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Protein

Histone H3.2

Gene

HTR2

more
Organism
Arabidopsis thaliana (Mouse-ear cress)
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
Sitei32 – 321Recognition by ATXR5 and ATXR61 Publication

GO - Molecular functioni

Complete GO annotation...

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H3.2
Alternative name(s):
Histone H3.1
Gene namesi
Name:HTR2
Ordered Locus Names:At1g09200
ORF Names:T12M4.9
AND
Name:HTR3
Ordered Locus Names:At3g27360
ORF Names:K1G2.8
AND
Name:HTR13
Ordered Locus Names:At5g10390
ORF Names:F12B17_260
AND
Name:HTR9
Ordered Locus Names:At5g10400
ORF Names:F12B17_250
AND
Name:HTR1
Ordered Locus Names:At5g65360
ORF Names:MNA5.9
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componentsi: Chromosome 1, Chromosome 3, Chromosome 5

Organism-specific databases

TAIRiAT1G09200.
AT3G27360.
AT5G10390.
AT5G10400.
AT5G65360.

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
Chaini1 – 136136Histone H3.2PRO_0000221267Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei5 – 51N6,N6,N6-trimethyllysine; alternate4 Publications
Modified residuei5 – 51N6,N6-dimethyllysine; alternate4 Publications
Modified residuei5 – 51N6-methyllysine; alternate4 Publications
Modified residuei10 – 101N6,N6,N6-trimethyllysine; alternate5 Publications
Modified residuei10 – 101N6,N6-dimethyllysine; alternate5 Publications
Modified residuei10 – 101N6-acetyllysine; alternate3 Publications
Modified residuei10 – 101N6-methyllysine; alternate5 Publications
Modified residuei11 – 111Phosphoserine2 Publications
Modified residuei12 – 121Phosphothreonine1 Publication
Modified residuei15 – 151N6-acetyllysine4 Publications
Modified residuei19 – 191N6-acetyllysine; alternate3 Publications
Modified residuei19 – 191N6-methyllysine; alternate1 Publication
Modified residuei24 – 241N6-acetyllysine; alternate2 Publications
Modified residuei24 – 241N6-methyllysine; alternate1 Publication
Modified residuei28 – 281N6,N6,N6-trimethyllysine; alternate6 Publications
Modified residuei28 – 281N6,N6-dimethyllysine; alternate6 Publications
Modified residuei28 – 281N6-methyllysine; alternate6 Publications
Modified residuei29 – 291Phosphoserine2 Publications
Modified residuei37 – 371N6,N6,N6-trimethyllysine; alternate2 Publications
Modified residuei37 – 371N6,N6-dimethyllysine; alternate2 Publications
Modified residuei37 – 371N6-methyllysine; alternate2 Publications

