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Protein

Histone H3.2

Gene

H3-I

more
Organism
Gallus gallus (Chicken)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei37 – 382Involved in HMGB1-binding

GO - Molecular functioni

Complete GO annotation...

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiREACT_276260. DNA methylation.
REACT_277792. RNA Polymerase I Chain Elongation.
REACT_286472. Factors involved in megakaryocyte development and platelet production.
REACT_299305. PRC2 methylates histones and DNA.
REACT_316866. Transcriptional regulation by small RNAs.
REACT_316940. SIRT1 negatively regulates rRNA Expression.
REACT_322027. RNA Polymerase I Promoter Opening.
REACT_340836. NoRC negatively regulates rRNA expression.
REACT_342239. Senescence-Associated Secretory Phenotype (SASP).
REACT_348443. Oxidative Stress Induced Senescence.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H3.2
Alternative name(s):
Histone H3 class I
Gene namesi
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
OrganismiGallus gallus (Chicken)
Taxonomic identifieri9031 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiArchelosauriaArchosauriaDinosauriaSaurischiaTheropodaCoelurosauriaAvesNeognathaeGalloanseraeGalliformesPhasianidaePhasianinaeGallus
ProteomesiUP000000539 Componenti: Chromosome 1

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 136135Histone H3.2PRO_0000221260Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei3 – 31Asymmetric dimethylarginine; by PRMT6By similarity
Modified residuei4 – 41Phosphothreonine; by GSG2By similarity
Modified residuei5 – 51Allysine; alternateBy similarity
Modified residuei5 – 51N6,N6,N6-trimethyllysine; alternate1 Publication
Modified residuei5 – 51N6,N6-dimethyllysine; alternate1 Publication
Modified residuei5 – 51N6-acetyllysine; alternateBy similarity
Modified residuei5 – 51N6-methyllysine1 Publication
Modified residuei7 – 71Phosphothreonine; by PKCBy similarity
Modified residuei10 – 101N6,N6,N6-trimethyllysine; alternate1 Publication
Modified residuei10 – 101N6,N6-dimethyllysine; alternate1 Publication
Modified residuei10 – 101N6-methyllysine; alternate1 Publication
Modified residuei11 – 111Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5By similarity
Modified residuei12 – 121Phosphothreonine; by PKCBy similarity
Modified residuei15 – 151N6,N6-dimethyllysine; alternate1 Publication
Modified residuei15 – 151N6-acetyllysine; alternate1 Publication
Modified residuei18 – 181Asymmetric dimethylarginineBy similarity
Modified residuei19 – 191N6-acetyllysine; alternate1 Publication
Modified residuei19 – 191N6-methylated lysine; alternateBy similarity
Modified residuei24 – 241N6-acetyllysine1 Publication
Modified residuei28 – 281N6-acetyllysine; alternateBy similarity
Modified residuei28 – 281N6-methylated lysine; alternate1 Publication
Modified residuei29 – 291Phosphoserine; by AURKB, AURKC and RPS6KA5By similarity
Modified residuei37 – 371N6-acetyllysine; alternateBy similarity
Modified residuei37 – 371N6-methylated lysine; alternate1 Publication
Modified residuei42 – 421PhosphotyrosineBy similarity
Modified residuei58 – 581PhosphoserineBy similarity
Modified residuei65 – 651N6-methylated lysineBy similarity
Modified residuei80 – 801N6,N6-dimethyllysine; alternate1 Publication
Modified residuei80 – 801N6-methyllysine; alternate1 Publication
Modified residuei81 – 811PhosphothreonineBy similarity
Modified residuei116 – 1161N6-acetyllysineBy similarity
Modified residuei123 – 1231N6-acetyllysine; alternateBy similarity
Modified residuei123 – 1231N6-methyllysine; alternateBy similarity

Post-translational modificationi

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).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).By similarityCurated
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).1 Publication
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).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

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiP84229.
PRIDEiP84229.

Expressioni

Developmental stagei

Expressed during S phase, then expression strongly decreases as cell division slows down during the process of differentiation.

Interactioni

Subunit structurei

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 HMGB1.3 Publications

Protein-protein interaction databases

IntActiP84229. 3 interactions.
STRINGi9031.ENSGALP00000019185.

Structurei

Secondary structure

1
136
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi34 – 374Combined sources
Helixi44 – 5714Combined sources
Helixi65 – 7915Combined sources
Beta strandi80 – 823Combined sources
Helixi87 – 11428Combined sources
Beta strandi118 – 1203Combined sources
Helixi122 – 13110Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EQZX-ray2.50C/G1-136[»]
1HIOX-ray3.10C44-136[»]
1HQ3X-ray2.15C/G1-136[»]
1TZYX-ray1.90C/G1-136[»]
2AROX-ray2.10C/G1-136[»]
2HIOX-ray3.10C1-136[»]
3C9Kelectron microscopy20.00C/G2-136[»]
ProteinModelPortaliP84229.
SMRiP84229. Positions 17-136.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP84229.

