Histone H3 - Caenorhabditis elegans

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P08898 (H3_CAEEL) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 124. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Histone H3

Gene names

Name:	his-2
ORF Names:	T10C6.13
AND
Name:	his-6
ORF Names:	F45F2.13
AND
Name:	his-9
ORF Names:	ZK131.3
AND
Name:	his-13
ORF Names:	ZK131.7
AND
Name:	his-17
ORF Names:	K06C4.5
AND
Name:	his-25
ORF Names:	ZK131.2
AND
Name:	his-27
ORF Names:	K06C4.13
AND
Name:	his-32
ORF Names:	F17E9.10
AND
Name:	his-42
ORF Names:	F08G2.3
AND
Name:	his-45
ORF Names:	B0035.10
AND
Name:	his-49
ORF Names:	F07B7.5
AND
Name:	his-55
ORF Names:	F54E12.1
AND
Name:	his-59
ORF Names:	F55G1.2
AND
Name:	his-63
ORF Names:	F22B3.2

Organism

Caenorhabditis elegans [Reference proteome]

Taxonomic identifier

6239 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Ecdysozoa › Nematoda › Chromadorea › Rhabditida › Rhabditoidea › Rhabditidae › Peloderinae › Caenorhabditis

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.
Post-translational modification	Phosphorylated at Ser-11 and Ser-29 during M phase. Phosphorylation of Ser-11 requires air-2 but not air-1. Dephosphorylated by gsp-1 and/or gsp-2 during chromosome segregation. Ref.5 Ref.6 Ref.7 Ref.9 Ref.10 Ref.11 Ref.13 Acetylation is generally linked to gene activation By similarity. Methylation at Lys-5 is linked to gene activation and is absent from male inactive X chromosome chromatin. Methylation at Lys-10 is linked to gene repression and is enriched in male inactive X chromosome chromatin. Methylation at Lys-37 occurs on the entire length of autosomes during meiotic prophase. Trimethylation at Lys-10 and Lys-37 is specifically antagonized by jmjd-2. Dimethylation and trimethylation at Lys-28 occurs in all nuclei. The mes-2-mes-3-mes-6 complex may be responsible for Lys-28 methylation in most of the germline and in the early embryo. Ref.4 Ref.7 Ref.8 Ref.9 Ref.12 Ref.13 Ref.14
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 Complete proteome Direct protein sequencing Reference proteome
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

Removed Ref.4

Chain

2 – 136

135

Histone H3

PRO_0000221297

Amino acid modifications

Modified residue

N6,N6,N6-trimethyllysine; alternate Ref.7 Ref.8 Ref.9 Ref.13

Modified residue

N6,N6-dimethyllysine; alternate Ref.7 Ref.8 Ref.9 Ref.13

Modified residue

N6-acetyllysine; alternate Ref.4

Modified residue

N6-methyllysine; alternate Ref.7 Ref.8 Ref.9 Ref.13

Modified residue

N6,N6,N6-trimethyllysine; alternate Ref.4 Ref.7 Ref.8 Ref.9 Ref.13 Ref.14

Modified residue

N6,N6-dimethyllysine; alternate Ref.4 Ref.7 Ref.8 Ref.9 Ref.13 Ref.14

Modified residue

N6-acetyllysine; alternate Ref.7 Ref.13

Modified residue

Phosphoserine Ref.5 Ref.6 Ref.7 Ref.9 Ref.10 Ref.11 Ref.13

Modified residue

N6-acetyllysine Ref.4 Ref.7 Ref.13

Modified residue

N6-acetyllysine Ref.4

Modified residue

N6,N6,N6-trimethyllysine; alternate Ref.4 Ref.12

Modified residue

N6,N6-dimethyllysine; alternate Ref.4 Ref.12

Modified residue

N6-methyllysine; alternate Ref.4 Ref.12

Modified residue

Phosphoserine Ref.6 Ref.11

Modified residue

N6,N6,N6-trimethyllysine; alternate Ref.4 Ref.9 Ref.14

Modified residue

N6,N6-dimethyllysine; alternate Ref.4 Ref.9 Ref.14

Modified residue

N6-methyllysine; alternate Ref.4 Ref.9 Ref.14

Modified residue

N6-methyllysine Ref.4

Natural variations

Natural variant

C → A.

Natural variant

101

L → I.

