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H33C_DICDI
ID   H33C_DICDI              Reviewed;         136 AA.
AC   Q55BP0;
DT   24-NOV-2009, integrated into UniProtKB/Swiss-Prot.
DT   24-MAY-2005, sequence version 1.
DT   03-AUG-2022, entry version 116.
DE   RecName: Full=Histone H3.3 type c;
DE   AltName: Full=Histone 3, variant 3 type c;
GN   Name=H3c; ORFNames=DDB_G0271092;
OS   Dictyostelium discoideum (Slime mold).
OC   Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC   Dictyosteliaceae; Dictyostelium.
OX   NCBI_TaxID=44689;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=AX4;
RX   PubMed=15875012; DOI=10.1038/nature03481;
RA   Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA   Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA   Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA   Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA   Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA   Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA   Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA   Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA   Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA   Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA   Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA   Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA   Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA   Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA   Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA   Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA   Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT   "The genome of the social amoeba Dictyostelium discoideum.";
RL   Nature 435:43-57(2005).
RN   [2]
RP   PARTIAL PROTEIN SEQUENCE.
RX   PubMed=497154; DOI=10.1021/bi00588a016;
RA   Bakke A.C., Bonner J.;
RT   "Purification and the histones of Dictyostelium discoideum chromatin.";
RL   Biochemistry 18:4556-4562(1979).
RN   [3]
RP   FUNCTION, NOMENCLATURE, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, AND
RP   METHYLATION AT LYS-5 BY SET1.
RX   PubMed=16469305; DOI=10.1016/j.ydbio.2005.12.054;
RA   Chubb J.R., Bloomfield G., Xu Q., Kaller M., Ivens A., Skelton J.,
RA   Turner B.M., Nellen W., Shaulsky G., Kay R.R., Bickmore W.A., Singer R.H.;
RT   "Developmental timing in Dictyostelium is regulated by the Set1 histone
RT   methyltransferase.";
RL   Dev. Biol. 292:519-532(2006).
RN   [4]
RP   METHYLATION AT LYS-10, AND SUBCELLULAR LOCATION.
RX   PubMed=16524908; DOI=10.1128/ec.5.3.530-543.2006;
RA   Kaller M., Euteneuer U., Nellen W.;
RT   "Differential effects of heterochromatin protein 1 isoforms on mitotic
RT   chromosome distribution and growth in Dictyostelium discoideum.";
RL   Eukaryot. Cell 5:530-543(2006).
RN   [5]
RP   METHYLATION AT LYS-80, SUBCELLULAR LOCATION, AND DEVELOPMENTAL STAGE.
RC   STRAIN=AX2;
RX   PubMed=21187070; DOI=10.1016/j.bbrc.2010.12.101;
RA   Muller-Taubenberger A., Bonisch C., Furbringer M., Wittek F., Hake S.B.;
RT   "The histone methyltransferase Dot1 is required for DNA damage repair and
RT   proper development in Dictyostelium.";
RL   Biochem. Biophys. Res. Commun. 404:1016-1022(2011).
CC   -!- FUNCTION: Core component of nucleosome. Nucleosomes wrap and compact
CC       DNA into chromatin, limiting DNA accessibility to the cellular
CC       machineries which require DNA as a template. Histones thereby play a
CC       central role in transcription regulation, DNA repair, DNA replication
CC       and chromosomal stability. DNA accessibility is regulated via a complex
CC       set of post-translational modifications of histones, also called
CC       histone code, and nucleosome remodeling. {ECO:0000269|PubMed:16469305}.
CC   -!- SUBUNIT: The nucleosome is a histone octamer containing two molecules
CC       each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and
CC       two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA
CC       (By similarity). {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Nucleus. Chromosome. Note=Associated with
CC       pericentromeric heterochromatin.
CC   -!- DEVELOPMENTAL STAGE: Levels relative to total cellular protein,
CC       increase as differentiation proceeds towards the final culminant. The
CC       levels of tri-methylation of Lys-5 (H3K4me3) diminish considerably
CC       during the process of differentiation. In contrast, the level of mono-
CC       methylation of Lys-5 (H3K4me1) becomes significantly enhanced during
CC       differentiation. There is a slight dip in di-methylation of Lys-5
CC       (H3K4me2) around the time of aggregation and the level of this mark
CC       again dips during the final stages of spore formation. The levels of
CC       H3K4me1 and H3K4me2 rise during the inactivation of rasG that occurs
CC       after the onset of differentiation. The level of dimethylation at this
CC       locus peaks coinciding with the loss of H3K4me3. This enrichment of
CC       dimethyl H3K4 declines as the rise in the level of H3K4me1 continues.
CC       H3K79me2 (di-methylation of Lys-80) is expressed during the whole life
CC       cycle. {ECO:0000269|PubMed:16469305, ECO:0000269|PubMed:21187070}.
CC   -!- PTM: Acetylation is generally linked to gene activation. {ECO:0000250}.
CC   -!- PTM: Different methylation states of H3K4 mark distinct developmental
CC       phases. H3K4me2 is associated with euchromatic regions. H3K4me3 is a
CC       mark of active chromatin. set1 is responsible for all mono-, di- and
CC       tri-methylation of H3K4. H3K4me facilitates subsequent acetylation of
CC       H3 and H4. Methylation at H3K9 is linked to gene repression (By
CC       similarity). {ECO:0000250}.
CC   -!- PTM: H3S10ph, which is linked to gene activation, prevents methylation
CC       at H3K9 but facilitates acetylation of H3 and H4. {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the histone H3 family. {ECO:0000305}.
