASEAY LVGLFEDTNL CAIHAKRVTI 

       130 
MPKDIQLARR IRGERA

« Hide

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References

[1]	"Inverted duplication of histone genes in chicken and disposition of regulatory sequences." Wang S.W., Robins A.J., D'Andrea R., Wells J.R.E. Nucleic Acids Res. 13:1369-1387(1985) [PubMed: 4000938] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"A chicken histone H3 gene contains intervening sequences." Engel J.D., Sugarman B.J., Dodgson J.B. Nature 297:434-436(1982) [PubMed: 7078654] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Nucleotide sequences of two members of the chicken H3 histone-encoding gene family." Nakayama T. Gene 102:289-290(1991) [PubMed: 1874451] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (H3-II AND H3-III).
[4]	"Nucleotide sequences of new members (H3-IV and H3-V) of the chicken H3 histone-encoding gene family." Setoguchi Y., Nakayama T. Nucleic Acids Res. 19:6327-6327(1991) [PubMed: 1956792] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (H3-IV AND H3-V). Strain: White leghorn.
[5]	"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] (H3-VI; H3-VII AND H3-VIII). Strain: White leghorn. Tissue: Liver.
[6]	"The determination of the primary structure of histone F3 from chicken erythrocytes by automatic Edman degradation. 2. Sequence analysis of histone F3." Brandt W.F., von Holt C. Eur. J. Biochem. 46:419-429(1974) [PubMed: 4859525] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-136.
[7]	"Identification of acetylation and methylation sites of histone H3 from chicken erythrocytes by high-accuracy matrix-assisted laser desorption ionization-time-of-flight, matrix-assisted laser desorption ionization-postsource decay, and nanoelectrospray ionization tandem mass spectrometry." Zhang K., Tang H., Huang L., Blankenship J.W., Jones P.R., Xiang F., Yau P.M., Burlingame A.L. Anal. Biochem. 306:259-269(2002) [PubMed: 12123664] [Abstract] Cited for: METHYLATION AT LYS-5; LYS-10; LYS-15; LYS-28; LYS-37 AND LYS-80, ACETYLATION AT LYS-15; LYS-19 AND LYS-24, MASS SPECTROMETRY.
[8]	"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).
[9]	"Asymmetries in the nucleosome core particle at 2.5 A resolution." Harp J.M., Hanson B.L., Timm D.E., Bunick G.J. Acta Crystallogr. D 56:1513-1534(2000) [PubMed: 11092917] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH H2A; H2B AND H4.
[10]	"Structure of the histone-core octamer in KCl/phosphate crystals at 2.15 A resolution." Chantalat L., Nicholson J.M., Lambert S.J., Reid A.J., Donovan M.J., Reynolds C.D., Wood C.M., Baldwin J.P. Acta Crystallogr. D 59:1395-1407(2003) [PubMed: 12876341] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH H2A AND H2B.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

X02218 Genomic DNA. Translation: CAA26138.1.
J00869 Genomic DNA. Translation: AAA48795.1. Sequence problems.
M61154 Genomic DNA. Translation: AAA48796.1.
M61155 Genomic DNA. Translation: AAA48797.1.
X62291 Genomic DNA. Translation: CAA44180.1.
X62292 Genomic DNA. Translation: CAA44181.1.
U37577 Genomic DNA. Translation: AAC60003.1.
U37578 Genomic DNA. Translation: AAC60004.1.
U37579 Genomic DNA. Translation: AAC60005.1.

IPI

IPI00683452.

PIR

HSCH3. S18716.

RefSeq

XP_001231209.1.
XP_001232833.1.
XP_001232932.1.
XP_001233028.1.
XP_416193.2.

UniGene

Gga.40179
Gga.44534
Gga.5274

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EQZ	X-ray	2.50	C/G	1-136	[»]
1HIO	X-ray	3.10	C	44-136	[»]
1HQ3	X-ray	2.15	C/G	1-136	[»]
1TZY	X-ray	1.90	C/G	1-136	[»]
2ARO	X-ray	2.10	C/G	1-136	[»]
2HIO	X-ray	3.10	C	1-136	[»]
3C9K	electron microscopy	20.00	C/G	2-136	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P84229. 3 interactions.

STRING

P84229.

Genome annotation databases

Ensembl

ENSGALT00000019190; ENSGALP00000019166; ENSGALG00000023231; Gallus gallus. [Genome view]
ENSGALT00000019209; ENSGALP00000019185; ENSGALG00000023219; Gallus gallus. [Genome view]
ENSGALT00000031955; ENSGALP00000031319; ENSGALG00000023215; Gallus gallus. [Genome view]
ENSGALT00000038085; ENSGALP00000037293; ENSGALG00000023219; Gallus gallus. [Genome view]
ENSGALT00000038086; ENSGALP00000037294; ENSGALG00000023220; Gallus gallus. [Genome view]
ENSGALT00000038102; ENSGALP00000037310; ENSGALG00000023228; Gallus gallus. [Genome view]
ENSGALT00000038109; ENSGALP00000037317; ENSGALG00000023231; Gallus gallus. [Genome view]

GeneID

417953.
427887.
768333.
769809.
770022.

KEGG

gga:417953.
gga:768333.
gga:769809.
gga:770022.

Organism-specific databases

CTD

427887.

Phylogenomic databases

HOVERGEN

P84229.

Family and domain databases

InterPro

IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3.
[Graphical view]

Gene3D

G3DSA:1.10.20.10. Histone-fold. 1 hit.

PANTHER

PTHR11426. Histone_H3. 1 hit.

Pfam

PF00125. Histone. 1 hit.
[Graphical view]

PRINTS

PR00622. HISTONEH3.

SMART

SM00428. H3. 1 hit.
[Graphical view]

PROSITE

PS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

H32_CHICK

Accession

Primary (citable) accession number: P84229
Secondary accession number(s): P02295

P17320

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	September 22, 2009
This is version 54 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

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Entry information

Relevant documents