Secondary structure

136

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P08898 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: 40D7DE0EF5BA6F1F
Show »

FASTA

136

15,376

        10         20         30         40         50         60 
MARTKQTARK STGGKAPRKQ LATKAARKSA PASGGVKKPH RYRPGTVALR EIRRYQKSTE 

        70         80         90        100        110        120 
LLIRRAPFQR LVREIAQDFK TDLRFQSSAV MALQEACEAY LVGLFEDTNL CAIHAKRVTI 

       130 
MPKDIQLARR IRGERA

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequences of Caenorhabditis elegans core histone genes. Genes for different histone classes share common flanking sequence elements." Roberts S.B., Emmons S.W., Childs G. J. Mol. Biol. 206:567-577(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HIS-10). Strain: Bristol N2.
[2]	"Genome sequence of the nematode C. elegans: a platform for investigating biology." The C. elegans sequencing consortium Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Bristol N2.
[3]	"The Caenorhabditis elegans transcriptome project, a complementary view of the genome." Kohara Y., Shin-i T., Suzuki Y., Sugano S., Potdevin M., Thierry-Mieg Y., Thierry-Mieg D., Thierry-Mieg J. Submitted (SEP-2000) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (HIS-4). Strain: Bristol N2.
[4]	"The primary structure of histone H3 from the nematode Caenorhabditis elegans." Vanfleteren J.R., van Bun S.M., van Beeumen J.J. FEBS Lett. 211:59-63(1987) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-136, ACETYLATION AT LYS-5; LYS-15 AND LYS-24, METHYLATION AT LYS-10; LYS-28; LYS-37 AND LYS-80. Strain: DR27.
[5]	"Mitotic phosphorylation of histone H3 is governed by Ipl1/aurora kinase and Glc7/PP1 phosphatase in budding yeast and nematodes." Hsu J.-Y., Sun Z.-W., Li X., Reuben M., Tatchell K., Bishop D.K., Grushcow J.M., Brame C.J., Caldwell J.A., Hunt D.F., Lin R., Smith M.M., Allis C.D. Cell 102:279-291(2000) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION AT SER-11.
[6]	"The aurora B kinase AIR-2 regulates kinetochores during mitosis and is required for separation of homologous Chromosomes during meiosis." Kaitna S., Pasierbek P., Jantsch M., Loidl J., Glotzer M. Curr. Biol. 12:798-812(2002) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION AT SER-11 AND SER-29.
[7]	"X-chromosome silencing in the germline of C. elegans." Kelly W.G., Schaner C.E., Dernburg A.F., Lee M.-H., Kim S.K., Villeneuve A.M., Reinke V. Development 129:479-492(2002) [PubMed] [Europe PMC] [Abstract] Cited for: METHYLATION AT LYS-5 AND LYS-10, PHOSPHORYLATION AT SER-11, ACETYLATION AT LYS-10 AND LYS-15.
[8]	"Germline X chromosomes exhibit contrasting patterns of histone H3 methylation in Caenorhabditis elegans." Reuben M., Lin R. Dev. Biol. 245:71-82(2002) [PubMed] [Europe PMC] [Abstract] Cited for: METHYLATION AT LYS-5 AND LYS-10.
[9]	"The C. elegans Tousled-like kinase (TLK-1) has an essential role in transcription." Han Z., Saam J.R., Adams H.P., Mango S.E., Schumacher J.M. Curr. Biol. 13:1921-1929(2003) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION AT SER-11, METHYLATION AT LYS-5; LYS-10 AND LYS-37.
[10]	"Role of Caenorhabditis elegans protein phosphatase type 1, CeGLC-7 beta, in metaphase to anaphase transition during embryonic development." Sassa T., Ueda-Ohba H., Kitamura K., Harada S., Hosono R. Exp. Cell Res. 287:350-360(2003) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION AT SER-11.
[11]	"Caenorhabditis elegans RBX1 is essential for meiosis, mitotic chromosomal condensation and segregation, and cytokinesis." Sasagawa Y., Urano T., Kohara Y., Takahashi H., Higashitani A. Genes Cells 8:857-872(2003) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION AT SER-11 AND SER-29.
[12]	"The MES-2/MES-3/MES-6 complex and regulation of histone H3 methylation in C. elegans." Bender L.B., Cao R., Zhang Y., Strome S. Curr. Biol. 14:1639-1643(2004) [PubMed] [Europe PMC] [Abstract] Cited for: METHYLATION AT LYS-28.
[13]	"Meiotic pairing and imprinted X chromatin assembly in Caenorhabditis elegans." Bean C.J., Schaner C.E., Kelly W.G. Nat. Genet. 36:100-105(2004) [PubMed] [Europe PMC] [Abstract] Cited for: ACETYLATION AT LYS-10 AND LYS-15, METHYLATION AT LYS-5 AND LYS-10, PHOSPHORYLATION AT SER-11.
[14]	"Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases." Whetstine J.R., Nottke A., Lan F., Huarte M., Smolikov S., Chen Z., Spooner E., Li E., Zhang G., Colaiacovo M., Shi Y. Cell 125:467-481(2006) [PubMed] [Europe PMC] [Abstract] Cited for: METHYLATION AT LYS-10 AND LYS-37.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X15634 Genomic DNA. Translation: CAA33644.1.
FO081018 Genomic DNA. Translation: CCD68531.1.
FO081059 Genomic DNA. Translation: CCD68868.1.
FO081135 Genomic DNA. Translation: CCD69390.1.
FO081223 Genomic DNA. Translation: CCD70027.1.
FO081551 Genomic DNA. Translation: CCD72363.1.
FO081551 Genomic DNA. Translation: CCD72373.1.
Z68336 Genomic DNA. Translation: CAA92733.1.
Z73102 Genomic DNA. Translation: CAA97411.1.
Z81495 Genomic DNA. Translation: CAB04057.1.
Z82271 Genomic DNA. Translation: CAB05209.1.
Z83245 Genomic DNA. Translation: CAB05831.1.
Z83245 Genomic DNA. Translation: CAB05833.1.
Z83245 Genomic DNA. Translation: CAB05834.1.
Z93388 Genomic DNA. Translation: CAB07653.1.
AF304122 mRNA. Translation: AAG50235.1.

