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P62799 (H4_XENLA) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 98. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Histone H4
OrganismXenopus laevis (African clawed frog)
Taxonomic identifier8355 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Protein attributes

Sequence length103 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Subunit structure

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.

Subcellular location

Nucleus. Chromosome.

Post-translational modification

Acetylation at Lys-6 (H4K5ac), Lys-9 (H4K8ac), Lys-13 (H4K12ac) and Lys-17 (H4K16ac) occurs in coding regions of the genome but not in heterochromatin By similarity.

Citrullination at Arg-4 (H4R3ci) by PADI4 impairs methylation By similarity.

Monomethylation and asymmetric dimethylation at Arg-4 (H4R3me1 and H4R3me2a, respectively) by PRMT1 favors acetylation at Lys-9 (H4K8ac) and Lys-13 (H4K12ac). Demethylation is performed by JMJD6. Symmetric dimethylation on Arg-4 (H4R3me2s) by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage By similarity.

Monomethylated, dimethylated or trimethylated at Lys-21 (H4K20me1, H4K20me2, H4K20me3). Monomethylation is performed by SET8. Trimethylation is performed by SUV420H1 and SUV420H2 and induces gene silencing By similarity.

Phosphorylated by pak2 at Ser-48 (H4S47ph). This phosphorylation increases the association of H3.3-H4 with the histone chaperone HIRA, thus promoting nucleosome assembly of H3.3-H4 and inhibiting nucleosome assembly of H3.1-H4 By similarity.

Ubiquitinated by the CUL4-DDB-RBX1 complex in response to ultraviolet irradiation. This may weaken the interaction between histones and DNA and facilitate DNA accessibility to repair proteins. Monoubiquitinated at Lys-92 of histone H4 (H4K91ub1) in response to DNA damage. The exact role of H4K91ub1 in DNA damage response is still unclear but it may function as a licensing signal for additional histone H4 post-translational modifications such as H4 Lys-21 methylation (H4K20me) By similarity.

Sumoylated, which is associated with transcriptional repression By similarity.

Sequence similarities

Belongs to the histone H4 family.

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

P842332EBI-302085,EBI-350041

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 103102Histone H4
PRO_0000158376

Regions

DNA binding17 – 215

Amino acid modifications

Modified residue21N-acetylserine By similarity
Modified residue21Phosphoserine By similarity
Modified residue41Asymmetric dimethylarginine; by PRMT1; alternate By similarity
Modified residue41Citrulline; alternate By similarity
Modified residue41Omega-N-methylarginine; by PRMT1; alternate By similarity
Modified residue41Symmetric dimethylarginine; by PRMT5 and PRMT7; alternate By similarity
Modified residue61N6-acetyllysine By similarity
Modified residue91N6-acetyllysine By similarity
Modified residue131N6-acetyllysine By similarity
Modified residue171N6-acetyllysine By similarity
Modified residue211N6,N6,N6-trimethyllysine; alternate By similarity
Modified residue211N6,N6-dimethyllysine; alternate By similarity
Modified residue211N6-methylated lysine By similarity
Modified residue211N6-methyllysine; alternate By similarity
Modified residue321N6-acetyllysine By similarity
Modified residue481Phosphoserine; by PAK2 By similarity
Modified residue521Phosphotyrosine By similarity
Modified residue601N6-acetyllysine By similarity
Modified residue801N6-acetyllysine By similarity
Modified residue891Phosphotyrosine By similarity
Modified residue921N6-acetyllysine; alternate By similarity
Cross-link92Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate By similarity

Secondary structure

................... 103
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P62799 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: A9E5DFD3F8B97598

FASTA10311,367
        10         20         30         40         50         60 
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK 

        70         80         90        100 
VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG 

