P62799 (H4_XENLA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Histone H4
Organism	Xenopus laevis (African clawed frog)
Taxonomic identifier	8355 [NCBI]
Taxonomic lineage	cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amphibia › Batrachia › Anura › Pipoidea › Pipidae › Xenopodinae › Xenopus › Xenopus

Protein attributes

Sequence length	103 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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

Keywords
Cellular component	Chromosome Nucleosome core Nucleus
Ligand	DNA-binding
PTM	Acetylation Citrullination Isopeptide bond Methylation Phosphoprotein Ubl conjugation
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	nucleosome assembly Inferred from electronic annotation. Source: InterPro
Cellular_component	nucleosome Inferred from electronic annotation. Source: UniProtKB-KW nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
	P84233	2	EBI-302085,EBI-350041

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed By similarity

Chain

2 – 103

102

Histone H4

PRO_0000158376

Regions

DNA binding

17 – 21

5

Amino acid modifications

Modified residue

2

1

N-acetylserine By similarity

Modified residue

2

1

Phosphoserine By similarity

Modified residue

4

1

Asymmetric dimethylarginine; by PRMT1; alternate By similarity

Modified residue

4

1

Citrulline; alternate By similarity

Modified residue

4

1

Omega-N-methylarginine; by PRMT1; alternate By similarity

Modified residue

4

1

Symmetric dimethylarginine; by PRMT5 and PRMT7; alternate By similarity

Modified residue

6

1

N6-acetyllysine By similarity

Modified residue

9

1

N6-acetyllysine By similarity

Modified residue

13

1

N6-acetyllysine By similarity

Modified residue

17

1

N6-acetyllysine By similarity

Modified residue

21

1

N6,N6,N6-trimethyllysine; alternate By similarity

Modified residue

21

1

N6,N6-dimethyllysine; alternate By similarity

Modified residue

21

1

N6-methylated lysine By similarity

Modified residue

21

1

N6-methyllysine; alternate By similarity

Modified residue

32

1

N6-acetyllysine By similarity

Modified residue

48

1

Phosphoserine; by PAK2 By similarity

Modified residue

52

1

Phosphotyrosine By similarity

Modified residue

60

1

N6-acetyllysine By similarity

Modified residue

80

1

N6-acetyllysine By similarity

Modified residue

89

1

Phosphotyrosine By similarity

Modified residue

92

1

N6-acetyllysine; alternate By similarity

Cross-link

92

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate By similarity

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

103

Helix Strand Turn

Details...

Beta strand

6 – 12

7

Helix

23 – 26

4

Helix

27 – 29

3

Helix

32 – 41

10

Beta strand

45 – 47

3

Helix

51 – 76

26

Beta strand

80 – 82

3

Helix

84 – 90

7

Turn

91 – 94

4

Beta strand

96 – 100

5

Sequences

	Sequence		Length	Mass (Da)
	P62799 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: A9E5DFD3F8B97598	FASTA	103	11,367
	10 20 30 40 50 60 MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK 70 80 90 100 VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

References

	« Hide 'large scale' referencesShow '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.

PIR

HSXL4. A02641.

RefSeq

NP_001087926.1. NM_001094457.1.

