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Protein

Histone H3.2

Gene
N/A
Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 4 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.

GO - Molecular functioni

Complete GO annotation...

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H3.2
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-866635. hist2h3c.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00002212652 – 136Histone H3.2Add BLAST135

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei3Asymmetric dimethylarginine; by PRMT6By similarity1
Modified residuei4Phosphothreonine; by GSG2By similarity1
Modified residuei5Allysine; alternateBy similarity1
Modified residuei5N6,N6,N6-trimethyllysine; alternate1 Publication1
Modified residuei5N6,N6-dimethyllysine; alternate1 Publication1
Modified residuei5N6-acetyllysine; alternateBy similarity1
Modified residuei5N6-methyllysine; alternate1 Publication1
Modified residuei7Phosphothreonine; by PKCBy similarity1
Modified residuei10N6-methylated lysine1 Publication1
Modified residuei11Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5By similarity1
Modified residuei12Phosphothreonine; by PKCBy similarity1
Modified residuei15N6-acetyllysine1 Publication1
Modified residuei18Asymmetric dimethylarginine1 Publication1
Modified residuei19N6-acetyllysine; alternateBy similarity1
Modified residuei19N6-methylated lysine; alternateBy similarity1
Modified residuei24N6-acetyllysineBy similarity1
Modified residuei28N6-acetyllysine; alternateBy similarity1
Modified residuei28N6-methylated lysine; alternateBy similarity1
Modified residuei29Phosphoserine; by AURKB, AURKC and RPS6KA5By similarity1
Modified residuei37N6-acetyllysine; alternateBy similarity1
Modified residuei37N6-methylated lysine; alternateBy similarity1
Modified residuei42PhosphotyrosineBy similarity1
Modified residuei58PhosphoserineBy similarity1
Modified residuei65N6-methylated lysineBy similarity1
Modified residuei80N6-methylated lysineBy similarity1
Modified residuei81PhosphothreonineBy similarity1
Modified residuei116N6-acetyllysineBy similarity1
Modified residuei123N6-acetyllysine; alternateBy similarity1
Modified residuei123N6-methyllysine; alternateBy similarity1

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
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' (By similarity).By similarity
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

PRIDEiP84233.

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.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
P627992EBI-350041,EBI-302085

Protein-protein interaction databases

BioGridi674575. 4 interactors.
DIPiDIP-37430N.
IntActiP84233. 4 interactors.

