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P08898 (H3_CAEEL) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 129. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismCaenorhabditis elegans [Reference proteome]
Taxonomic identifier6239 [NCBI]
Taxonomic lineageEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis

Protein attributes

Sequence length136 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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. Ref.4 Ref.7 Ref.13

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 componentChromosome
Nucleosome core
Nucleus
   LigandDNA-binding
   PTMAcetylation
Methylation
Phosphoprotein
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processnucleosome assembly

Inferred from electronic annotation. Source: InterPro

   Cellular_componentnucleosome

Inferred from electronic annotation. Source: UniProtKB-KW

nucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.4
Chain2 – 136135Histone H3
PRO_0000221297

Amino acid modifications

Modified residue51N6,N6,N6-trimethyllysine; alternate Ref.7 Ref.8 Ref.9 Ref.13
Modified residue51N6,N6-dimethyllysine; alternate Ref.7 Ref.8 Ref.9 Ref.13
Modified residue51N6-acetyllysine; alternate Ref.4
Modified residue51N6-methyllysine; alternate Ref.7 Ref.8 Ref.9 Ref.13
Modified residue101N6,N6,N6-trimethyllysine; alternate Ref.4 Ref.7 Ref.8 Ref.9 Ref.13 Ref.14
Modified residue101N6,N6-dimethyllysine; alternate Ref.4 Ref.7 Ref.8 Ref.9 Ref.13 Ref.14
Modified residue101N6-acetyllysine; alternate Ref.7 Ref.13
Modified residue111Phosphoserine Ref.5 Ref.6 Ref.7 Ref.9 Ref.10 Ref.11 Ref.13
Modified residue151N6-acetyllysine Ref.4 Ref.7 Ref.13
Modified residue241N6-acetyllysine Ref.4
Modified residue281N6,N6,N6-trimethyllysine; alternate Ref.4 Ref.12
Modified residue281N6,N6-dimethyllysine; alternate Ref.4 Ref.12
Modified residue281N6-methyllysine; alternate Ref.4 Ref.12
Modified residue291Phosphoserine Ref.6 Ref.11
Modified residue371N6,N6,N6-trimethyllysine; alternate Ref.4 Ref.9 Ref.14
Modified residue371N6,N6-dimethyllysine; alternate Ref.4 Ref.9 Ref.14
Modified residue371N6-methyllysine; alternate Ref.4 Ref.9 Ref.14
Modified residue801N6-methyllysine Ref.4

Natural variations

Natural variant971C → A.
Natural variant1011L → I.

Secondary structure

..... 136
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P08898 [UniParc].

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

FASTA13615,376
        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' 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.
PIRHSKW3. S04241.
RefSeqNP_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.
UniGeneCel.12716.
Cel.12871.
Cel.21447.
Cel.21596.
Cel.21806.
Cel.21871.
Cel.2350.
Cel.27007.
Cel.29106.
Cel.29299.
Cel.32605.
Cel.32856.
Cel.33056.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3N9LX-ray2.80B2-16[»]
3N9NX-ray2.30B/C2-33[»]
3N9OX-ray2.31B2-16[»]
C2-18[»]
3N9PX-ray2.39B/C2-33[»]
3N9QX-ray2.30B2-16[»]
C20-36[»]
ProteinModelPortalP08898.
SMRP08898. Positions 17-136.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid42741. 1 interaction.
45065. 3 interactions.
50996. 1 interaction.
IntActP08898. 1 interaction.
STRING6239.F07B7.5.

Proteomic databases

PaxDbP08898.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID175030.
175031.
177628.
180074.
181821.
184113.
184200.
184804.
186250.
186325.
191668.
191672.
191673.
246024.
KEGGcel: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.
UCSCZK131.7. c. elegans.

Organism-specific databases

CTD175030.
175031.
177628.
180074.
181821.
184113.
184200.
184804.
186250.
186325.
191668.
191672.
191673.
246024.
WormBaseB0035.10; CE03253; WBGene00001919; his-45.
F07B7.5; CE03253; WBGene00001923; his-49.
F08G2.3; CE03253; WBGene00001916; his-42.
F17E9.10; CE03253; WBGene00001906; his-32.
F22B3.2; CE03253; WBGene00001937; his-63.
F45F2.13; CE03253; WBGene00001880; his-6.
F54E12.1; CE03253; WBGene00001929; his-55.
F55G1.2; CE03253; WBGene00001933; his-59.
K06C4.13; CE03253; WBGene00001901; his-27.
K06C4.5; CE03253; WBGene00001891; his-17.
T10C6.13; CE03253; WBGene00001876; his-2.
ZK131.2; CE03253; WBGene00001899; his-25.
ZK131.3; CE03253; WBGene00001883; his-9.
ZK131.7; CE03253; WBGene00001887; his-13.

Phylogenomic databases

eggNOGCOG2036.
HOGENOMHOG000155290.
InParanoidP08898.
KOK11253.
OrthoDBEOG7HB5C2.
PhylomeDBP08898.

Family and domain databases

Gene3D1.10.20.10. 1 hit.
InterProIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3.
[Graphical view]
PANTHERPTHR11426. PTHR11426. 1 hit.
PfamPF00125. Histone. 1 hit.
[Graphical view]
PRINTSPR00622. HISTONEH3.
SMARTSM00428. H3. 1 hit.
[Graphical view]
SUPFAMSSF47113. SSF47113. 1 hit.
PROSITEPS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP08898.
NextBio886476.

Entry information

Entry nameH3_CAEEL
AccessionPrimary (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: April 16, 2014
This is version 129 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Caenorhabditis elegans

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