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Q6PI79

- H33_XENLA

UniProt

Q6PI79 - H33_XENLA

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Protein

Histone H3.3

Gene
N/A
Organism
Xenopus laevis (African clawed frog)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli

Functioni

Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes. Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes, suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. 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 – 321Interaction with zmynd11By similarity

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
Complete GO annotation...

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H3.3
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-488762. h3f3b.

Subcellular locationi

GO - Cellular componenti

  1. nucleosome Source: UniProtKB-KW
  2. nucleus 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 H3.3PRO_0000253957Add
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.1 Publication
Asymmetric dimethylation at Arg-18 (H3R17me2a) is linked to gene activation. 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 similarity
Specifically enriched in modifications associated with active chromatin such as 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. Phosphorylation on Ser-32 (H3S31ph) is specific to regions bordering centromeres in metaphase chromosomes (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

PRIDEiQ6PI79.

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 zmynd11; when trimethylated at 'Lys-36' (H3.3K36me3).

Structurei

3D structure databases

ProteinModelPortaliQ6PI79.
SMRiQ6PI79. Positions 17-136.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

Specific interaction of trimethylated form at 'Lys-36' (H3.3K36me3) with zmynd11 is mediated by the encapsulation of Ser-32 residue with a composite pocket formed by the tandem bromo-PWWP domains.By similarity

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.

Q6PI79-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR
60 70 80 90 100
EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAAI GALQEASEAY
110 120 130
LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA
Length:136
Mass (Da):15,328
Last modified:January 23, 2007 - v3
Checksum:i5158ED279E6F9E1C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC041218 mRNA. Translation: AAH41218.1.
BC042290 mRNA. Translation: AAH42290.1.
BC042309 mRNA. Translation: AAH42309.1.
BC070966 mRNA. Translation: AAH70966.1.
BC074158 mRNA. Translation: AAH74158.1.
BC106302 mRNA. Translation: AAI06303.1.
BC123120 mRNA. Translation: AAI23121.1.
RefSeqiNP_001079375.1. NM_001085906.1.
NP_001080065.1. NM_001086596.1.
NP_001085048.1. NM_001091579.1.
NP_001086074.1. NM_001092605.1.
NP_001091902.1. NM_001098432.1.
UniGeneiXl.36404.
Xl.39769.
Xl.4043.
Xl.77438.
Xl.86817.

Genome annotation databases

GeneIDi379062.
379757.
399418.
432115.
444503.
KEGGixla:379062.
xla:379757.
xla:399418.
xla:432115.
xla:444503.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC041218 mRNA. Translation: AAH41218.1 .
BC042290 mRNA. Translation: AAH42290.1 .
BC042309 mRNA. Translation: AAH42309.1 .
BC070966 mRNA. Translation: AAH70966.1 .
BC074158 mRNA. Translation: AAH74158.1 .
BC106302 mRNA. Translation: AAI06303.1 .
BC123120 mRNA. Translation: AAI23121.1 .
RefSeqi NP_001079375.1. NM_001085906.1.
NP_001080065.1. NM_001086596.1.
NP_001085048.1. NM_001091579.1.
NP_001086074.1. NM_001092605.1.
NP_001091902.1. NM_001098432.1.
UniGenei Xl.36404.
Xl.39769.
Xl.4043.
Xl.77438.
Xl.86817.

3D structure databases

ProteinModelPortali Q6PI79.
SMRi Q6PI79. Positions 17-136.
ModBasei Search...
MobiDBi Search...

Proteomic databases

PRIDEi Q6PI79.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 379062.
379757.
399418.
432115.
444503.
KEGGi xla:379062.
xla:379757.
xla:399418.
xla:432115.
xla:444503.

Organism-specific databases

CTDi 3020.
3021.
653604.
Xenbasei XB-GENE-488762. h3f3b.

Phylogenomic databases

HOVERGENi HBG001172.
KOi K11253.

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. NIH - Xenopus Gene Collection (XGC) project
    Submitted (SEP-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Embryo.
  2. "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.

Entry informationi

Entry nameiH33_XENLA
AccessioniPrimary (citable) accession number: Q6PI79
Secondary accession number(s): Q05AX9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 17, 2006
Last sequence update: January 23, 2007
Last modified: October 29, 2014
This is version 80 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3