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P84233

- H32_XENLA

UniProt

P84233 - H32_XENLA

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Protein

Histone H3.2

Gene
N/A
Organism
Xenopus laevis (African clawed frog)
Status
Reviewed - 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

  1. DNA binding Source: UniProtKB-KW
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

  1. nucleoplasm Source: Reactome
  2. nucleosome Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 136135Histone H3.2PRO_0000221265Add
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-methyllysine; alternate1 Publication
Modified residuei7 – 71Phosphothreonine; by PKCBy similarity
Modified residuei10 – 101N6-methylated lysine1 Publication
Modified residuei11 – 111Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5By similarity
Modified residuei12 – 121Phosphothreonine; by PKCBy similarity
Modified residuei15 – 151N6-acetyllysine1 Publication
Modified residuei18 – 181Asymmetric dimethylarginine1 Publication
Modified residuei19 – 191N6-acetyllysine; alternateBy similarity
Modified residuei19 – 191N6-methylated lysine; alternateBy similarity
Modified residuei24 – 241N6-acetyllysineBy similarity
Modified residuei28 – 281N6-acetyllysine; alternateBy similarity
Modified residuei28 – 281N6-methylated lysine; alternateBy similarity
Modified residuei29 – 291Phosphoserine; by AURKB, AURKC and RPS6KA5By similarity
Modified residuei37 – 371N6-acetyllysine; alternateBy similarity
Modified residuei37 – 371N6-methylated lysine; alternateBy similarity
Modified residuei42 – 421PhosphotyrosineBy similarity
Modified residuei58 – 581PhosphoserineBy similarity
Modified residuei65 – 651N6-methylated lysineBy similarity
Modified residuei80 – 801N6-methylated lysineBy similarity
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
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. 2 interactions.
DIPiDIP-37430N.
IntActiP84233. 4 interactions.

Structurei

Secondary structure

1
136
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi7 – 104
Beta strandi19 – 213
Beta strandi27 – 293
Beta strandi31 – 344
Helixi46 – 5712
Helixi65 – 7713
Beta strandi80 – 823
Helixi87 – 11428
Beta strandi118 – 1203
Helixi122 – 13110
Turni132 – 1354

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliP84233.
SMRiP84233. Positions 17-136.
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_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.

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:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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 .
PIRi A93596. HSXL31.
I51448.
RefSeqi NP_001091428.1. NM_001097959.1.
UniGenei Xl.85517.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1F66 X-ray 2.60 A/E 1-136 [» ]
1KX3 X-ray 2.00 A/E 2-136 [» ]
1KX4 X-ray 2.60 A/E 2-136 [» ]
1KX5 X-ray 1.94 A/E 2-136 [» ]
1P34 X-ray 2.70 A/E 2-136 [» ]
1P3A X-ray 3.00 A/E 2-136 [» ]
1P3B X-ray 3.00 A/E 2-136 [» ]
1P3F X-ray 2.90 A/E 2-136 [» ]
1P3G X-ray 2.70 A/E 2-136 [» ]
1P3I X-ray 2.30 A/E 2-136 [» ]
1P3K X-ray 2.90 A/E 2-136 [» ]
1P3L X-ray 2.40 A/E 2-136 [» ]
1P3M X-ray 2.90 A/E 2-136 [» ]
1P3O X-ray 2.75 A/E 2-136 [» ]
1P3P X-ray 2.70 A/E 2-136 [» ]
1S32 X-ray 2.05 A/E 2-136 [» ]
1ZBB X-ray 9.00 A/E/a/e 2-136 [» ]
1ZLA X-ray 2.90 A/E 2-136 [» ]
2F8N X-ray 2.90 A/E 1-136 [» ]
2FJ7 X-ray 3.20 A/E 2-136 [» ]
2HUE X-ray 1.70 B 62-136 [» ]
2IO5 X-ray 2.70 B 2-136 [» ]
2NZD X-ray 2.65 A/E 2-136 [» ]
3B6F X-ray 3.45 A/E 2-136 [» ]
3B6G X-ray 3.45 A/E 2-136 [» ]
3C1B X-ray 2.20 A/E 2-136 [» ]
3C1C X-ray 3.15 A/E 2-136 [» ]
3GV6 X-ray 1.76 B 2-16 [» ]
3KUY X-ray 2.90 A/E 2-136 [» ]
3KWQ X-ray 3.50 A/E 39-136 [» ]
3KXB X-ray 3.20 A/E 2-136 [» ]
3LEL X-ray 2.95 A/E/K/O 1-136 [» ]
3LJA X-ray 2.75 A/E 2-136 [» ]
3LZ0 X-ray 2.50 A/E 2-136 [» ]
3LZ1 X-ray 2.50 A/E 2-136 [» ]
3MGP X-ray 2.44 A/E 2-136 [» ]
3MGQ X-ray 2.65 A/E 2-136 [» ]
3MGR X-ray 2.30 A/E 2-136 [» ]
3MGS X-ray 3.15 A/E 2-136 [» ]
3MNN X-ray 2.50 A/E 2-136 [» ]
3MVD X-ray 2.90 A/E 2-136 [» ]
3O62 X-ray 3.22 A/E 2-136 [» ]
3REH X-ray 2.50 A/E 2-136 [» ]
3REI X-ray 2.65 A/E 2-136 [» ]
3REJ X-ray 2.55 A/E 2-136 [» ]
3REK X-ray 2.60 A/E 2-136 [» ]
3REL X-ray 2.70 A/E 2-136 [» ]
3TU4 X-ray 3.00 A/E 2-136 [» ]
3UT9 X-ray 2.20 A/E 2-136 [» ]
3UTA X-ray 2.07 A/E 2-136 [» ]
3UTB X-ray 2.20 A/E 2-136 [» ]
4EO5 X-ray 2.35 B 62-136 [» ]
4J8U X-ray 2.38 A/E 2-136 [» ]
4J8V X-ray 2.58 A/E 2-136 [» ]
4J8W X-ray 2.41 A/E 2-136 [» ]
4J8X X-ray 2.87 A/E 2-136 [» ]
4KGC X-ray 2.69 A/E 1-136 [» ]
4LD9 X-ray 3.31 A/E 1-136 [» ]
ProteinModelPortali P84233.
SMRi P84233. Positions 17-136.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 674575. 2 interactions.
DIPi DIP-37430N.
IntActi P84233. 4 interactions.