PIR

HSKW3. S04241.

RefSeq

NP_001263958.1. NM_001277029.1.
NP_496890.1. NM_064489.1.
NP_496894.1. NM_064493.5.
NP_496895.1. NM_064494.1.
NP_496899.1. NM_064498.1.
NP_501204.1. NM_068803.3.
NP_501407.1. NM_069006.3.
NP_502134.1. NM_069733.3.
NP_502138.1. NM_069737.1.
NP_502153.1. NM_069752.3.
NP_505199.1. NM_072798.1.
NP_505276.1. NM_072875.1.
NP_505292.1. NM_072891.1.
NP_505297.1. NM_072896.3.
NP_507033.1. NM_074632.3.

UniGene

Cel.21871.
Cel.2350.
Cel.29106.
Cel.29299.
Cel.32605.
Cel.32856.
Cel.33056.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3N9L	X-ray	2.80	B	2-16	[»]
3N9N	X-ray	2.30	B/C	2-33	[»]
3N9O	X-ray	2.31	B	2-16	[»]
			C	2-18	[»]
3N9P	X-ray	2.39	B/C	2-33	[»]
3N9Q	X-ray	2.30	B	2-16	[»]
			C	20-36	[»]

ProteinModelPortal

P08898.

SMR

P08898. Positions 17-136.

ModBase

Search...

Protein-protein interaction databases

IntAct

P08898. 1 interaction.

STRING

6239.F07B7.5.

Proteomic databases

PaxDb

P08898.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

175030.
175031.
177628.
180074.
181821.
184113.
184200.
184804.
186250.
186325.
191668.
191672.
191673.
246024.

KEGG

cel:CELE_B0035.10.
cel:CELE_F07B7.5.
cel:CELE_F08G2.3.
cel:CELE_F17E9.10.
cel:CELE_F22B3.2.
cel:CELE_F45F2.13.
cel:CELE_F54E12.1.
cel:CELE_F55G1.2.
cel:CELE_K06C4.13.
cel:CELE_K06C4.5.
cel:CELE_T10C6.13.
cel:CELE_ZK131.2.
cel:CELE_ZK131.3.
cel:CELE_ZK131.7.

UCSC

ZK131.7. c. elegans.

Organism-specific databases

CTD

175030.
175031.
177628.
180074.
181821.
184113.
184200.
184804.
186250.
186325.
191668.
191672.
191673.
246024.

WormBase

Phylogenomic databases

eggNOG

COG2036.

HOGENOM

HOG000155290.

InParanoid

P08898.

K11253.

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

P08898.

NextBio

886476.

Entry information

Entry name

H3_CAEEL

Accession

Primary (citable) accession number: P08898
Secondary accession number(s): Q9TW44

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1988
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 124 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Caenorhabditis annotation project

Relevant documents

Caenorhabditis elegans

Caenorhabditis elegans: entries, gene names and cross-references to WormBase

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Amino acid modifications

Natural variations

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Other

Entry information

Relevant documents