CC   -!- CAUTION: To ensure consistency between histone entries, we follow the
CC       'Brno' nomenclature for histone modifications, with positions referring
CC       to those used in the literature for the 'closest' model organism. Due
CC       to slight variations in histone sequences between organisms and to the
CC       presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the
CC       actual positions of modified amino acids in the sequence generally
CC       differ. In this entry the following conventions are used: H3K4me1/2/3 =
CC       mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me1
CC       = monomethylated Lys-10; H3S10ph = phosphorylated Ser-11; H3K14ac =
CC       acetylated Lys-15; H3K14me2 = dimethylated Lys-15; H3K18ac = acetylated
CC       Lys-19; H3K18me1 = monomethylated Lys-19; H3K23ac = acetylated Lys-24;
CC       H3K23me1 = monomethylated Lys-24; H3K27ac = acetylated Lys-28;
CC       H3K27me1/2/3 = mono-, di- and trimethylated Lys-28; H3K36ac =
CC       acetylated Lys-37; H3K36me1/2/3 = mono-, di- and trimethylated Lys-37;
CC       H3K56ac = acetylated Lys-57; H3K64ac = acetylated Lys-68; H3K79me1/2/3
CC       = mono-, di- and trimethylated Lys-80. {ECO:0000305}.
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DR   EMBL; AAFI02000005; EAL72896.1; -; Genomic_DNA.
DR   RefSeq; XP_646791.1; XM_641699.1.
DR   AlphaFoldDB; Q55BP0; -.
DR   SMR; Q55BP0; -.
DR   STRING; 44689.DDB0231141; -.
DR   iPTMnet; Q55BP0; -.
DR   PaxDb; Q55BP0; -.
DR   EnsemblProtists; EAL72896; EAL72896; DDB_G0271092.
DR   GeneID; 8617764; -.
DR   KEGG; ddi:DDB_G0271092; -.
DR   dictyBase; DDB_G0271092; H3c.
DR   eggNOG; KOG1745; Eukaryota.
DR   HOGENOM; CLU_078295_4_0_1; -.
DR   InParanoid; Q55BP0; -.
DR   OMA; ASHPKKN; -.
DR   PhylomeDB; Q55BP0; -.
DR   PRO; PR:Q55BP0; -.
DR   Proteomes; UP000002195; Chromosome 1.
DR   GO; GO:0000786; C:nucleosome; IEA:UniProtKB-KW.
DR   GO; GO:0005634; C:nucleus; IDA:dictyBase.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0046982; F:protein heterodimerization activity; IEA:InterPro.
DR   GO; GO:0030527; F:structural constituent of chromatin; IEA:InterPro.
DR   Gene3D; 1.10.20.10; -; 1.
DR   InterPro; IPR009072; Histone-fold.
DR   InterPro; IPR007125; Histone_H2A/H2B/H3.
DR   InterPro; IPR000164; Histone_H3/CENP-A.
DR   PANTHER; PTHR11426; PTHR11426; 1.
DR   Pfam; PF00125; Histone; 1.
DR   PRINTS; PR00622; HISTONEH3.
DR   SMART; SM00428; H3; 1.
DR   SUPFAM; SSF47113; SSF47113; 1.
DR   PROSITE; PS00959; HISTONE_H3_2; 1.
PE   1: Evidence at protein level;
KW   Acetylation; Chromosome; Direct protein sequencing; DNA-binding;
KW   Methylation; Nucleosome core; Nucleus; Phosphoprotein; Reference proteome.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0000250"
FT   CHAIN           2..136
FT                   /note="Histone H3.3 type c"
FT                   /id="PRO_0000389162"
FT   REGION          1..30
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOD_RES         5
FT                   /note="N6,N6,N6-trimethyllysine; by set1; alternate"
FT                   /evidence="ECO:0000269|PubMed:16469305"
FT   MOD_RES         5
FT                   /note="N6,N6-dimethyllysine; by set1; alternate"
FT                   /evidence="ECO:0000269|PubMed:16469305"
FT   MOD_RES         5
FT                   /note="N6-acetyllysine; alternate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         5
FT                   /note="N6-methyllysine; by set1; alternate"
FT                   /evidence="ECO:0000269|PubMed:16469305"
FT   MOD_RES         10
FT                   /note="N6,N6,N6-trimethyllysine; alternate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         10
FT                   /note="N6,N6-dimethyllysine; alternate"
FT                   /evidence="ECO:0000269|PubMed:16524908"
FT   MOD_RES         10
FT                   /note="N6-acetyllysine; alternate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         10
FT                   /note="N6-methyllysine; alternate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         11
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         15
FT                   /note="N6-acetyllysine"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         19
FT                   /note="N6-acetyllysine; alternate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         19
FT                   /note="N6-methyllysine; alternate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         24
FT                   /note="N6-acetyllysine; alternate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         24
FT                   /note="N6-methyllysine; alternate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         37
FT                   /note="N6,N6,N6-trimethyllysine; alternate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         37
FT                   /note="N6,N6-dimethyllysine; alternate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         37
FT                   /note="N6-acetyllysine; alternate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         37
FT                   /note="N6-methyllysine; alternate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         57
FT                   /note="N6-acetyllysine"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         80
FT                   /note="N6,N6,N6-trimethyllysine; alternate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         80
FT                   /note="N6,N6-dimethyllysine; alternate"
FT                   /evidence="ECO:0000269|PubMed:21187070"
FT   MOD_RES         80
FT                   /note="N6-methyllysine; alternate"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   136 AA;  15601 MW;  93BA28E20910424A CRC64;
     MARTKQTARK STGAKVPRKH LSSKSSFPSK PVNEVLKKTH RFRPGTVALR EIRRYQKSSD
     LLIKKLPFQR LVREIAQEFK TDLRFQAAAI EALQEATEAY LVGLFEDTNL CAIHAKRVTI
     MVKDIQLARR IRGERA
 
 
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