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Probable histone-binding protein lin-53 (Abnormal cell lineage protein 53) (Synthetic multivulva protein p48)

 LIN53_CAEEL             Reviewed;         417 AA.
P90916; A2JDY3; O62411;
15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
07-FEB-2006, sequence version 2.
25-OCT-2017, entry version 127.
RecName: Full=Probable histone-binding protein lin-53;
AltName: Full=Abnormal cell lineage protein 53;
AltName: Full=Synthetic multivulva protein p48;
Name=lin-53 {ECO:0000312|WormBase:K07A1.12};
Synonyms=rba-2 {ECO:0000312|WormBase:K07A1.12};
ORFNames=K07A1.12 {ECO:0000312|WormBase:K07A1.12};
Caenorhabditis elegans.
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis.
NCBI_TaxID=6239;
[1]
NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INTERACTION WITH LIN-35 AND
HDA-1, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, DISRUPTION
PHENOTYPE, AND MUTAGENESIS OF LEU-292.
PubMed=9875852; DOI=10.1016/S0092-8674(00)81722-5;
Lu X., Horvitz H.R.;
"lin-35 and lin-53, two genes that antagonize a C. elegans Ras
pathway, encode proteins similar to Rb and its binding protein
RbAp48.";
Cell 95:981-991(1998).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Bristol N2;
PubMed=9851916; DOI=10.1126/science.282.5396.2012;
The C. elegans sequencing consortium;
"Genome sequence of the nematode C. elegans: a platform for
investigating biology.";
Science 282:2012-2018(1998).
[3]
FUNCTION.
PubMed=10704416; DOI=10.1016/S0960-9822(00)00343-2;
Solari F., Ahringer J.;
"NURD-complex genes antagonise Ras-induced vulval development in
Caenorhabditis elegans.";
Curr. Biol. 10:223-226(2000).
[4]
FUNCTION, IDENTIFICATION IN THE DRM COMPLEX, IDENTIFICATION IN COMPLEX
WITH HDA-1, AND DISRUPTION PHENOTYPE.
PubMed=17075059; DOI=10.1073/pnas.0608461103;
Harrison M.M., Ceol C.J., Lu X., Horvitz H.R.;
"Some C. elegans class B synthetic multivulva proteins encode a
conserved LIN-35 Rb-containing complex distinct from a NuRD-like
complex.";
Proc. Natl. Acad. Sci. U.S.A. 103:16782-16787(2006).
[5]
DISRUPTION PHENOTYPE.
PubMed=17237514; DOI=10.1534/genetics.106.068148;
Reddien P.W., Andersen E.C., Huang M.C., Horvitz H.R.;
"DPL-1 DP, LIN-35 Rb and EFL-1 E2F act with the MCD-1 zinc-finger
protein to promote programmed cell death in Caenorhabditis elegans.";
Genetics 175:1719-1733(2007).
[6]
FUNCTION, INTERACTION WITH HCP-3, SUBCELLULAR LOCATION, AND DISRUPTION
PHENOTYPE.
PubMed=26904949; DOI=10.1016/j.celrep.2016.01.065;
Lee B.C., Lin Z., Yuen K.W.;
"RbAp46/48(LIN-53) is required for holocentromere assembly in
Caenorhabditis elegans.";
Cell Rep. 14:1819-1828(2016).
-!- FUNCTION: Core histone-binding subunit that may target chromatin
assembly factors, chromatin remodeling factors and histone
deacetylases to their histone substrates in a manner that is
regulated by nucleosomal DNA (By similarity). Required for hcp-3
and his-1 stabilization, localization of hcp-3 to centromeres and
for proper chromosome segregation (PubMed:26904949). Synthetic
multivulva class B (synMuvB) protein (PubMed:9875852). SynMuvB
proteins are required to repress the induction of vulval
development by Ras signaling and probably act by forming the
multiprotein DRM complex that represses transcription
(PubMed:9875852, PubMed:10704416, PubMed:17075059).
{ECO:0000250|UniProtKB:Q09028, ECO:0000269|PubMed:10704416,
ECO:0000269|PubMed:17075059, ECO:0000269|PubMed:26904949,
ECO:0000269|PubMed:9875852}.
-!- SUBUNIT: Binds directly to helix 1 of the histone fold of histone
H4, a region that is not accessible when H4 is in chromatin (By
similarity). Probable component of a NuRD-like complex, composed
of at least lin-53 and hda-1 (PubMed:17075059). Interacts with
lin-35 (PubMed:9875852). Interacts with hda-1; the interaction is
direct (PubMed:9875852, PubMed:17075059). Component of the DRM
complex, at least composed of lin-9, lin-35, lin-37, lin-52, lin-
53, lin-54- dpl-1 and efl-1 (PubMed:17075059). Interacts with hcp-
3 (PubMed:26904949). {ECO:0000250|UniProtKB:Q24572,
ECO:0000269|PubMed:17075059, ECO:0000269|PubMed:26904949,
ECO:0000269|PubMed:9875852, ECO:0000305}.
-!- INTERACTION:
Q23482:lin-37; NbExp=5; IntAct=EBI-324314, EBI-324325;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:9875852}.
Chromosome, centromere {ECO:0000269|PubMed:26904949}.
Note=Localizes to centromeres during metaphase. Requires hcp-3 and
knl-2 for nuclear and centromere localization.
{ECO:0000269|PubMed:26904949}.
-!- DEVELOPMENTAL STAGE: Ubiquitously expressed in embryos and newly
hatched larvae. Expressed in all P(3-8).p vulval precursor cells
at the time of vulval induction and until after all cell divisions
and vulval morphogenesis are complete.
