LIN53_CAEEL
ID LIN53_CAEEL Reviewed; 417 AA.
AC P90916; A2JDY3; O62411;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 07-FEB-2006, sequence version 2.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=Probable histone-binding protein lin-53;
DE AltName: Full=Abnormal cell lineage protein 53;
DE AltName: Full=Synthetic multivulva protein p48;
GN Name=lin-53 {ECO:0000312|WormBase:K07A1.12};
GN Synonyms=rba-2 {ECO:0000312|WormBase:K07A1.12};
GN ORFNames=K07A1.12 {ECO:0000312|WormBase:K07A1.12};
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INTERACTION WITH LIN-35 AND HDA-1,
RP SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE, AND
RP MUTAGENESIS OF LEU-292.
RX PubMed=9875852; DOI=10.1016/s0092-8674(00)81722-5;
RA Lu X., Horvitz H.R.;
RT "lin-35 and lin-53, two genes that antagonize a C. elegans Ras pathway,
RT encode proteins similar to Rb and its binding protein RbAp48.";
RL Cell 95:981-991(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2;
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
RN [3]
RP FUNCTION.
RX PubMed=10704416; DOI=10.1016/s0960-9822(00)00343-2;
RA Solari F., Ahringer J.;
RT "NURD-complex genes antagonise Ras-induced vulval development in
RT Caenorhabditis elegans.";
RL Curr. Biol. 10:223-226(2000).
RN [4]
RP FUNCTION, IDENTIFICATION IN THE DRM COMPLEX, IDENTIFICATION IN COMPLEX WITH
RP HDA-1, AND DISRUPTION PHENOTYPE.
RX PubMed=17075059; DOI=10.1073/pnas.0608461103;
RA Harrison M.M., Ceol C.J., Lu X., Horvitz H.R.;
RT "Some C. elegans class B synthetic multivulva proteins encode a conserved
RT LIN-35 Rb-containing complex distinct from a NuRD-like complex.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:16782-16787(2006).
RN [5]
RP DISRUPTION PHENOTYPE.
RX PubMed=17237514; DOI=10.1534/genetics.106.068148;
RA Reddien P.W., Andersen E.C., Huang M.C., Horvitz H.R.;
RT "DPL-1 DP, LIN-35 Rb and EFL-1 E2F act with the MCD-1 zinc-finger protein
RT to promote programmed cell death in Caenorhabditis elegans.";
RL Genetics 175:1719-1733(2007).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=25446273; DOI=10.1016/j.ydbio.2014.10.014;
RA Krueger A.V., Jelier R., Dzyubachyk O., Zimmerman T., Meijering E.,
RA Lehner B.;
RT "Comprehensive single cell-resolution analysis of the role of chromatin
RT regulators in early C. elegans embryogenesis.";
RL Dev. Biol. 398:153-162(2015).
RN [7]
RP FUNCTION, INTERACTION WITH HCP-3, SUBCELLULAR LOCATION, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=26904949; DOI=10.1016/j.celrep.2016.01.065;
RA Lee B.C., Lin Z., Yuen K.W.;
RT "RbAp46/48(LIN-53) is required for holocentromere assembly in
RT Caenorhabditis elegans.";
RL Cell Rep. 14:1819-1828(2016).
CC -!- FUNCTION: Core histone-binding subunit that may target chromatin
CC assembly factors, chromatin remodeling factors and histone deacetylases
CC to their histone substrates in a manner that is regulated by
CC nucleosomal DNA (By similarity). Required for hcp-3 and his-1
CC stabilization, localization of hcp-3 to centromeres and for proper
CC chromosome segregation (PubMed:25446273, PubMed:26904949). Synthetic
CC multivulva class B (synMuvB) protein (PubMed:9875852). SynMuvB proteins
CC are required to repress the induction of vulval development by Ras
CC signaling and probably act by forming the multiprotein DRM complex that
CC represses transcription (PubMed:10704416, PubMed:17075059,
CC PubMed:9875852). {ECO:0000250|UniProtKB:Q09028,
CC ECO:0000269|PubMed:10704416, ECO:0000269|PubMed:17075059,
CC ECO:0000269|PubMed:25446273, ECO:0000269|PubMed:26904949,
CC ECO:0000269|PubMed:9875852}.
CC -!- SUBUNIT: Binds directly to helix 1 of the histone fold of histone H4, a
CC region that is not accessible when H4 is in chromatin (By similarity).
CC Probable component of a NuRD-like complex, composed of at least lin-53
CC and hda-1 (PubMed:17075059). Interacts with lin-35 (PubMed:9875852).