Post-translational modificationi

Can be acetylated to form H3K9ac, H3K14ac, H3K18ac and H3K23ac. H3K9ac could compete with H3K9me and prevent gene silencing. H3K9acK14ac molecules are 30-fold less abundant than H3K9ac or H3K14ac. Very low level of H3K9meK14ac. H3K14 is specifically acetylated by HAG1 and deacetylated by HDA6. H3K9ac is deacetylated by HDT1. H3K9ac is restricted to euchromatin. H3K18ac, but not H3K9ac, is cell-cycle dependent and linked to replication. Reduced H4R3me2s increases H3K14ac in the FLC chromatin and activates or maintains its transcription. Vernalization decreases H3K9/14ac in the promoter region of FLC.5 Publications
Mono-, di- or trimethylated to form mainly H3K4me1/2/3, H3K9me1/2/3, H3K27me1/2/3 and H3K36me1/2/3. Very low monomethylation at H3K18me1 or H3K23me1. H3K4me1/2/3, H3K9me3, H3K27me3 and H3K36me1/2/3 are typical marks for euchromatin, whereas heterochromatic chromocenters are enriched in H3K9me1/2 and H3K27me1/2. H3K27me3 is largely restricted to the transcribed regions of single genes and not associated with low-nucleosome density regions. SUVR1 to SUVR5, ASHH1 to ASHH3, ASHR1 to ASHR3, and ATXR5 and ATXR6 methylate H3, with ASHH2 methylating specifically H3K4 and H3K36 and ATXR5 and ATXR6 monomethylating specifically H3K27me1. The Su(var)3-9 homolog proteins (SUVH1 to SUVH10) are H3K9-specific methyltransferases. Among them, KRYPTONITE (SUVH4) is only involved in di- or trimethylation. Regarding H3K9, the major forms are H3K9me1 (20%) and H3K9me2 (10%), while H3K9me3 is rare (0.2%). H3K9me is controlled by DNA methylation and is not required for the formation of constitutive heterochromatin, but double methylation H3K9meK27me is required for the recruitment of CMT3 to methylate heterochromatin and silence euchromatic loci. Very low level of H3K9meK14ac. 60% of H3K27 is found under the form of H3K27me1, 16% of H3K27me2 and 5% of H3K27me3. When associated with H3K27me, H3K36 can only be mono- or di-methylated. H327me2K36me1 or H3K27me1K36me2 are both found in 3% of the proteins. When not associated with H3K27me, H3K36 is only trimethylated. H3K36me3 is found in 3% of the proteins. H2BK143ub1 is probably prerequisite for H3K4me. Elevated H3K4me3 and H3K36me2 formed by ASHH2 are required for high FLC expression. Vernalization increases H3K9me2 and H3K27me2/3 and decreases H3K4me2 at the FLC locus, resulting in the epigenetic silencing of this floral repressor.11 Publications
In meta- and anaphase, H3T11ph is found on the entire length of the condensed chromosomes, whereas H3S10ph and H3S28ph are confined to the pericentromeric regions. During the first meiotic division, H3S10ph and H3S28ph are found on the entire length of the chromosome. Both sites may be involved in sister chromatid cohesion. No phosphorylation detected during interphase. AUR1 and AUR2 phosphorylate only H3S10, while AUR3 phosphorylates both H3S10 and H3S28.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei15 – 151Not N6-methylated1 Publication
Sitei28 – 281Not N6-acetylated1 Publication
Sitei37 – 371Not N6-acetylated1 Publication

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

PaxDbiP59226.
PRIDEiP59226.

PTM databases

iPTMnetiP59226.

Expressioni

Tissue specificityi

Expressed in inflorescences, buds and seedlings.1 Publication

Developmental stagei

Expressed during the S phase.1 Publication

Gene expression databases

ExpressionAtlasiP59226. baseline and differential.
GenevisibleiP59226. AT.

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. The H3K9meK27me dimethylated N-terminal tail of histone H3 can directly interact with the chromodomains of CMT3 and/or LHP1. Interacts with ORTH2. Interacts (via N-terminus) with ATXR5 and ATXR6 (via PHD domain).4 Publications

Protein-protein interaction databases

BioGridi21903. 8 interactions.
22681. 5 interactions.
DIPiDIP-48531N.
STRINGi3702.AT5G65360.1.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4FT2X-ray3.20P2-16[»]
4FT4X-ray2.70P/Q2-33[»]
4IURX-ray2.50C2-16[»]
4IUTX-ray2.70C2-16[»]
4IUUX-ray2.70C2-16[»]
4IUVX-ray2.80C2-16[»]
5HH7X-ray1.90P2-16[»]
ProteinModelPortaliP59226.
SMRiP59226. Positions 17-136.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H3 family.Curated

Phylogenomic databases

eggNOGiKOG1745. Eukaryota.
COG2036. LUCA.
HOGENOMiHOG000155290.
InParanoidiP59226.
KOiK11253.
OMAiASEAYLX.
OrthoDBiEOG09360S2A.
PhylomeDBiP59226.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
IPR000164. Histone_H3/CENP-A.
[Graphical view]
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.

