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Protein

Histone H3

Gene

hh3

Organism
Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

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.

GO - Molecular functioni

Complete GO annotation...

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H3
Gene namesi
Name:hh3
ORF Names:B7K22.030, NCU01635
OrganismiNeurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Taxonomic identifieri367110 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaPezizomycotinaSordariomycetesSordariomycetidaeSordarialesSordariaceaeNeurospora
ProteomesiUP000001805 Componenti: Chromosome 6, Linkage Group II

Organism-specific databases

EuPathDBiFungiDB:NCU01635.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 136135Histone H3PRO_0000221364Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei5 – 51N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei5 – 51N6,N6-dimethyllysine; alternateBy similarity
Modified residuei5 – 51N6-methyllysine; alternateBy similarity
Modified residuei10 – 101N6,N6,N6-trimethyllysine; alternate1 Publication
Modified residuei10 – 101N6-acetyllysine; alternateBy similarity
Modified residuei11 – 111PhosphoserineBy similarity
Modified residuei15 – 151N6,N6-dimethyllysine; alternateBy similarity
Modified residuei15 – 151N6-acetyllysine; alternateBy similarity
Modified residuei15 – 151N6-methyllysine; alternateBy similarity
Modified residuei19 – 191N6-acetyllysine; alternateBy similarity
Modified residuei19 – 191N6-methyllysine; alternateBy similarity
Modified residuei24 – 241N6-acetyllysine; alternateBy similarity
Modified residuei24 – 241N6-methyllysine; alternateBy similarity
Modified residuei28 – 281N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei28 – 281N6,N6-dimethyllysine; alternateBy similarity
Modified residuei28 – 281N6-acetyllysine; alternateBy similarity
Modified residuei28 – 281N6-methyllysine; alternateBy similarity
Modified residuei37 – 371N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei37 – 371N6,N6-dimethyllysine; alternateBy similarity
Modified residuei37 – 371N6-acetyllysine; alternateBy similarity
Modified residuei37 – 371N6-methyllysine; alternateBy similarity
Modified residuei57 – 571N6-acetyllysineBy similarity
Modified residuei65 – 651N6-acetyllysineBy similarity
Modified residuei80 – 801N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei80 – 801N6,N6-dimethyllysine; alternateBy similarity
Modified residuei80 – 801N6-methyllysine; alternateBy similarity

Post-translational modificationi

Phosphorylated to form H3S10ph. H3S10ph promotes subsequent H3K14ac formation and is required for transcriptional activation through TBP recruitment to the promoters (By similarity).By similarity
Mono-, di- and trimethylated by the COMPASS complex to form H3K4me1/2/3. H3K4me activates gene expression by regulating transcription elongation and plays a role in telomere length maintenance. H3K4me enrichment correlates with transcription levels, and occurs in a 5' to 3' gradient with H3K4me3 enrichment at the 5'-end of genes, shifting to H3K4me2 and then H3K4me1. Trimethylated by methyltransferase dim-5 to form H3K9me3. H3K9me3, but not H3K9me2, marks chromatin regions for cytosine methylation. Methylated by set-2 to form H3K36me. H3K36me represses gene expression. Methylated by dot-1 to form H3K79me. H3K79me is required for association of SIR proteins with telomeric regions and for telomeric silencing. The COMPASS-mediated formation of H3K4me2/3 and the dot-1-mediated formation of H3K79me require H2BK123ub1 (By similarity).By similarity
Acetylation of histone H3 leads to transcriptional activation. H3K14ac formation by gcn-5 is promoted by H3S10ph. H3K14ac can also be formed by esa-1. H3K56ac formation occurs predominantly in newly synthesized H3 molecules during G1, S and G2/M of the cell cycle and may be involved in DNA repair (By similarity).By similarity

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Interactioni

Subunit structurei

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.

Binary interactionsi

WithEntry#Exp.IntActNotes
dim-5Q8X2252EBI-1270655,EBI-1268994

Protein-protein interaction databases

DIPiDIP-39601N.
IntActiP07041. 1 interaction.
STRINGi5141.EFNCRP00000001782.

Structurei

3D structure databases

ProteinModelPortaliP07041.
SMRiP07041. Positions 2-135.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H3 family.Curated

Phylogenomic databases

eggNOGiCOG2036.
HOGENOMiHOG000155290.
InParanoidiP07041.
KOiK11253.
OrthoDBiEOG7T4MZ6.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3/CENP-A.
[Graphical view]
PANTHERiPTHR11426. PTHR11426. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00622. HISTONEH3.
SMARTiSM00428. H3. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P07041-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARTKQTARK STGGKAPRKQ LASKAARKSA PSTGGVKKPH RYKPGTVALR
60 70 80 90 100
EIRRYQKSTE LLIRKLPFQR LVREIAQDFK SDLRFQSSAI GALQESVESY
110 120 130
LVSLFEDTNL CAIHAKRVTI QSKDIQLARR LRGERN
Length:136
Mass (Da):15,392
Last modified:January 23, 2007 - v3
Checksum:i9AF51E808E698349
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti92 – 921A → L in CAA25761 (PubMed:6310494).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X01612 Genomic DNA. Translation: CAA25761.1.
AY062173 Genomic DNA. Translation: AAL38973.1.
AL670543 Genomic DNA. Translation: CAD21510.1.
CM002237 Genomic DNA. Translation: EAA26767.1.
PIRiS07350.
RefSeqiXP_956003.1. XM_950910.3.