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H3 family.Curated

Phylogenomic databases

eggNOGiCOG2036.
GeneTreeiENSGT00760000118967.
HOGENOMiHOG000155290.
HOVERGENiHBG001172.
InParanoidiP84229.
KOiK11253.
OMAiRISKMAR.
PhylomeDBiP84229.
TreeFamiTF314241.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3/CENP-A.
[Graphical view]
PANTHERiPTHR11426. PTHR11426. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00622. HISTONEH3.
SMARTiSM00428. H3. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P84229-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR
60 70 80 90 100
EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEASEAY
110 120 130
LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA
Length:136
Mass (Da):15,388
Last modified:January 23, 2007 - v2
Checksum:i6FD8508EA50A0EEC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiS18716. HSCH3.
RefSeqiNP_001268409.1. NM_001281480.1.
NP_001268438.1. NM_001281509.1.
XP_001232833.1. XM_001232832.3.
XP_001233028.1. XM_001233027.3.
XP_004937729.1. XM_004937672.1.
XP_416193.2. XM_416193.3.
UniGeneiGga.5274.

Genome annotation databases

EnsembliENSGALT00000042655; ENSGALP00000042290; ENSGALG00000027064.
ENSGALT00000043934; ENSGALP00000040958; ENSGALG00000027257.
GeneIDi100858681.
417953.
768333.
769809.
769852.
770022.
KEGGigga:100858681.
gga:417953.
gga:768333.
gga:769809.
gga:769852.
gga:770022.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiS18716. HSCH3.
RefSeqiNP_001268409.1. NM_001281480.1.
NP_001268438.1. NM_001281509.1.
XP_001232833.1. XM_001232832.3.
XP_001233028.1. XM_001233027.3.
XP_004937729.1. XM_004937672.1.
XP_416193.2. XM_416193.3.
UniGeneiGga.5274.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EQZX-ray2.50C/G1-136[»]
1HIOX-ray3.10C44-136[»]
1HQ3X-ray2.15C/G1-136[»]
1TZYX-ray1.90C/G1-136[»]
2AROX-ray2.10C/G1-136[»]
2HIOX-ray3.10C1-136[»]
3C9Kelectron microscopy20.00C/G2-136[»]
ProteinModelPortaliP84229.
SMRiP84229. Positions 17-136.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP84229. 3 interactions.
STRINGi9031.ENSGALP00000019185.

Proteomic databases

PaxDbiP84229.
PRIDEiP84229.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSGALT00000042655; ENSGALP00000042290; ENSGALG00000027064.
ENSGALT00000043934; ENSGALP00000040958; ENSGALG00000027257.
GeneIDi100858681.
417953.
768333.
769809.
769852.
770022.
KEGGigga:100858681.
gga:417953.
gga:768333.
gga:769809.
gga:769852.
gga:770022.

Phylogenomic databases

eggNOGiCOG2036.
GeneTreeiENSGT00760000118967.
HOGENOMiHOG000155290.
HOVERGENiHBG001172.
InParanoidiP84229.
KOiK11253.
OMAiRISKMAR.
PhylomeDBiP84229.
TreeFamiTF314241.

Enzyme and pathway databases

ReactomeiREACT_276260. DNA methylation.
REACT_277792. RNA Polymerase I Chain Elongation.
REACT_286472. Factors involved in megakaryocyte development and platelet production.
REACT_299305. PRC2 methylates histones and DNA.
REACT_316866. Transcriptional regulation by small RNAs.
REACT_316940. SIRT1 negatively regulates rRNA Expression.
REACT_322027. RNA Polymerase I Promoter Opening.
REACT_340836. NoRC negatively regulates rRNA expression.
REACT_342239. Senescence-Associated Secretory Phenotype (SASP).
REACT_348443. Oxidative Stress Induced Senescence.

Miscellaneous databases

EvolutionaryTraceiP84229.
NextBioi20821179.
PROiP84229.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3/CENP-A.
[Graphical view]
PANTHERiPTHR11426. PTHR11426. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00622. HISTONEH3.
SMARTiSM00428. H3. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [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, IDENTIFICATION BY MASS SPECTROMETRY.
  8. "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.
  9. "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).
  10. "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.
  11. "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.

Entry informationi

Entry nameiH32_CHICK
AccessioniPrimary (citable) accession number: P84229
Secondary accession number(s): P02295
, P02297, P16105, P17269, P17320
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: June 24, 2015
This is version 104 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.