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P02302

- H3C_XENLA

UniProt

P02302 - H3C_XENLA

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Protein
Histone H3.3C
Gene
h3f3c
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

GO - Biological processi

  1. nucleosome assembly Source: InterPro
Complete GO annotation...

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H3.3C
Gene namesi
Name:h3f3c
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Subcellular locationi

GO - Cellular componenti

  1. nucleosome Source: UniProtKB-KW
  2. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed By similarity
Chaini2 – 136135Histone H3.3C
PRO_0000221266Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei3 – 31Asymmetric dimethylarginine; by PRMT6 By similarity
Modified residuei4 – 41Phosphothreonine; by GSG2 By similarity
Modified residuei5 – 51Allysine; alternate By similarity
Modified residuei5 – 51N6,N6,N6-trimethyllysine; alternate By similarity
Modified residuei5 – 51N6,N6-dimethyllysine; alternate By similarity
Modified residuei5 – 51N6-acetyllysine; alternate By similarity
Modified residuei5 – 51N6-methyllysine; alternate By similarity
Modified residuei7 – 71Phosphothreonine; by PKC By similarity
Modified residuei10 – 101N6-methylated lysine By similarity
Modified residuei11 – 111Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 By similarity
Modified residuei12 – 121Phosphothreonine; by PKC By similarity
Modified residuei15 – 151N6-acetyllysine By similarity
Modified residuei18 – 181Asymmetric dimethylarginine By similarity
Modified residuei19 – 191N6-acetyllysine; alternate By similarity
Modified residuei19 – 191N6-methylated lysine; alternate By similarity
Modified residuei24 – 241N6-acetyllysine By similarity
Modified residuei28 – 281N6-acetyllysine; alternate By similarity
Modified residuei28 – 281N6-methylated lysine; alternate By similarity
Modified residuei37 – 371N6-acetyllysine; alternate By similarity
Modified residuei37 – 371N6-methylated lysine; alternate By similarity
Modified residuei42 – 421Phosphotyrosine By similarity
Modified residuei58 – 581Phosphoserine By similarity
Modified residuei65 – 651N6-methylated lysine By similarity
Modified residuei80 – 801N6-methylated lysine By similarity
Modified residuei81 – 811Phosphothreonine By similarity
Modified residuei116 – 1161N6-acetyllysine By similarity
Modified residuei123 – 1231N6-acetyllysine; alternate By similarity
Modified residuei123 – 1231N6-methylated lysine; alternate By 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.
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.
Methylation at Lys-5 (H3K4me) 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.
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. 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.
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

Proteomic databases

PRIDEiP02302.

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.2 Publications

Protein-protein interaction databases

DIPiDIP-39145N.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi46 – 5510
Helixi65 – 7713
Beta strandi80 – 823
Helixi87 – 11428
Beta strandi118 – 1203
Helixi122 – 13211

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AOIX-ray2.80A/E21-136[»]
1M18X-ray2.45A/E2-136[»]
1M19X-ray2.30A/E2-136[»]
1M1AX-ray2.65A/E2-136[»]
ProteinModelPortaliP02302.
SMRiP02302. Positions 2-136.

Miscellaneous databases

EvolutionaryTraceiP02302.

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H3 family.

Phylogenomic databases

HOVERGENiHBG001172.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3.
[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.

P02302-1 [UniParc]FASTAAdd to Basket

« Hide

MARTKQTARK STGGKAPRKQ LVTKAAKKCA PATGGVKKPH RYRPGTVALR    50
EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQRSAV MALQEASEAY 100
LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA 136
Length:136
Mass (Da):15,487
Last modified:January 23, 2007 - v2
Checksum:iFE1B7E45DBBC7D95
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J00982 Genomic DNA. No translation available.
J00984 Genomic DNA. No translation available.
PIRiA02634. HSXL32.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J00982 Genomic DNA. No translation available.
J00984 Genomic DNA. No translation available.
PIRi A02634. HSXL32.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1AOI X-ray 2.80 A/E 21-136 [» ]
1M18 X-ray 2.45 A/E 2-136 [» ]
1M19 X-ray 2.30 A/E 2-136 [» ]
1M1A X-ray 2.65 A/E 2-136 [» ]
ProteinModelPortali P02302.
SMRi P02302. Positions 2-136.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-39145N.

Proteomic databases

PRIDEi P02302.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Phylogenomic databases

HOVERGENi HBG001172.

Miscellaneous databases

EvolutionaryTracei P02302.

Family and domain databases

Gene3Di 1.10.20.10. 1 hit.
InterProi IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3.
[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

  1. "Primary structure of the histone H3 and H4 genes and their flanking sequences in a minor histone gene cluster of Xenopus laevis."
    Moorman A.F.M., de Boer P.A.J., de Laaf R.T.M., van Dongen W.M.A.M., Destree O.H.J.
    FEBS Lett. 136:45-52(1981) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (GENE CLUSTER X1H1).
  2. "Crystal structure of the nucleosome core particle at 2.8 A resolution."
    Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J.
    Nature 389:251-260(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF NUCLEOSOME CORE COMPLEX, SUBUNIT.
  3. "Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands."
    Suto R.K., Edayathumangalam R.S., White C.L., Melander C., Gottesfeld J.M., Dervan P.B., Luger K.
    J. Mol. Biol. 326:371-380(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF NUCLEOSOME CORE COMPLEX, SUBUNIT.

Entry informationi

Entry nameiH3C_XENLA
AccessioniPrimary (citable) accession number: P02302
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: May 14, 2014
This is version 98 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

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