Genome annotation databases

EnsemblFungiiEFNCRT00000001782; EFNCRP00000001782; EFNCRG00000001780.
GeneIDi3872150.
KEGGincr:NCU01635.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X01612 Genomic DNA. Translation: CAA25761.1.
AY062173 Genomic DNA. Translation: AAL38973.1.
AL670543 Genomic DNA. Translation: CAD21510.1.
CM002237 Genomic DNA. Translation: EAA26767.1.
PIRiS07350.
RefSeqiXP_956003.1. XM_950910.3.

3D structure databases

ProteinModelPortaliP07041.
SMRiP07041. Positions 2-135.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-39601N.
IntActiP07041. 1 interaction.
STRINGi5141.EFNCRP00000001782.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiEFNCRT00000001782; EFNCRP00000001782; EFNCRG00000001780.
GeneIDi3872150.
KEGGincr:NCU01635.

Organism-specific databases

EuPathDBiFungiDB:NCU01635.

Phylogenomic databases

eggNOGiCOG2036.
HOGENOMiHOG000155290.
InParanoidiP07041.
KOiK11253.
OrthoDBiEOG7T4MZ6.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3/CENP-A.
[Graphical view]
PANTHERiPTHR11426. PTHR11426. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00622. HISTONEH3.
SMARTiSM00428. H3. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The genes coding for histone H3 and H4 in Neurospora crassa are unique and contain intervening sequences."
    Woudt L.P., Pastink A., Kempers-Veenstra A.E., Jansen A.E.M., Mager W.H., Planta R.J.
    Nucleic Acids Res. 11:5347-5360(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Identification and characterization of the genes encoding the core histones and histone variants of Neurospora crassa."
    Hays S.M., Swanson J., Selker E.U.
    Genetics 160:961-973(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence."
    Mannhaupt G., Montrone C., Haase D., Mewes H.-W., Aign V., Hoheisel J.D., Fartmann B., Nyakatura G., Kempken F., Maier J., Schulte U.
    Nucleic Acids Res. 31:1944-1954(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987.
  4. "The genome sequence of the filamentous fungus Neurospora crassa."
    Galagan J.E., Calvo S.E., Borkovich K.A., Selker E.U., Read N.D., Jaffe D.B., FitzHugh W., Ma L.-J., Smirnov S., Purcell S., Rehman B., Elkins T., Engels R., Wang S., Nielsen C.B., Butler J., Endrizzi M., Qui D.
    , Ianakiev P., Bell-Pedersen D., Nelson M.A., Werner-Washburne M., Selitrennikoff C.P., Kinsey J.A., Braun E.L., Zelter A., Schulte U., Kothe G.O., Jedd G., Mewes H.-W., Staben C., Marcotte E., Greenberg D., Roy A., Foley K., Naylor J., Stange-Thomann N., Barrett R., Gnerre S., Kamal M., Kamvysselis M., Mauceli E.W., Bielke C., Rudd S., Frishman D., Krystofova S., Rasmussen C., Metzenberg R.L., Perkins D.D., Kroken S., Cogoni C., Macino G., Catcheside D.E.A., Li W., Pratt R.J., Osmani S.A., DeSouza C.P.C., Glass N.L., Orbach M.J., Berglund J.A., Voelker R., Yarden O., Plamann M., Seiler S., Dunlap J.C., Radford A., Aramayo R., Natvig D.O., Alex L.A., Mannhaupt G., Ebbole D.J., Freitag M., Paulsen I., Sachs M.S., Lander E.S., Nusbaum C., Birren B.W.
    Nature 422:859-868(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987.
  5. "Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa."
    Tamaru H., Zhang X., McMillen D., Singh P.B., Nakayama J., Grewal S.I., Allis C.D., Cheng X., Selker E.U.
    Nat. Genet. 34:75-79(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: METHYLATION AT LYS-10.

Entry informationi

Entry nameiH3_NEUCR
AccessioniPrimary (citable) accession number: P07041
Secondary accession number(s): Q7RV46, Q8WZD9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: January 23, 2007
Last modified: June 24, 2015
This is version 133 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Caution

To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me3 = trimethylated Lys-10; H3S10ph = phosphorylated Ser-11; H3K14ac = acetylated Lys-15; H3K14me2 = dimethylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me1 = monomethylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me1 = monomethylated Lys-24; H3K27ac = acetylated Lys-28; H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3K36ac = acetylated Lys-37; H3K36me1/2/3 = mono-, di- and trimethylated Lys-37; H3K56ac = acetylated Lys-57; H3K64ac = acetylated Lys-65; H3K79me1/2/3 = mono-, di- and trimethylated Lys-80.Curated

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.