Structurei

Secondary structure

1136
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi7 – 10Combined sources4
Beta strandi19 – 21Combined sources3
Beta strandi27 – 29Combined sources3
Beta strandi31 – 34Combined sources4
Helixi46 – 57Combined sources12
Helixi65 – 77Combined sources13
Beta strandi80 – 82Combined sources3
Helixi87 – 114Combined sources28
Beta strandi118 – 120Combined sources3
Helixi122 – 131Combined sources10
Turni132 – 135Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1F66X-ray2.60A/E1-136[»]
1KX3X-ray2.00A/E2-136[»]
1KX4X-ray2.60A/E2-136[»]
1KX5X-ray1.94A/E2-136[»]
1P34X-ray2.70A/E2-136[»]
1P3AX-ray3.00A/E2-136[»]
1P3BX-ray3.00A/E2-136[»]
1P3FX-ray2.90A/E2-136[»]
1P3GX-ray2.70A/E2-136[»]
1P3IX-ray2.30A/E2-136[»]
1P3KX-ray2.90A/E2-136[»]
1P3LX-ray2.40A/E2-136[»]
1P3MX-ray2.90A/E2-136[»]
1P3OX-ray2.75A/E2-136[»]
1P3PX-ray2.70A/E2-136[»]
1S32X-ray2.05A/E2-136[»]
1ZBBX-ray9.00A/E/a/e2-136[»]
1ZLAX-ray2.90A/E2-136[»]
2F8NX-ray2.90A/E1-136[»]
2FJ7X-ray3.20A/E2-136[»]
2HUEX-ray1.70B62-136[»]
2IO5X-ray2.70B2-136[»]
2NZDX-ray2.65A/E2-136[»]
3B6FX-ray3.45A/E2-136[»]
3B6GX-ray3.45A/E2-136[»]
3C1BX-ray2.20A/E2-136[»]
3C1CX-ray3.15A/E2-136[»]
3GV6X-ray1.76B2-16[»]
3KUYX-ray2.90A/E2-136[»]
3KWQX-ray3.50A/E39-136[»]
3KXBX-ray3.20A/E2-136[»]
3LELX-ray2.95A/E/K/O1-136[»]
3LJAX-ray2.75A/E2-136[»]
3LZ0X-ray2.50A/E2-136[»]
3LZ1X-ray2.50A/E2-136[»]
3MGPX-ray2.44A/E2-136[»]
3MGQX-ray2.65A/E2-136[»]
3MGRX-ray2.30A/E2-136[»]
3MGSX-ray3.15A/E2-136[»]
3MNNX-ray2.50A/E2-136[»]
3MVDX-ray2.90A/E2-136[»]
3O62X-ray3.22A/E2-136[»]
3REHX-ray2.50A/E2-136[»]
3REIX-ray2.65A/E2-136[»]
3REJX-ray2.55A/E2-136[»]
3REKX-ray2.60A/E2-136[»]
3RELX-ray2.70A/E2-136[»]
3TU4X-ray3.00A/E2-136[»]
3UT9X-ray2.20A/E2-136[»]
3UTAX-ray2.07A/E2-136[»]
3UTBX-ray2.20A/E2-136[»]
4EO5X-ray2.35B62-136[»]
4J8UX-ray2.38A/E2-136[»]
4J8VX-ray2.58A/E2-136[»]
4J8WX-ray2.41A/E2-136[»]
4J8XX-ray2.87A/E2-136[»]
4KGCX-ray2.69A/E1-136[»]
4LD9X-ray3.31A/E1-136[»]
4R8PX-ray3.28A/E2-136[»]
4WU8X-ray2.45A/E2-136[»]
4WU9X-ray2.60A/E2-136[»]
4XUJX-ray3.18A/E2-136[»]
4XZQX-ray2.40A/E39-136[»]
4YS3X-ray3.00A/E39-136[»]
4Z66X-ray2.50A/E39-136[»]
4ZUXX-ray3.82A/E/K/O1-136[»]
5BS7X-ray3.30A/B26-136[»]
5BSAX-ray4.61A/B27-136[»]
5CP6X-ray2.60A/E2-136[»]
5DNMX-ray2.81A/E2-136[»]
5DNNX-ray2.80A/E2-136[»]
5E5AX-ray2.81A/E1-136[»]
5F99X-ray2.63A/E2-136[»]
5HQ2X-ray4.50A2-136[»]
5KGFelectron microscopy4.54A/E1-136[»]
ProteinModelPortaliP84233.
SMRiP84233.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP84233.

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H3 family.Curated

Phylogenomic databases

HOVERGENiHBG001172.
KOiK11253.

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]
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.

P84233-1 [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
X03104 Genomic DNA. Translation: CAA26890.1.
X03017 Genomic DNA. Translation: CAA26813.1.
X03018 Genomic DNA. Translation: CAA26818.1.
M21286 Genomic DNA. Translation: AAA49765.1.
M21287 Genomic DNA. Translation: AAA49770.1.
BC133776 mRNA. Translation: AAI33777.1.
PIRiA93596. HSXL31.
I51448.
RefSeqiNP_001091428.1. NM_001097959.1.
UniGeneiXl.85517.

