H33B_DICDI
ID H33B_DICDI Reviewed; 136 AA.
AC Q55BN9;
DT 24-NOV-2009, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=Histone H3.3 type b;
DE AltName: Full=Histone 3, variant 3 type b;
GN Name=H3b; ORFNames=DDB_G0270838;
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 IDENTIFICATION.
RX PubMed=17878305; DOI=10.1073/pnas.0705996104;
RA Van Driessche N., Alexander H., Min J., Kuspa A., Alexander S.,
RA Shaulsky G.;
RT "Global transcriptional responses to cisplatin in Dictyostelium discoideum
RT identify potential drug targets.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:15406-15411(2007).
RN [6]
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 and H3K27 are linked to gene repression
CC (By 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; EAL72769.1; -; Genomic_DNA.
DR RefSeq; XP_646792.1; XM_641700.1.
DR AlphaFoldDB; Q55BN9; -.
DR SMR; Q55BN9; -.
DR STRING; 44689.DDB0216291; -.
DR iPTMnet; Q55BN9; -.
DR PaxDb; Q55BN9; -.
DR EnsemblProtists; EAL72769; EAL72769; DDB_G0270838.
DR GeneID; 8617765; -.
DR KEGG; ddi:DDB_G0270838; -.
DR dictyBase; DDB_G0270838; H3b.
DR eggNOG; KOG1745; Eukaryota.
DR HOGENOM; CLU_078295_4_0_1; -.
DR InParanoid; Q55BN9; -.
DR OMA; ASEAYYL; -.
DR PhylomeDB; Q55BN9; -.
DR PRO; PR:Q55BN9; -.
DR Proteomes; UP000002195; Chromosome 1.
DR GO; GO:0000786; C:nucleosome; IEA:UniProtKB-KW.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
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 GO; GO:0046689; P:response to mercury ion; IDA:dictyBase.
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 b"
FT /id="PRO_0000389161"
FT REGION 1..41
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 28
FT /note="N6,N6,N6-trimethyllysine; alternate"
FT /evidence="ECO:0000250"
FT MOD_RES 28
FT /note="N6,N6-dimethyllysine; alternate"
FT /evidence="ECO:0000250"
FT MOD_RES 28
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250"
FT MOD_RES 28
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; 15560 MW; 87A13694F0FE2C98 CRC64;
MARTKQTARK STGAKVPRKH LGNKSSQKSF PSTQGLKKTH RFRPGTVALR EIRRYQKSSE
LLIKKLPFQR LVREIAQEFK TDLRFQAAAI QALQEASEAY LVGLFEDTNL CAIHAKRVTI
MVKDIQLARR IRGERA