{ECO:0000269|PubMed:9875852}.
-!- DISRUPTION PHENOTYPE: Decreased protein levels of DRM complex
components including lin-9, lin-37, lin-52 and lin-54
(PubMed:17075059). Double knockout with the programmed cell death
regulator mcd-1 results slow larval growth (PubMed:17237514).
RNAi-mediated knockdown results in embryonic lethality
(PubMed:9875852). RNAi-mediated knockdown leads to a reduction of
hcp-3 and his-1 protein levels and to a depletion of hcp-3 on
centromeres, a reduction of H3K27me3 levels on metaphase
chromosomes and to chromosome segregation defects
(PubMed:26904949). {ECO:0000269|PubMed:17075059,
ECO:0000269|PubMed:17237514, ECO:0000269|PubMed:26904949,
ECO:0000269|PubMed:9875852}.
-!- SIMILARITY: Belongs to the WD repeat RBAP46/RBAP48/MSI1 family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AF116530; AAD05571.1; -; mRNA.
EMBL; Z81097; CAB03178.1; -; Genomic_DNA.
EMBL; AL023833; CAB03178.1; JOINED; Genomic_DNA.
PIR; T23391; T23391.
RefSeq; NP_492552.1; NM_060151.6.
UniGene; Cel.19610; -.
ProteinModelPortal; P90916; -.
SMR; P90916; -.
BioGrid; 38227; 6.
DIP; DIP-24440N; -.
IntAct; P90916; 9.
MINT; MINT-114323; -.
STRING; 6239.K07A1.12.2; -.
EPD; P90916; -.
PaxDb; P90916; -.
PeptideAtlas; P90916; -.
PRIDE; P90916; -.
EnsemblMetazoa; K07A1.12; K07A1.12; WBGene00003036.
GeneID; 172802; -.
KEGG; cel:CELE_K07A1.12; -.
UCSC; K07A1.12.1; c. elegans.
CTD; 172802; -.
WormBase; K07A1.12; CE16234; WBGene00003036; lin-53.
eggNOG; KOG0264; Eukaryota.
eggNOG; ENOG410XNU9; LUCA.
GeneTree; ENSGT00570000079069; -.
HOGENOM; HOG000160330; -.
InParanoid; P90916; -.
KO; K10752; -.
OMA; VAWHVLH; -.
OrthoDB; EOG091G0A20; -.
PhylomeDB; P90916; -.
Reactome; R-CEL-2559580; Oxidative Stress Induced Senescence.
Reactome; R-CEL-3214847; HATs acetylate histones.
Reactome; R-CEL-8943724; Regulation of PTEN gene transcription.
Reactome; R-CEL-8951664; Neddylation.
SignaLink; P90916; -.
PRO; PR:P90916; -.
Proteomes; UP000001940; Chromosome I.
Bgee; WBGene00003036; -.
GO; GO:0000775; C:chromosome, centromeric region; IEA:UniProtKB-SubCell.
GO; GO:0070176; C:DRM complex; IDA:UniProtKB.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0017053; C:transcriptional repressor complex; IDA:UniProtKB.
GO; GO:0042826; F:histone deacetylase binding; IPI:UniProtKB.
GO; GO:0001708; P:cell fate specification; IMP:WormBase.
GO; GO:0016569; P:covalent chromatin modification; IEA:UniProtKB-KW.
GO; GO:0009792; P:embryo development ending in birth or egg hatching; IMP:UniProtKB.
GO; GO:0048557; P:embryonic digestive tract morphogenesis; IGI:WormBase.
GO; GO:0040035; P:hermaphrodite genitalia development; IMP:UniProtKB.
GO; GO:0045892; P:negative regulation of transcription, DNA-templated; NAS:UniProtKB.
GO; GO:0045138; P:nematode male tail tip morphogenesis; IMP:WormBase.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
Gene3D; 2.130.10.10; -; 1.
InterPro; IPR020472; G-protein_beta_WD-40_rep.
InterPro; IPR022052; Histone-bd_RBBP4_N.
InterPro; IPR015943; WD40/YVTN_repeat-like_dom.
InterPro; IPR001680; WD40_repeat.
InterPro; IPR019775; WD40_repeat_CS.
InterPro; IPR017986; WD40_repeat_dom.
InterPro; IPR036322; WD40_repeat_dom_sf.
Pfam; PF12265; CAF1C_H4-bd; 1.
Pfam; PF00400; WD40; 5.
PRINTS; PR00320; GPROTEINBRPT.
SMART; SM00320; WD40; 6.
SUPFAM; SSF50978; SSF50978; 1.
PROSITE; PS00678; WD_REPEATS_1; 2.
PROSITE; PS50082; WD_REPEATS_2; 5.
PROSITE; PS50294; WD_REPEATS_REGION; 1.
1: Evidence at protein level;
Centromere; Chromatin regulator; Chromosome; Complete proteome;
Developmental protein; Nucleus; Reference proteome; Repeat; Repressor;
Transcription; Transcription regulation; WD repeat.
CHAIN 1 417 Probable histone-binding protein lin-53.
/FTId=PRO_0000051059.
REPEAT 118 158 WD 1.
REPEAT 170 210 WD 2.
REPEAT 220 260 WD 3.
REPEAT 263 303 WD 4.
REPEAT 307 347 WD 5.
REPEAT 364 404 WD 6.
MUTAGEN 292 292 L->F: In semidominant alleles n883 and
n2978; causes development of multiple
vulvas. {ECO:0000269|PubMed:9875852}.
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


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