CC Interacts with hda-1; the interaction is direct (PubMed:9875852,
CC PubMed:17075059). Component of the DRM complex, at least composed of
CC lin-9, lin-35, lin-37, lin-52, lin-53, lin-54- dpl-1 and efl-1
CC (PubMed:17075059). Interacts with hcp-3 (PubMed:26904949).
CC {ECO:0000250|UniProtKB:Q24572, ECO:0000269|PubMed:17075059,
CC ECO:0000269|PubMed:26904949, ECO:0000269|PubMed:9875852, ECO:0000305}.
CC -!- INTERACTION:
CC P90916; Q23482: lin-37; NbExp=5; IntAct=EBI-324314, EBI-324325;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:9875852}. Chromosome,
CC centromere {ECO:0000269|PubMed:26904949}. Note=Localizes to centromeres
CC during metaphase. Requires hcp-3 and knl-2 for nuclear and centromere
CC localization. {ECO:0000269|PubMed:26904949}.
CC -!- DEVELOPMENTAL STAGE: Ubiquitously expressed in embryos and newly
CC hatched larvae. Expressed in all P(3-8).p vulval precursor cells at the
CC time of vulval induction and until after all cell divisions and vulval
CC morphogenesis are complete. {ECO:0000269|PubMed:9875852}.
CC -!- DISRUPTION PHENOTYPE: Decreased protein levels of DRM complex
CC components including lin-9, lin-37, lin-52 and lin-54
CC (PubMed:17075059). Double knockout with the programmed cell death
CC regulator mcd-1 results slow larval growth (PubMed:17237514). RNAi-
CC mediated knockdown results in embryonic lethality (PubMed:9875852,
CC PubMed:26904949). RNAi-mediated knockdown leads to a reduction of hcp-3
CC and his-1 protein levels and to a depletion of hcp-3 on centromeres and
CC a reduction of H3K27me3 levels on metaphase chromosomes
CC (PubMed:26904949). RNAi-mediated knockdown results in chromosome
CC segregation defects during mitosis (PubMed:25446273, PubMed:26904949).
CC {ECO:0000269|PubMed:17075059, ECO:0000269|PubMed:17237514,
CC ECO:0000269|PubMed:25446273, ECO:0000269|PubMed:26904949,
CC ECO:0000269|PubMed:9875852}.
CC -!- SIMILARITY: Belongs to the WD repeat RBAP46/RBAP48/MSI1 family.
CC {ECO:0000305}.
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DR EMBL; AF116530; AAD05571.1; -; mRNA.
DR EMBL; Z81097; CAB03178.1; -; Genomic_DNA.
DR EMBL; AL023833; CAB03178.1; JOINED; Genomic_DNA.
DR PIR; T23391; T23391.
DR RefSeq; NP_492552.1; NM_060151.6.
DR AlphaFoldDB; P90916; -.
DR SMR; P90916; -.
DR BioGRID; 38227; 479.
DR ComplexPortal; CPX-1100; DRM complex.
DR DIP; DIP-24440N; -.
DR IntAct; P90916; 10.
DR MINT; P90916; -.
DR STRING; 6239.K07A1.12; -.
DR EPD; P90916; -.
DR PaxDb; P90916; -.
DR PeptideAtlas; P90916; -.
DR EnsemblMetazoa; K07A1.12.1; K07A1.12.1; WBGene00003036.
DR GeneID; 172802; -.
DR KEGG; cel:CELE_K07A1.12; -.
DR UCSC; K07A1.12.1; c. elegans.
DR CTD; 172802; -.
DR WormBase; K07A1.12; CE16234; WBGene00003036; lin-53.
DR eggNOG; KOG0264; Eukaryota.
DR GeneTree; ENSGT00940000154748; -.
DR HOGENOM; CLU_020445_3_1_1; -.
DR InParanoid; P90916; -.
DR OMA; PITDFNW; -.
DR OrthoDB; 831322at2759; -.
DR PhylomeDB; P90916; -.
DR Reactome; R-CEL-1538133; G0 and Early G1.
DR Reactome; R-CEL-212300; PRC2 methylates histones and DNA.
DR Reactome; R-CEL-2559580; Oxidative Stress Induced Senescence.
DR Reactome; R-CEL-3214815; HDACs deacetylate histones.
DR Reactome; R-CEL-3214847; HATs acetylate histones.
DR Reactome; R-CEL-3214858; RMTs methylate histone arginines.
DR Reactome; R-CEL-8943724; Regulation of PTEN gene transcription.
DR Reactome; R-CEL-8951664; Neddylation.
DR PRO; PR:P90916; -.
DR Proteomes; UP000001940; Chromosome I.
