P02302 (H3C_XENLA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone H3.3C

Gene names

Name:

h3f3c

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	136 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. Ref.2 Ref.3
Subcellular location	Nucleus. Chromosome.
Post-translational modification	Acetylation is generally linked to gene activation. Acetylation on Lys-19 (H3K18ac) and Lys-24 (H3K24ac) favors methylation at Arg-18 (H3R17me) 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.
Sequence similarities	Belongs to the histone H3 family.

Ontologies

Keywords
Cellular component	Chromosome Nucleosome core Nucleus
Ligand	DNA-binding
PTM	Acetylation Methylation Phosphoprotein
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...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed By similarity

Chain

2 – 136

135

Histone H3.3C

PRO_0000221266

Amino acid modifications

Modified residue

3

1

Asymmetric dimethylarginine; by PRMT6 By similarity

Modified residue

4

1

Phosphothreonine; by GSG2 By similarity

Modified residue

5

1

Allysine; alternate By similarity

Modified residue

5

1

N6,N6,N6-trimethyllysine; alternate By similarity

Modified residue

5

1

N6,N6-dimethyllysine; alternate By similarity

Modified residue

5

1

N6-acetyllysine; alternate By similarity

Modified residue

5

1

N6-methyllysine; alternate By similarity

Modified residue

7

1

Phosphothreonine; by PKC By similarity

Modified residue

10

1

N6-methylated lysine By similarity

Modified residue

11

1

Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 By similarity

Modified residue

12

1

Phosphothreonine; by PKC By similarity

Modified residue

15

1

N6-acetyllysine By similarity

Modified residue

18

1

Asymmetric dimethylarginine By similarity

Modified residue

19

1

N6-acetyllysine; alternate By similarity

Modified residue

19

1

N6-methylated lysine; alternate By similarity

Modified residue

24

1

N6-acetyllysine By similarity

Modified residue

28

1

N6-acetyllysine; alternate By similarity

Modified residue

28

1

N6-methylated lysine; alternate By similarity

Modified residue

37

1

N6-acetyllysine; alternate By similarity

Modified residue

37

1

N6-methylated lysine; alternate By similarity

Modified residue

42

1

Phosphotyrosine By similarity

Modified residue

58

1

Phosphoserine By similarity

Modified residue

65

1

N6-methylated lysine By similarity

Modified residue

80

1

N6-methylated lysine By similarity

Modified residue

81

1

Phosphothreonine By similarity

Modified residue

123

1

N6-methylated lysine By similarity

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

136

Helix Strand Turn

Details...

Helix

46 – 55

10

Helix

65 – 77

13

Beta strand

80 – 82

3

Helix

87 – 114

28

Beta strand

118 – 120

3

Helix

122 – 132

11

Sequences

	Sequence		Length	Mass (Da)
	P02302 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: FE1B7E45DBBC7D95	FASTA	136	15,487
	10 20 30 40 50 60 MARTKQTARK STGGKAPRKQ LVTKAAKKCA PATGGVKKPH RYRPGTVALR EIRRYQKSTE 70 80 90 100 110 120 LLIRKLPFQR LVREIAQDFK TDLRFQRSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI 130 MPKDIQLARR IRGERA

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] (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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J00982 Genomic DNA. No translation available.
J00984 Genomic DNA. No translation available.

PIR

HSXL32. A02634.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AOI	X-ray	2.80	A/E	23-136	[»]
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	[»]

ProteinModelPortal

P02302.

SMR

P02302. Positions 2-136.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-39145N.

Proteomic databases

PRIDE

P02302.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Phylogenomic databases

HOVERGEN

HBG001172.

Family and domain databases

Gene3D

1.10.20.10. 1 hit.

InterPro

IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3.
[Graphical view]

PANTHER

PTHR11426. PTHR11426. 1 hit.

Pfam

PF00125. Histone. 1 hit.
[Graphical view]

PRINTS

PR00622. HISTONEH3.

SMART

SM00428. H3. 1 hit.
[Graphical view]

SUPFAM

SSF47113. Histone-fold. 1 hit.

PROSITE

PS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P02302.

Entry information

Entry name

H3C_XENLA

Accession

Primary (citable) accession number: P02302

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 96 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program