« Hide

References

« Hide 'large scale' references
[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].
[2]"Transcription of a cloned Xenopus laevis H4 histone gene in the homologous frog oocyte system depends on an evolutionary conserved sequence motif in the -50 region."
Clerc R.G., Bucher P., Strub K., Birnstiel M.L.
Nucleic Acids Res. 11:8641-8657(1983) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"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].
[4]NIH - Xenopus Gene Collection (XGC) project
Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Embryo.
[5]"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 17-103.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X00224 Genomic DNA. Translation: CAA25042.1.
X03017 Genomic DNA. Translation: CAA26809.1.
X03017 Genomic DNA. Translation: CAA26814.1.
X03018 Genomic DNA. Translation: CAA26819.1.
M21286 Genomic DNA. Translation: AAA49761.1.
M21286 Genomic DNA. Translation: AAA49766.1.
M21287 Genomic DNA. Translation: AAA49771.1.
BC078038 mRNA. Translation: AAH78038.1.
PIRHSXL4. A02641.
RefSeqNP_001087926.1. NM_001094457.1.
UniGeneXl.85592.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1AOIX-ray2.80B/F17-103[»]
1KX3X-ray2.00B/F2-103[»]
1KX4X-ray2.60B/F2-103[»]
1KX5X-ray1.94B/F2-103[»]
1M18X-ray2.45B/F2-103[»]
1M19X-ray2.30B/F2-103[»]
1M1AX-ray2.65B/F2-103[»]
1P34X-ray2.70B/F2-103[»]
1P3AX-ray3.00B/F2-103[»]
1P3BX-ray3.00B/F2-103[»]
1P3FX-ray2.90B/F2-103[»]
1P3GX-ray2.70B/F2-103[»]
1P3IX-ray2.30B/F2-103[»]
1P3KX-ray2.90B/F2-103[»]
1P3LX-ray2.40B/F2-103[»]
1P3MX-ray2.90B/F2-103[»]
1P3OX-ray2.75B/F2-103[»]
1P3PX-ray2.70B/F2-103[»]
1S32X-ray2.05B/F2-103[»]
1ZBBX-ray9.00B/F/b/f2-103[»]
1ZLAX-ray2.90B/F2-103[»]
2F8NX-ray2.90B/F1-103[»]
2FJ7X-ray3.20B/F2-103[»]
2HUEX-ray1.70C21-103[»]
2IO5X-ray2.70C2-103[»]
2NZDX-ray2.65B/F2-103[»]
3B6FX-ray3.45B/F2-103[»]
3B6GX-ray3.45B/F2-103[»]
3C1BX-ray2.20B/F2-103[»]
3C1CX-ray3.15B/F2-103[»]
3KUYX-ray2.90B/F2-103[»]
3KWQX-ray3.50B/F21-103[»]
3KXBX-ray3.20B/F2-103[»]
3LELX-ray2.95B/F/L/P2-103[»]
3LJAX-ray2.75B/F2-103[»]
3LZ0X-ray2.50B/F2-103[»]
3LZ1X-ray2.50B/F2-103[»]
3MGPX-ray2.44B/F2-103[»]
3MGQX-ray2.65B/F2-103[»]
3MGRX-ray2.30B/F2-103[»]
3MGSX-ray3.15B/F2-103[»]
3MNNX-ray2.50B/F2-103[»]
3MVDX-ray2.90B/F2-103[»]
3O62X-ray3.22B/F2-103[»]
3REHX-ray2.50B/F2-103[»]
3REIX-ray2.65B/F2-103[»]
3REJX-ray2.55B/F2-103[»]
3REKX-ray2.60B/F2-103[»]
3RELX-ray2.70B/F2-103[»]
3TU4X-ray3.00B/F2-103[»]
3UT9X-ray2.20B/F2-103[»]
3UTAX-ray2.07B/F2-103[»]
3UTBX-ray2.20B/F2-103[»]
4EO5X-ray2.35C21-103[»]
4J8UX-ray2.38B/F2-103[»]
4J8VX-ray2.58B/F2-103[»]
4J8WX-ray2.41B/F2-103[»]
4J8XX-ray2.87B/F2-103[»]
4KGCX-ray2.69B/F1-103[»]
4LD9X-ray3.31B/F1-103[»]
ProteinModelPortalP62799.
SMRP62799. Positions 21-102.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid104647. 12 interactions.
DIPDIP-37429N.
IntActP62799. 4 interactions.

Proteomic databases

PRIDEP62799.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID447787.
KEGGxla:447787.

Organism-specific databases

CTD8359.
XenbaseXB-GENE-6493984. hist1h4a.

Phylogenomic databases

HOVERGENHBG051878.
KOK11254.

Family and domain databases

Gene3D1.10.20.10. 1 hit.
InterProIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR001951. Histone_H4.
IPR019809. Histone_H4_CS.
[Graphical view]
PfamPF00125. Histone. 1 hit.
[Graphical view]
PRINTSPR00623. HISTONEH4.
SMARTSM00417. H4. 1 hit.
[Graphical view]
SUPFAMSSF47113. SSF47113. 1 hit.
PROSITEPS00047. HISTONE_H4. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP62799.

Entry information

Entry nameH4_XENLA
AccessionPrimary (citable) accession number: P62799
Secondary accession number(s): P02304, P02305, Q6AZG5
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 98 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references