P84229 (H32_CHICK) Reviewed, UniProtKB/Swiss-Prot
Last modified November 13, 2013. Version 89. History...
Names and origin
|Protein names||Recommended name:|
Histone H3 class I
|Organism||Gallus gallus (Chicken) [Reference proteome]|
|Taxonomic identifier||9031 [NCBI]|
|Taxonomic lineage||Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Testudines + Archosauria group › Archosauria › Dinosauria › Saurischia › Theropoda › Coelurosauria › Aves › Neognathae › Galliformes › Phasianidae › Phasianinae › Gallus|
|Sequence length||136 AA.|
|Sequence processing||The displayed sequence is further processed into a mature form.|
|Protein existence||Evidence at protein level|
General annotation (Comments)
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.
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 HMGB1. Ref.8
Expressed during S phase, then expression strongly decreases as cell division slows down during the process of differentiation.
Acetylation is generally linked to gene activation. Acetylation on Lys-19 (H3K18ac) and Lys-24 (H3K24ac) favors methylation at Arg-18 (H3R17me). Acetylation at Lys-123 (H3K122ac) by EP300/p300 plays a central role in chromatin structure: localizes at the surface of the histone octamer and stimulates transcription, possibly by promoting nucleosome instability 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. Ref.7
Phosphorylated at Thr-4 (H3T3ph) by GSG2/haspin during prophase and dephosphorylated during anaphase. 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. 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. Phosphorylation at Ser-11 (H3S10ph) is also an essential regulatory mechanism for neoplastic cell transformation. Phosphorylated at Ser-29 (H3S28ph) by MLTK isoform 1, RPS6KA5 or AURKB during mitosis or upon ultraviolet B irradiation. Phosphorylation at Thr-7 (H3T6ph) by PRKCB is a specific tag for epigenetic transcriptional activation that prevents demethylation of Lys-5 (H3K4me) by LSD1/KDM1A. At centromeres, specifically phosphorylated at Thr-12 (H3T11ph) from prophase to early anaphase, by DAPK3 and PKN1. Phosphorylation at Thr-12 (H3T11ph) by PKN1 is a specific tag for epigenetic transcriptional activation that promotes demethylation of Lys-10 (H3K9me) by KDM4C/JMJD2C. Phosphorylation at Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin By similarity.
Monoubiquitinated by RAG1 in lymphoid cells, monoubiquitination is required for V(D)J recombination By similarity.
Lysine deamination at Lys-5 (H3K4all) to form allysine only takes place on H3K4me3 and results in gene repression By similarity.
Belongs to the histone H3 family.
Direct protein sequencing
|Gene Ontology (GO)|
Inferred from electronic annotation. Source: InterPro
Inferred from electronic annotation. Source: UniProtKB-KWnucleus
Inferred from electronic annotation. Source: UniProtKB-SubCell
Inferred from electronic annotation. Source: UniProtKB-KW
|Complete GO annotation...|
Sequence annotation (Features)
|Feature key||Position(s)||Length||Description||Graphical view||Feature identifier|
|Initiator methionine||1||1||Removed Ref.6|
|Chain||2 – 136||135||Histone H3.2||PRO_0000221260|
|Site||37 – 38||2||Involved in HMGB1-binding|
Amino acid modifications
|Modified residue||3||1||Asymmetric dimethylarginine; by PRMT6 By similarity|
|Modified residue||4||1||Phosphothreonine; by GSG2 By similarity|
|Modified residue||5||1||Allysine; alternate By similarity|
|Modified residue||5||1||N6,N6,N6-trimethyllysine; alternate Ref.7|
|Modified residue||5||1||N6,N6-dimethyllysine; alternate Ref.7|
|Modified residue||5||1||N6-acetyllysine; alternate By similarity|
|Modified residue||5||1||N6-methyllysine Ref.7|
|Modified residue||7||1||Phosphothreonine; by PKC By similarity|
|Modified residue||10||1||N6,N6,N6-trimethyllysine; alternate Ref.7|
|Modified residue||10||1||N6,N6-dimethyllysine; alternate Ref.7|
|Modified residue||10||1||N6-methyllysine; alternate Ref.7|
|Modified residue||11||1||Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 By similarity|