DR Bgee; WBGene00003036; Expressed in embryo and 4 other tissues.
DR GO; GO:0000775; C:chromosome, centromeric region; IEA:UniProtKB-SubCell.
DR GO; GO:0070176; C:DRM complex; IDA:UniProtKB.
DR GO; GO:0035098; C:ESC/E(Z) complex; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0016581; C:NuRD complex; IMP:UniProtKB.
DR GO; GO:0017053; C:transcription repressor complex; IDA:UniProtKB.
DR GO; GO:0042393; F:histone binding; IBA:GO_Central.
DR GO; GO:0042826; F:histone deacetylase binding; IPI:UniProtKB.
DR GO; GO:0001708; P:cell fate specification; IMP:WormBase.
DR GO; GO:0006325; P:chromatin organization; IMP:UniProtKB.
DR GO; GO:0006338; P:chromatin remodeling; IBA:GO_Central.
DR GO; GO:0009792; P:embryo development ending in birth or egg hatching; IMP:UniProtKB.
DR GO; GO:0048557; P:embryonic digestive tract morphogenesis; IGI:WormBase.
DR GO; GO:0040035; P:hermaphrodite genitalia development; IMP:UniProtKB.
DR GO; GO:0016575; P:histone deacetylation; IBA:GO_Central.
DR GO; GO:0034514; P:mitochondrial unfolded protein response; IMP:UniProtKB.
DR GO; GO:1903507; P:negative regulation of nucleic acid-templated transcription; IC:ComplexPortal.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; NAS:UniProtKB.
DR GO; GO:0040027; P:negative regulation of vulval development; IDA:ComplexPortal.
DR GO; GO:0045138; P:nematode male tail tip morphogenesis; IMP:WormBase.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IBA:GO_Central.
DR Gene3D; 2.130.10.10; -; 1.
DR InterPro; IPR020472; G-protein_beta_WD-40_rep.
DR InterPro; IPR022052; Histone-bd_RBBP4_N.
DR InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR InterPro; IPR001680; WD40_repeat.
DR InterPro; IPR019775; WD40_repeat_CS.
DR InterPro; IPR036322; WD40_repeat_dom_sf.
DR Pfam; PF12265; CAF1C_H4-bd; 1.
DR Pfam; PF00400; WD40; 5.
DR PRINTS; PR00320; GPROTEINBRPT.
DR SMART; SM00320; WD40; 6.
DR SUPFAM; SSF50978; SSF50978; 1.
DR PROSITE; PS00678; WD_REPEATS_1; 2.
DR PROSITE; PS50082; WD_REPEATS_2; 5.
DR PROSITE; PS50294; WD_REPEATS_REGION; 1.
PE 1: Evidence at protein level;
KW Centromere; Chromatin regulator; Chromosome; Developmental protein;
KW Nucleus; Reference proteome; Repeat; Repressor; Transcription;
KW Transcription regulation; WD repeat.
FT CHAIN 1..417
FT /note="Probable histone-binding protein lin-53"
FT /id="PRO_0000051059"
FT REPEAT 118..158
FT /note="WD 1"
FT REPEAT 170..210
FT /note="WD 2"
FT REPEAT 220..260
FT /note="WD 3"
FT REPEAT 263..303
FT /note="WD 4"
FT REPEAT 307..347
FT /note="WD 5"
FT REPEAT 364..404
FT /note="WD 6"
FT MUTAGEN 292
FT /note="L->F: In semidominant alleles n883 and n2978; causes
FT development of multiple vulvas."
FT /evidence="ECO:0000269|PubMed:9875852"
SQ SEQUENCE 417 AA; 47166 MW; AE388CFB048CE51B CRC64;
MATLEDGTSE DRVANDEYKI WKKNTPFLYD LVMTHALEWP SLSVQWLPDV AKDNSDHTIH
RLILGTHTSD EQNHLLISKI CMPTDDAQFD ASRYDTERSE YGGFGAVNGK VEPDIRINHE
GEVNRARYMP QKSNIIATKS PHADVYIFDY LKHSAVPRDN TFNPLIRLKG HTKEGYGLSW
NPNKEGLILS ASDDQTVCHW DINANQNVAG ELQAKDVFKG HESVVEDVAW HVLHDGVFGS
VGDDKKLLIW DVRTSTPGHC IDAHSAEVNC LAFNPYSEFI LATGSADKTV ALWDLRNLRM
KLHSFESHRD EIFQVQWSPH NETILASSGT DKRLHVWDLS KIGEDQSAED AEDGPPELLF
IHGGHTAKIS DFSWNPNEPW VVCSVSEDNI LQVWQMADNI YNEVDEETPA DVVERQQ
