P07041 (H3_NEUCR) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone H3

Gene names

Name:	hh3
ORF Names:	B7K22.030, NCU01635

Organism

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) [Reference proteome]

Taxonomic identifier

367110 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Pezizomycotina › leotiomyceta › sordariomyceta › Sordariomycetes › Sordariomycetidae › Sordariales › Sordariaceae › Neurospora › Neurospora crassa

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 By similarity. Chromosome By similarity.
Post-translational modification	Phosphorylated to form H3S10ph. H3S10ph promotes subsequent H3K14ac formation and is required for transcriptional activation through TBP recruitment to the promoters 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. Ref.5 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.
Sequence similarities	Belongs to the histone H3 family.
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.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Chromosome Nucleosome core Nucleus
Ligand	DNA-binding
PTM	Acetylation Methylation Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW 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...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
dim-5	Q8X225	2	EBI-1270655,EBI-1268994

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		PRO_0000221364
Amino acid modifications
	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-methyllysine; alternate By similarity
	Modified residue	10	1	N6,N6,N6-trimethyllysine; alternate Ref.5
	Modified residue	10	1	N6-acetyllysine; alternate By similarity
	Modified residue	11	1	Phosphoserine By similarity
	Modified residue	15	1	N6,N6-dimethyllysine; alternate By similarity
	Modified residue	15	1	N6-acetyllysine; alternate By similarity
	Modified residue	15	1	N6-methyllysine; alternate By similarity
	Modified residue	19	1	N6-acetyllysine; alternate By similarity
	Modified residue	19	1	N6-methyllysine; alternate By similarity
	Modified residue	24	1	N6-acetyllysine; alternate By similarity
	Modified residue	24	1	N6-methyllysine; alternate By similarity
	Modified residue	28	1	N6,N6,N6-trimethyllysine; alternate By similarity
	Modified residue	28	1	N6,N6-dimethyllysine; alternate By similarity
	Modified residue	28	1	N6-acetyllysine; alternate By similarity
	Modified residue	28	1	N6-methyllysine; alternate By similarity
	Modified residue	37	1	N6,N6,N6-trimethyllysine; alternate By similarity
	Modified residue	37	1	N6,N6-dimethyllysine; alternate By similarity
	Modified residue	37	1	N6-acetyllysine; alternate By similarity
	Modified residue	37	1	N6-methyllysine; alternate By similarity
	Modified residue	57	1	N6-acetyllysine By similarity
	Modified residue	65	1	N6-acetyllysine By similarity
	Modified residue	80	1	N6,N6,N6-trimethyllysine; alternate By similarity
	Modified residue	80	1	N6,N6-dimethyllysine; alternate By similarity
	Modified residue	80	1	N6-methyllysine; alternate By similarity
Experimental info
	Sequence conflict	92	1	A → L in CAA25761. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P07041 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 9AF51E808E698349	FASTA	136	15,392
	10 20 30 40 50 60 MARTKQTARK STGGKAPRKQ LASKAARKSA PSTGGVKKPH RYKPGTVALR EIRRYQKSTE 70 80 90 100 110 120 LLIRKLPFQR LVREIAQDFK SDLRFQSSAI GALQESVESY LVSLFEDTNL CAIHAKRVTI 130 QSKDIQLARR LRGERN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X01612 Genomic DNA. Translation: CAA25761.1. AY062173 Genomic DNA. Translation: AAL38973.1. AL670543 Genomic DNA. Translation: CAD21510.1. AABX02000005 Genomic DNA. Translation: EAA26767.1.
PIR	S07350.
RefSeq	XP_956003.1. XM_950910.2.
UniGene	Ncr.23461.
3D structure databases
ProteinModelPortal	P07041.
SMR	P07041. Positions 2-135.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-39601N.
IntAct	P07041. 1 interaction.
STRING	5141.NCU01635.1.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	EFNCRT00000001782; EFNCRP00000001782; EFNCRG00000001780.
GeneID	3872150.
KEGG	ncr:NCU01635.
Phylogenomic databases
eggNOG	COG2036.
HOGENOM	HOG000155290.
KO	K11253.
OrthoDB	EOG4B01ZS.
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...

Entry information

Entry name

H3_NEUCR

Accession

Primary (citable) accession number: P07041
Secondary accession number(s): Q7RV46, Q8WZD9

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 119 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program