Proteomic databases

PRIDEi P84233.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 100049126.
KEGGi xla:100049126.

Organism-specific databases

CTDi 126961.
Xenbasei XB-GENE-866635. hist2h3c.

Phylogenomic databases

HOVERGENi HBG001172.
KOi K11253.

Miscellaneous databases

EvolutionaryTracei P84233.

Family and domain databases

Gene3Di 1.10.20.10. 1 hit.
InterProi IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3/CENP-A.
[Graphical view ]
PANTHERi PTHR11426. PTHR11426. 1 hit.
Pfami PF00125. Histone. 1 hit.
[Graphical view ]
PRINTSi PR00622. HISTONEH3.
SMARTi SM00428. H3. 1 hit.
[Graphical view ]
SUPFAMi SSF47113. SSF47113. 1 hit.
PROSITEi PS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Individual Xenopus histone genes are replication-independent in oocytes and replication-dependent in Xenopus or mouse somatic cells."
    Old R.W., Sheikh S.A., Chambers A., Newton C.A., Mohammed A., Aldridge T.C.
    Nucleic Acids Res. 13:7341-7358(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Genomic organization and nucleotide sequence of two distinct histone gene clusters from Xenopus laevis. Identification of novel conserved upstream sequence elements."
    Perry M., Thomsen G.H., Roeder R.G.
    J. Mol. Biol. 185:479-499(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (GENE CLUSTERS X1H1 AND X1H3).
  3. NIH - Xenopus Gene Collection (XGC) project
    Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Embryo.
  4. "Involvement of histone methylation and phosphorylation in regulation of transcription by thyroid hormone receptor."
    Li J., Lin Q., Yoon H.-G., Huang Z.-Q., Strahl B.D., Allis C.D., Wong J.
    Mol. Cell. Biol. 22:5688-5697(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: METHYLATION AT LYS-5; LYS-10 AND ARG-18, PHOSPHORYLATION AT SER-11, ACETYLATION AT LYS-15.
  5. "Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 A resolution."
    Davey C.A., Sargent D.F., Luger K., Maeder A.W., Richmond T.J.
    J. Mol. Biol. 319:1097-1113(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH H2A; H2B AND H4.

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: October 29, 2014
This is version 86 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

External Data

Dasty 3