P59226-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RFRPGTVALR
60 70 80 90 100
EIRKYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAV AALQEAAEAY
110 120 130
LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA
Length:136
Mass (Da):15,268
Last modified:January 23, 2007 - v2
Checksum:iF1FB03A849777A61
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M35387 Genomic DNA. Translation: AAA79889.1.
M17131 Genomic DNA. Translation: AAA32809.1.
M17130 Genomic DNA. Translation: AAA32808.1.
AC003114 Genomic DNA. Translation: AAC24084.1.
AB024028 Genomic DNA. Translation: BAA95712.1.
AL353995 Genomic DNA. Translation: CAB89403.1.
AL353995 Genomic DNA. Translation: CAB89404.1.
AB011479 Genomic DNA. Translation: BAB11558.1.
CP002684 Genomic DNA. Translation: AEE28413.1.
CP002686 Genomic DNA. Translation: AEE77308.1.
CP002688 Genomic DNA. Translation: AED91535.1.
CP002688 Genomic DNA. Translation: AED91536.1.
CP002688 Genomic DNA. Translation: AED98043.1.
AK117157 mRNA. Translation: BAC41835.1.
AF370577 mRNA. Translation: AAK49583.1.
AY037250 mRNA. Translation: AAK59851.1.
AY039904 mRNA. Translation: AAK64008.1.
AY077654 mRNA. Translation: AAL76132.1.
AY081741 mRNA. Translation: AAL87394.1.
BT003051 mRNA. Translation: AAO23616.1.
BT003162 mRNA. Translation: AAO24594.1.
BT005805 mRNA. Translation: AAO64207.1.
BT006068 mRNA. Translation: AAP04053.1.
AY084316 mRNA. Translation: AAM60903.1.
PIRiS06250.
RefSeqiNP_189372.1. NM_113651.2.
NP_201339.1. NM_125934.2.
NP_563838.1. NM_100790.2.
NP_568227.1. NM_121077.3.
NP_568228.1. NM_121078.2.
UniGeneiAt.17610.
At.1824.
At.20804.
At.21310.
At.21486.
At.22540.
At.32384.
At.63772.
At.71559.
At.73076.

Genome annotation databases

EnsemblPlantsiAT1G09200.1; AT1G09200.1; AT1G09200.
AT3G27360.1; AT3G27360.1; AT3G27360.
AT5G10390.1; AT5G10390.1; AT5G10390.
AT5G10400.1; AT5G10400.1; AT5G10400.
AT5G65360.1; AT5G65360.1; AT5G65360.
GeneIDi822357.
830903.
830904.
836661.
837440.
GrameneiAT1G09200.1; AT1G09200.1; AT1G09200.
AT3G27360.1; AT3G27360.1; AT3G27360.
AT5G10390.1; AT5G10390.1; AT5G10390.
AT5G10400.1; AT5G10400.1; AT5G10400.
AT5G65360.1; AT5G65360.1; AT5G65360.
KEGGiath:AT1G09200.
ath:AT3G27360.
ath:AT5G10390.
ath:AT5G10400.
ath:AT5G65360.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M35387 Genomic DNA. Translation: AAA79889.1.
M17131 Genomic DNA. Translation: AAA32809.1.
M17130 Genomic DNA. Translation: AAA32808.1.
AC003114 Genomic DNA. Translation: AAC24084.1.
AB024028 Genomic DNA. Translation: BAA95712.1.
AL353995 Genomic DNA. Translation: CAB89403.1.
AL353995 Genomic DNA. Translation: CAB89404.1.
AB011479 Genomic DNA. Translation: BAB11558.1.
CP002684 Genomic DNA. Translation: AEE28413.1.
CP002686 Genomic DNA. Translation: AEE77308.1.
CP002688 Genomic DNA. Translation: AED91535.1.
CP002688 Genomic DNA. Translation: AED91536.1.
CP002688 Genomic DNA. Translation: AED98043.1.
AK117157 mRNA. Translation: BAC41835.1.
AF370577 mRNA. Translation: AAK49583.1.
AY037250 mRNA. Translation: AAK59851.1.
AY039904 mRNA. Translation: AAK64008.1.
AY077654 mRNA. Translation: AAL76132.1.
AY081741 mRNA. Translation: AAL87394.1.
BT003051 mRNA. Translation: AAO23616.1.
BT003162 mRNA. Translation: AAO24594.1.
BT005805 mRNA. Translation: AAO64207.1.
BT006068 mRNA. Translation: AAP04053.1.
AY084316 mRNA. Translation: AAM60903.1.
PIRiS06250.
RefSeqiNP_189372.1. NM_113651.2.
NP_201339.1. NM_125934.2.
NP_563838.1. NM_100790.2.
NP_568227.1. NM_121077.3.
NP_568228.1. NM_121078.2.
UniGeneiAt.17610.
At.1824.
At.20804.
At.21310.
At.21486.
At.22540.
At.32384.
At.63772.
At.71559.
At.73076.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4FT2X-ray3.20P2-16[»]
4FT4X-ray2.70P/Q2-33[»]
4IURX-ray2.50C2-16[»]
4IUTX-ray2.70C2-16[»]
4IUUX-ray2.70C2-16[»]
4IUVX-ray2.80C2-16[»]
5HH7X-ray1.90P2-16[»]
ProteinModelPortaliP59226.
SMRiP59226. Positions 17-136.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi21903. 8 interactions.
22681. 5 interactions.
DIPiDIP-48531N.
STRINGi3702.AT5G65360.1.