Genome annotation databases

GeneIDi100049126.
KEGGixla:100049126.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03104 Genomic DNA. Translation: CAA26890.1.
X03017 Genomic DNA. Translation: CAA26813.1.
X03018 Genomic DNA. Translation: CAA26818.1.
M21286 Genomic DNA. Translation: AAA49765.1.
M21287 Genomic DNA. Translation: AAA49770.1.
BC133776 mRNA. Translation: AAI33777.1.
PIRiA93596. HSXL31.
I51448.
RefSeqiNP_001091428.1. NM_001097959.1.
UniGeneiXl.85517.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1F66X-ray2.60A/E1-136[»]
1KX3X-ray2.00A/E2-136[»]
1KX4X-ray2.60A/E2-136[»]
1KX5X-ray1.94A/E2-136[»]
1P34X-ray2.70A/E2-136[»]
1P3AX-ray3.00A/E2-136[»]
1P3BX-ray3.00A/E2-136[»]
1P3FX-ray2.90A/E2-136[»]
1P3GX-ray2.70A/E2-136[»]
1P3IX-ray2.30A/E2-136[»]
1P3KX-ray2.90A/E2-136[»]
1P3LX-ray2.40A/E2-136[»]
1P3MX-ray2.90A/E2-136[»]
1P3OX-ray2.75A/E2-136[»]
1P3PX-ray2.70A/E2-136[»]
1S32X-ray2.05A/E2-136[»]
1ZBBX-ray9.00A/E/a/e2-136[»]
1ZLAX-ray2.90A/E2-136[»]
2F8NX-ray2.90A/E1-136[»]
2FJ7X-ray3.20A/E2-136[»]
2HUEX-ray1.70B62-136[»]
2IO5X-ray2.70B2-136[»]
2NZDX-ray2.65A/E2-136[»]
3B6FX-ray3.45A/E2-136[»]
3B6GX-ray3.45A/E2-136[»]
3C1BX-ray2.20A/E2-136[»]
3C1CX-ray3.15A/E2-136[»]
3GV6X-ray1.76B2-16[»]
3KUYX-ray2.90A/E2-136[»]
3KWQX-ray3.50A/E39-136[»]
3KXBX-ray3.20A/E2-136[»]
3LELX-ray2.95A/E/K/O1-136[»]
3LJAX-ray2.75A/E2-136[»]
3LZ0X-ray2.50A/E2-136[»]
3LZ1X-ray2.50A/E2-136[»]
3MGPX-ray2.44A/E2-136[»]
3MGQX-ray2.65A/E2-136[»]
3MGRX-ray2.30A/E2-136[»]
3MGSX-ray3.15A/E2-136[»]
3MNNX-ray2.50A/E2-136[»]
3MVDX-ray2.90A/E2-136[»]
3O62X-ray3.22A/E2-136[»]
3REHX-ray2.50A/E2-136[»]
3REIX-ray2.65A/E2-136[»]
3REJX-ray2.55A/E2-136[»]
3REKX-ray2.60A/E2-136[»]
3RELX-ray2.70A/E2-136[»]
3TU4X-ray3.00A/E2-136[»]
3UT9X-ray2.20A/E2-136[»]
3UTAX-ray2.07A/E2-136[»]
3UTBX-ray2.20A/E2-136[»]
4EO5X-ray2.35B62-136[»]
4J8UX-ray2.38A/E2-136[»]
4J8VX-ray2.58A/E2-136[»]
4J8WX-ray2.41A/E2-136[»]
4J8XX-ray2.87A/E2-136[»]
4KGCX-ray2.69A/E1-136[»]
4LD9X-ray3.31A/E1-136[»]
4R8PX-ray3.28A/E2-136[»]
4WU8X-ray2.45A/E2-136[»]
4WU9X-ray2.60A/E2-136[»]
4XUJX-ray3.18A/E2-136[»]
4XZQX-ray2.40A/E39-136[»]
4YS3X-ray3.00A/E39-136[»]
4Z66X-ray2.50A/E39-136[»]
4ZUXX-ray3.82A/E/K/O1-136[»]
5BS7X-ray3.30A/B26-136[»]
5BSAX-ray4.61A/B27-136[»]
5CP6X-ray2.60A/E2-136[»]
5DNMX-ray2.81A/E2-136[»]
5DNNX-ray2.80A/E2-136[»]
5E5AX-ray2.81A/E1-136[»]
5F99X-ray2.63A/E2-136[»]
5HQ2X-ray4.50A2-136[»]
5KGFelectron microscopy4.54A/E1-136[»]
ProteinModelPortaliP84233.
SMRiP84233.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi674575. 4 interactors.
DIPiDIP-37430N.
IntActiP84233. 4 interactors.

Proteomic databases

PRIDEiP84233.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi100049126.
KEGGixla:100049126.

Organism-specific databases

CTDi126961.
XenbaseiXB-GENE-866635. hist2h3c.

Phylogenomic databases

HOVERGENiHBG001172.
KOiK11253.

Miscellaneous databases

EvolutionaryTraceiP84233.

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]
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...

Entry informationi

Entry nameiH32_XENLA
AccessioniPrimary (citable) accession number: P84233
Secondary accession number(s): A4FVE2
, P02295, P02297, P16105, P17269, P17320
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 100 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

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.