P84233 (H32_XENLA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Histone H3.2
Organism	Xenopus laevis (African clawed frog)
Taxonomic identifier	8355 [NCBI]
Taxonomic lineage	Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Amphibia › Batrachia › Anura › Mesobatrachia › 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.
Subcellular location	Nucleus. Chromosome.
Developmental stage	Expressed during S phase, then expression strongly decreases as cell division slows down during the process of differentiation.
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. Methylation at Lys-5 (H3K4me), Lys-37 (H3K36me) 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. Phosphorylated at Ser-29 (H3S28ph) by mltk isoform 1, rps6ka5 or aurkb during mitosis or upon ultraviolet B irradiation. 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. Ref.4 Monoubiquitinated by rag1 in lymphoid cells, monoubiquitination is required for V(D)J recombination 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 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 protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
	P62799	2	EBI-350041,EBI-302085

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 H3.2

PRO_0000221265

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

N6-methylated lysine Ref.4

Modified residue

7

1

Phosphothreonine; by PKC By similarity

Modified residue

10

1

N6-methylated lysine Ref.4

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 Ref.4

Modified residue

18

1

Asymmetric dimethylarginine Ref.4

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

29

1

Phosphoserine; by AURKB, AURKC and RPS6KA5 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 – 57

12

Helix

65 – 77

13

Beta strand

80 – 82

3

Helix

87 – 114

28

Beta strand

118 – 120

3

Helix

122 – 131

10

Sequences

	Sequence		Length	Mass (Da)
	P84233 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 6FD8508EA50A0EEC	FASTA	136	15,388
	10 20 30 40 50 60 MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE 70 80 90 100 110 120 LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEASEAY LVGLFEDTNL CAIHAKRVTI 130 MPKDIQLARR IRGERA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Individual Xenopus histone genes are replication-independent in oocytes and replication-dependent in Xenopus or mouse somatic cells." Old R.W., Sheikh S.A., Chambers A., Newton C.A., Mohammed A., Aldridge T.C. Nucleic Acids Res. 13:7341-7358(1985) [PubMed: 4059058] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"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: 3863963] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (GENE CLUSTERS X1H1 AND X1H3).
[3]	NIH - Xenopus Gene Collection (XGC) project Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Embryo.
[4]	"Involvement of histone methylation and phosphorylation in regulation of transcription by thyroid hormone receptor." Li J., Lin Q., Yoon H.-G., Huang Z.-Q., Strahl B.D., Allis C.D., Wong J. Mol. Cell. Biol. 22:5688-5697(2002) [PubMed: 12138181] [Abstract] Cited for: METHYLATION AT LYS-5; LYS-10 AND ARG-18, PHOSPHORYLATION AT SER-11, ACETYLATION AT LYS-15.
[5]	"Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 A resolution." Davey C.A., Sargent D.F., Luger K., Maeder A.W., Richmond T.J. J. Mol. Biol. 319:1097-1113(2002) [PubMed: 12079350] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH H2A; H2B AND H4.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X03104 Genomic DNA. Translation: CAA26890.1.
X03017 Genomic DNA. Translation: CAA26813.1.
X03018 Genomic DNA. Translation: CAA26818.1.
M21286 Genomic DNA. Translation: AAA49765.1.
M21287 Genomic DNA. Translation: AAA49770.1.
BC133776 mRNA. Translation: AAI33777.1.

PIR

HSXL31. A93596.
I51448.

RefSeq

NP_001091428.1. NM_001097959.1.

UniGene

Xl.78138.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1F66	X-ray	2.60	A/E	1-136	[»]
1KX3	X-ray	2.00	A/E	2-136	[»]
1KX4	X-ray	2.60	A/E	2-136	[»]
1KX5	X-ray	1.94	A/E	2-136	[»]
1P34	X-ray	2.70	A/E	2-136	[»]
1P3A	X-ray	3.00	A/E	2-136	[»]
1P3B	X-ray	3.00	A/E	2-136	[»]
1P3F	X-ray	2.90	A/E	2-136	[»]
1P3G	X-ray	2.70	A/E	2-136	[»]
1P3I	X-ray	2.30	A/E	2-136	[»]
1P3K	X-ray	2.90	A/E	2-136	[»]
1P3L	X-ray	2.40	A/E	2-136	[»]
1P3M	X-ray	2.90	A/E	2-136	[»]
1P3O	X-ray	2.75	A/E	2-136	[»]
1P3P	X-ray	2.70	A/E	2-136	[»]
1S32	X-ray	2.05	A/E	2-136	[»]
1ZBB	X-ray	9.00	A/E/a/e	2-136	[»]
1ZLA	X-ray	2.90	A/E	2-136	[»]
2F8N	X-ray	2.90	A/E	1-135	[»]
2FJ7	X-ray	3.20	A/E	2-136	[»]
2HUE	X-ray	1.70	B	62-136	[»]
2IO5	X-ray	2.70	B	2-136	[»]
2NZD	X-ray	2.65	A/E	2-136	[»]
3B6F	X-ray	3.45	A/E	2-136	[»]
3B6G	X-ray	3.45	A/E	2-136	[»]
3C1B	X-ray	2.20	A/E	2-136	[»]
3C1C	X-ray	3.15	A/E	2-136	[»]
3GV6	X-ray	1.76	B	2-16	[»]
3KUY	X-ray	2.90	A/E	2-136	[»]
3KWQ	X-ray	3.50	A/E	39-136	[»]
3KXB	X-ray	3.20	A/E	2-136	[»]
3LEL	X-ray	2.95	A/E/K/O	1-136	[»]
3LJA	X-ray	2.75	A/E	2-136	[»]
3LZ0	X-ray	2.50	A/E	2-136	[»]
3LZ1	X-ray	2.50	A/E	2-136	[»]
3MGP	X-ray	2.44	A/E	2-136	[»]
3MGQ	X-ray	2.65	A/E	2-136	[»]
3MGR	X-ray	2.30	A/E	2-136	[»]
3MGS	X-ray	3.15	A/E	2-136	[»]
3MNN	X-ray	2.50	A/E	2-136	[»]
3MVD	X-ray	2.90	A/E	2-136	[»]
3O62	X-ray	3.22	A/E	2-136	[»]
3TU4	X-ray	3.00	A/E	2-136	[»]

ProteinModelPortal

P84233.

SMR

P84233. Positions 17-136.

ModBase

Search...

Protein-protein interaction databases

IntAct

P84233. 4 interactions.

Proteomic databases

PRIDE

P84233.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

100049126.

KEGG

xla:100049126.

Organism-specific databases

CTD

126961.

Xenbase

XB-GENE-866635. hist2h3c.

Phylogenomic databases

HOVERGEN

HBG001172.

Family and domain databases

InterPro

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

Gene3D

G3DSA:1.10.20.10. Histone-fold. 1 hit.

KO

K11253.

PANTHER

PTHR11426. Histone_H3. 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...

Entry information

Entry name

H32_XENLA

Accession

Primary (citable) accession number: P84233
Secondary accession number(s): A4FVE2 , P02295, P02297, P16105, P17269, P17320

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 63 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program