|Modified residue||12||1||Phosphothreonine; by PKC By similarity|
|Modified residue||15||1||N6,N6-dimethyllysine; alternate Ref.7|
|Modified residue||15||1||N6-acetyllysine; alternate Ref.7|
|Modified residue||18||1||Asymmetric dimethylarginine By similarity|
|Modified residue||19||1||N6-acetyllysine; alternate Ref.7|
|Modified residue||19||1||N6-methylated lysine; alternate By similarity|
|Modified residue||24||1||N6-acetyllysine Ref.7|
|Modified residue||28||1||N6-acetyllysine; alternate By similarity|
|Modified residue||28||1||N6-methylated lysine; alternate Ref.7|
|Modified residue||29||1||Phosphoserine; by AURKB, AURKC and RPS6KA5 By similarity|
|Modified residue||37||1||N6-acetyllysine; alternate By similarity|
|Modified residue||37||1||N6-methylated lysine; alternate Ref.7|
|Modified residue||42||1||Phosphotyrosine By similarity|
|Modified residue||58||1||Phosphoserine By similarity|
|Modified residue||65||1||N6-methylated lysine By similarity|
|Modified residue||80||1||N6,N6-dimethyllysine; alternate Ref.7|
|Modified residue||80||1||N6-methyllysine; alternate Ref.7|
|Modified residue||81||1||Phosphothreonine By similarity|
|Modified residue||116||1||N6-acetyllysine By similarity|
|Modified residue||123||1||N6-acetyllysine; alternate By similarity|
|Modified residue||123||1||N6-methyllysine; alternate By similarity|
Helix Strand Turn
|Beta strand||34 – 37||4|
|Helix||44 – 57||14|
|Helix||65 – 79||15|
|Beta strand||80 – 82||3|
|Helix||87 – 114||28|
|Beta strand||118 – 120||3|
|Helix||122 – 131||10|
|||"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
|||"A chicken histone H3 gene contains intervening sequences."|
Engel J.D., Sugarman B.J., Dodgson J.B.
Nature 297:434-436(1982) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
|||"Nucleotide sequences of two members of the chicken H3 histone-encoding gene family."|
Gene 102:289-290(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (H3-II AND H3-III).
|||"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (H3-IV AND H3-V).
Strain: White leghorn.
|||"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (H3-VI; H3-VII AND H3-VIII).
Strain: White leghorn.
|||"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] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-136.
|||"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] [Europe PMC] [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.
|||"Distinct domains in HMGB1 are involved in specific intramolecular and nucleosomal interactions."|
Kawase T., Sato K., Ueda T., Yoshida M.
Biochemistry 47:13991-13996(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH HMGB1.
|||"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] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS).
|||"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] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH H2A; H2B AND H4.
|||"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] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH H2A AND H2B.
|+||Additional computationally mapped references.|
|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.
|PIR||HSCH3. S18716. |
|RefSeq||NP_001268409.1. NM_001281480.1. |
3D structure databases
|SMR||P84229. Positions 17-136. |
Protein-protein interaction databases
|IntAct||P84229. 3 interactions.|
Protocols and materials databases
Genome annotation databases
|Ensembl||ENSGALT00000042655; ENSGALP00000042290; ENSGALG00000027064. |
ENSGALT00000043934; ENSGALP00000040958; ENSGALG00000027257.
Gene expression databases
Family and domain databases
|Gene3D||184.108.40.206. 1 hit. |
|InterPro||IPR009072. Histone-fold. |
|PANTHER||PTHR11426. PTHR11426. 1 hit. |
|Pfam||PF00125. Histone. 1 hit. |
|PRINTS||PR00622. HISTONEH3. |
|SMART||SM00428. H3. 1 hit. |
|SUPFAM||SSF47113. SSF47113. 1 hit. |
|PROSITE||PS00322. HISTONE_H3_1. 1 hit. |
PS00959. HISTONE_H3_2. 1 hit.
|Accession||Primary (citable) accession number: P84229|
Secondary accession number(s): P02295 P17320
|Entry status||Reviewed (UniProtKB/Swiss-Prot)|
|Annotation program||Chordata Protein Annotation Program|