UniGene

Xl.85592.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AOI	X-ray	2.80	B/F	17-103	[»]
1KX3	X-ray	2.00	B/F	2-102	[»]
1KX4	X-ray	2.60	B/F	2-103	[»]
1KX5	X-ray	1.94	B/F	2-103	[»]
1M18	X-ray	2.45	B/F	2-103	[»]
1M19	X-ray	2.30	B/F	2-103	[»]
1M1A	X-ray	2.65	B/F	2-103	[»]
1P34	X-ray	2.70	B/F	2-103	[»]
1P3A	X-ray	3.00	B/F	2-103	[»]
1P3B	X-ray	3.00	B/F	2-103	[»]
1P3F	X-ray	2.90	B/F	2-103	[»]
1P3G	X-ray	2.70	B/F	2-103	[»]
1P3I	X-ray	2.30	B/F	2-103	[»]
1P3K	X-ray	2.90	B/F	2-103	[»]
1P3L	X-ray	2.40	B/F	2-103	[»]
1P3M	X-ray	2.90	B/F	2-103	[»]
1P3O	X-ray	2.75	B/F	2-103	[»]
1P3P	X-ray	2.70	B/F	2-103	[»]
1S32	X-ray	2.05	B/F	2-103	[»]
1ZBB	X-ray	9.00	B/F/b/f	2-103	[»]
1ZLA	X-ray	2.90	B/F	2-102	[»]
2F8N	X-ray	2.90	B/F	1-102	[»]
2FJ7	X-ray	3.20	B/F	2-103	[»]
2HUE	X-ray	1.70	C	21-103	[»]
2IO5	X-ray	2.70	C	2-103	[»]
2NZD	X-ray	2.65	B/F	2-103	[»]
3B6F	X-ray	3.45	B/F	2-103	[»]
3B6G	X-ray	3.45	B/F	2-103	[»]
3C1B	X-ray	2.20	B/F	2-103	[»]
3C1C	X-ray	3.15	B/F	2-103	[»]
3KUY	X-ray	2.90	B/F	2-103	[»]
3KWQ	X-ray	3.50	B/F	21-103	[»]
3KXB	X-ray	3.20	B/F	2-103	[»]
3LEL	X-ray	2.95	B/F/L/P	2-103	[»]
3LJA	X-ray	2.75	B/F	2-103	[»]
3LZ0	X-ray	2.50	B/F	2-103	[»]
3LZ1	X-ray	2.50	B/F	2-103	[»]
3MGP	X-ray	2.44	B/F	2-103	[»]
3MGQ	X-ray	2.65	B/F	2-103	[»]
3MGR	X-ray	2.30	B/F	2-103	[»]
3MGS	X-ray	3.15	B/F	2-103	[»]
3MNN	X-ray	2.50	B/F	2-103	[»]
3MVD	X-ray	2.90	B/F	2-103	[»]
3O62	X-ray	3.22	B/F	2-103	[»]
3REH	X-ray	2.50	B/F	2-103	[»]
3REI	X-ray	2.65	B/F	2-103	[»]
3REJ	X-ray	2.55	B/F	2-103	[»]
3REK	X-ray	2.60	B/F	2-103	[»]
3REL	X-ray	2.70	B/F	2-103	[»]
3TU4	X-ray	3.00	B/F	2-103	[»]
3UT9	X-ray	2.20	B/F	2-103	[»]
3UTA	X-ray	2.07	B/F	2-103	[»]
3UTB	X-ray	2.20	B/F	2-103	[»]
4EO5	X-ray	2.35	C	21-103	[»]

ProteinModelPortal

P62799.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-37429N.

IntAct

P62799. 4 interactions.

Proteomic databases

PRIDE

P62799.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

447787.

KEGG

xla:447787.

Organism-specific databases

CTD

8359.

Xenbase

XB-GENE-6493984. hist1h4a.

Phylogenomic databases

HOVERGEN

HBG051878.

KO

K11254.

Family and domain databases

Gene3D

1.10.20.10. 1 hit.

InterPro

IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR001951. Histone_H4.
IPR019809. Histone_H4_CS.
[Graphical view]

PANTHER

PTHR10484. PTHR10484. 1 hit.

Pfam

PF00125. Histone. 1 hit.
[Graphical view]

PRINTS

PR00623. HISTONEH4.

SMART

SM00417. H4. 1 hit.
[Graphical view]

SUPFAM

SSF47113. Histone-fold. 1 hit.

PROSITE

PS00047. HISTONE_H4. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P62799.

Entry information

Entry name

H4_XENLA

Accession

Primary (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:	May 1, 2013
This is version 89 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program