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Protein

Histone H4

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

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi17 – 215

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H4
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-6493984 hist1h4a

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00001583762 – 103Histone H4Add BLAST102

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineBy similarity1
Modified residuei2PhosphoserineBy similarity1
Modified residuei4Asymmetric dimethylarginine; by PRMT1; alternateBy similarity1
Modified residuei4Citrulline; alternateBy similarity1
Modified residuei4Omega-N-methylarginine; by PRMT1; alternateBy similarity1
Modified residuei4Symmetric dimethylarginine; by PRMT5 and PRMT7; alternateBy similarity1
Modified residuei6N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei6N6-acetyllysineBy similarity1
Modified residuei6N6-butyryllysine; alternateBy similarity1
Modified residuei9N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei9N6-acetyllysineBy similarity1
Modified residuei9N6-butyryllysine; alternateBy similarity1
Modified residuei9N6-propionyllysine; alternateBy similarity1
Modified residuei13N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei13N6-acetyllysineBy similarity1
Modified residuei13N6-butyryllysine; alternateBy similarity1
Modified residuei17N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei17N6-acetyllysineBy similarity1
Modified residuei17N6-butyryllysine; alternateBy similarity1
Modified residuei17N6-propionyllysine; alternateBy similarity1
Modified residuei21N6,N6,N6-trimethyllysine; alternateBy similarity1
Modified residuei21N6,N6-dimethyllysine; alternateBy similarity1
Modified residuei21N6-methylated lysineBy similarity1
Modified residuei21N6-methyllysine; alternateBy similarity1
Modified residuei32N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei32N6-acetyllysineBy similarity1
Modified residuei32N6-butyryllysine; alternateBy similarity1
Modified residuei32N6-propionyllysine; alternateBy similarity1
Modified residuei32N6-succinyllysine; alternateBy similarity1
Modified residuei45N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei45N6-butyryllysine; alternateBy similarity1
Modified residuei45N6-propionyllysine; alternateBy similarity1
Modified residuei48Phosphoserine; by PAK2By similarity1
Modified residuei52PhosphotyrosineBy similarity1
Modified residuei60N6-(2-hydroxyisobutyryl)lysineBy similarity1
Modified residuei60N6-acetyllysineBy similarity1
Modified residuei78N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei78N6-butyryllysine; alternateBy similarity1
Modified residuei78N6-propionyllysine; alternateBy similarity1
Modified residuei78N6-succinyllysineBy similarity1
Modified residuei80N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei80N6-acetyllysineBy similarity1
Modified residuei80N6-butyryllysine; alternateBy similarity1
Modified residuei80N6-propionyllysine; alternateBy similarity1
Modified residuei89PhosphotyrosineBy similarity1
Modified residuei92N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei92N6-acetyllysine; alternateBy similarity1
Modified residuei92N6-butyryllysine; alternateBy similarity1
Modified residuei92N6-propionyllysine; alternateBy similarity1
Modified residuei92N6-succinyllysine; alternateBy similarity1
Cross-linki92Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternateBy similarity

Post-translational modificationi

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).By similarity
Monomethylated, dimethylated or trimethylated at Lys-21 (H4K20me1, H4K20me2, H4K20me3). Monomethylation is performed by SET8. Trimethylation is performed by KMT5B and KMT5C and induces gene silencing (By similarity).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).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).By similarity
Sumoylated, which is associated with transcriptional repression.By similarity
Butyrylation of histones marks active promoters and competes with histone acetylation.By similarity

Keywords - PTMi

Acetylation, Citrullination, Hydroxylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

PRIDEiP62799

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.