PTM databases

iPTMnetiP59226.

Proteomic databases

PaxDbiP59226.
PRIDEiP59226.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G09200.1; AT1G09200.1; AT1G09200.
AT3G27360.1; AT3G27360.1; AT3G27360.
AT5G10390.1; AT5G10390.1; AT5G10390.
AT5G10400.1; AT5G10400.1; AT5G10400.
AT5G65360.1; AT5G65360.1; AT5G65360.
GeneIDi822357.
830903.
830904.
836661.
837440.
GrameneiAT1G09200.1; AT1G09200.1; AT1G09200.
AT3G27360.1; AT3G27360.1; AT3G27360.
AT5G10390.1; AT5G10390.1; AT5G10390.
AT5G10400.1; AT5G10400.1; AT5G10400.
AT5G65360.1; AT5G65360.1; AT5G65360.
KEGGiath:AT1G09200.
ath:AT3G27360.
ath:AT5G10390.
ath:AT5G10400.
ath:AT5G65360.

Organism-specific databases

TAIRiAT1G09200.
AT3G27360.
AT5G10390.
AT5G10400.
AT5G65360.

Phylogenomic databases

eggNOGiKOG1745. Eukaryota.
COG2036. LUCA.
HOGENOMiHOG000155290.
InParanoidiP59226.
KOiK11253.
OMAiASEAYLX.
OrthoDBiEOG09360S2A.
PhylomeDBiP59226.

Miscellaneous databases

PROiP59226.

Gene expression databases

ExpressionAtlasiP59226. baseline and differential.
GenevisibleiP59226. AT.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
IPR000164. Histone_H3/CENP-A.
[Graphical view]
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...

Entry informationi

Entry nameiH32_ARATH
AccessioniPrimary (citable) accession number: P59226
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 17, 2003
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 129 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9me1/2/3 = mono-, di- and trimethylated Lys-10; H3K9ac = acetylated Lys-10; H3S10ph = phosphorylated Ser-11; H3T11ph = phosphorylated Thr-12; H3K14ac = acetylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me1 = monomethylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me1 = monomethylated Lys-24; H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3S28ph = phosphorylated Ser-29; H3K36me1/2/3 = mono-, di- and trimethylated Lys-37.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.