Binary interactionsi

Show more details

GO - Molecular functioni

Protein-protein interaction databases

BioGridi104647, 12 interactors
DIPiDIP-37429N
IntActiP62799, 9 interactors

Structurei

Secondary structure

1103
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 12Combined sources7
Beta strandi13 – 17Combined sources5
Helixi23 – 26Combined sources4
Helixi27 – 29Combined sources3
Helixi32 – 41Combined sources10
Beta strandi45 – 47Combined sources3
Helixi51 – 76Combined sources26
Beta strandi80 – 82Combined sources3
Helixi84 – 90Combined sources7
Turni91 – 94Combined sources4
Beta strandi96 – 100Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
4R8PX-ray3.28B/F2-103[»]
4WU8X-ray2.45B/F2-103[»]
4WU9X-ray2.60B/F2-103[»]
4XUJX-ray3.18B/F2-103[»]
4XZQX-ray2.40B/F25-103[»]
4YS3X-ray3.00B/F25-103[»]
4Z66X-ray2.50B/F22-103[»]
4ZBJX-ray2.25C21-103[»]
4ZUXX-ray3.82B/F/L/P1-103[»]
5BS7X-ray3.30C/D2-103[»]
5BSAX-ray4.61C/D2-103[»]
5CP6X-ray2.60B/F2-103[»]
5DNMX-ray2.81B/F2-103[»]
5DNNX-ray2.80B/F2-103[»]
5E5AX-ray2.81B/F1-103[»]
5F99X-ray2.63B/F1-103[»]
5HQ2X-ray4.50B2-103[»]
5KGFelectron microscopy4.54B/F1-103[»]
5MLUX-ray2.80B/F20-103[»]
5NL0X-ray5.40B/F/L2-103[»]
5O9Gelectron microscopy4.80B/F1-103[»]
5OMXX-ray2.32B/F1-103[»]
5ONGX-ray2.80B/F1-103[»]
5ONWX-ray2.80B/F1-103[»]
5OXVX-ray6.72B/F/L/P2-103[»]
5OY7X-ray5.77B/F/J/N/R/V/Z/d2-103[»]
5X0Xelectron microscopy3.97B/F1-103[»]
5X0Yelectron microscopy3.97B/F2-103[»]
5XF6X-ray2.63B/F2-103[»]
6ESFelectron microscopy3.70B/F2-103[»]
6ESGelectron microscopy5.40B/F2-103[»]
6ESHelectron microscopy5.10B/F2-103[»]
6ESIelectron microscopy6.30B/F2-103[»]
ProteinModelPortaliP62799
SMRiP62799
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP62799

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H4 family.Curated

Phylogenomic databases

HOVERGENiHBG051878
KOiK11254

Family and domain databases

CDDicd00076 H4, 1 hit
Gene3Di1.10.20.10, 1 hit
InterProiView protein in InterPro
IPR035425 CENP-T/H4_C
IPR009072 Histone-fold
IPR001951 Histone_H4
IPR019809 Histone_H4_CS
IPR004823 TAF_TATA-bd
PfamiView protein in Pfam
PF15511 CENP-T_C, 1 hit
PRINTSiPR00623 HISTONEH4
SMARTiView protein in SMART
SM00417 H4, 1 hit
SM00803 TAF, 1 hit
SUPFAMiSSF47113 SSF47113, 1 hit
PROSITEiView protein in PROSITE
PS00047 HISTONE_H4, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P62799-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL
60 70 80 90 100
IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG

FGG
Length:103
Mass (Da):11,367
Last modified:January 23, 2007 - v2
Checksum:iA9E5DFD3F8B97598
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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
PIRiA02641 HSXL4
RefSeqiNP_001087926.1, NM_001094457.1
XP_018095104.1, XM_018239615.1
XP_018095605.1, XM_018240116.1
XP_018095606.1, XM_018240117.1
XP_018096302.1, XM_018240813.1
XP_018097458.1, XM_018241969.1
XP_018098137.1, XM_018242648.1
XP_018118237.1, XM_018262748.1
XP_018120359.1, XM_018264870.1
XP_018120360.1, XM_018264871.1
UniGeneiXl.32880
Xl.85592

Genome annotation databases

GeneIDi108703479
108703798
108703799
108704306
108705162
108705878
108716550
108717647
108717648
447787
KEGGixla:108703479
xla:108703798
xla:108703799
xla:108704306
xla:108705162
xla:108705878
xla:108716550
xla:108717647
xla:108717648
xla:447787

Similar proteinsi

Entry informationi

Entry nameiH4_XENLA
AccessioniPrimary (citable) accession number: P62799
Secondary accession number(s): P02304, P02305, Q6AZG5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: March 28, 2018
This is version 128 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

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