LIN54_CAEEL
ID LIN54_CAEEL Reviewed; 435 AA.
AC Q95QD7; O62295;
DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=Protein lin-54;
DE AltName: Full=Abnormal cell lineage protein 54;
GN Name=lin-54 {ECO:0000312|WormBase:JC8.6a};
GN ORFNames=JC8.6 {ECO:0000312|WormBase:JC8.6a};
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 [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 [2]
RP FUNCTION, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, IDENTIFICATION IN THE
RP DRM COMPLEX, 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 [3]
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 [4]
RP DISRUPTION PHENOTYPE.
RX PubMed=27650246; DOI=10.1038/srep33884;
RA Al-Amin M., Min H., Shim Y.H., Kawasaki I.;
RT "Somatically expressed germ-granule components, PGL-1 and PGL-3, repress
RT programmed cell death in C. elegans.";
RL Sci. Rep. 6:33884-33884(2016).
CC -!- FUNCTION: Synthetic multivulva class B (synMuvB) protein. SynMuvB
CC proteins are required to repress the induction of vulval development by
CC Ras signaling and probably act by forming the multiprotein DRM complex
CC that repress transcription. {ECO:0000269|PubMed:17075059}.
CC -!- SUBUNIT: Component of the DRM complex, at least composed of lin-9, lin-
CC 35, lin-37, lin-52, lin-53, lin-54- dpl-1 and efl-1.
CC {ECO:0000269|PubMed:17075059}.
CC -!- INTERACTION:
CC Q95QD7; Q23482: lin-37; NbExp=6; IntAct=EBI-6762766, EBI-324325;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:17075059}. Chromosome
CC {ECO:0000269|PubMed:17075059}. Note=Localizes to condensed chromosomes
CC during the diakinesis phase of meiosis. {ECO:0000269|PubMed:17075059}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=a {ECO:0000312|WormBase:JC8.6a};
CC IsoId=Q95QD7-1; Sequence=Displayed;
CC Name=b {ECO:0000312|WormBase:JC8.6b};
CC IsoId=Q95QD7-2; Sequence=VSP_034280, VSP_034281;
CC -!- DEVELOPMENTAL STAGE: Widely expressed. Present in most cells from the
CC embryo through the adulthood. {ECO:0000269|PubMed:17075059}.
CC -!- DOMAIN: The CRC domain mediates DNA-binding. It contains two CXC
CC subdomains (joined by a flexible linker) which are both required for
CC efficient association with target DNA. Each CXC subdomain coordinates
CC three Zn(2+) ions. {ECO:0000250|UniProtKB:Q6MZP7}.
CC -!- DISRUPTION PHENOTYPE: Decreased protein levels of DRM complex
CC components including lin-9 and lin-52 (PubMed:17075059). Double
CC knockout with the programmed cell death regulator mcd-1 results in 100%
CC lethality during the L1 stage of larval development (PubMed:17237514).
CC RNAi-mediated knockdown in a ced-1 mutant background results in reduced
CC somatic cell apoptosis (PubMed:27650246). {ECO:0000269|PubMed:17075059,
CC ECO:0000269|PubMed:17237514, ECO:0000269|PubMed:27650246}.
CC -!- SIMILARITY: Belongs to the lin-54 family. {ECO:0000305}.
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DR EMBL; Z82274; CAB05229.1; -; Genomic_DNA.
DR EMBL; Z82274; CAB05228.1; -; Genomic_DNA.
DR PIR; T23152; T23152.
DR RefSeq; NP_502544.1; NM_070143.3. [Q95QD7-1]
DR RefSeq; NP_502545.1; NM_070144.3. [Q95QD7-2]
DR AlphaFoldDB; Q95QD7; -.
DR SMR; Q95QD7; -.
DR BioGRID; 43369; 3.
DR ComplexPortal; CPX-1100; DRM complex.
DR DIP; DIP-61306N; -.
DR IntAct; Q95QD7; 5.
DR STRING; 6239.JC8.6a; -.
DR EPD; Q95QD7; -.
DR PaxDb; Q95QD7; -.
DR EnsemblMetazoa; JC8.6a.1; JC8.6a.1; WBGene00003037. [Q95QD7-1]
DR EnsemblMetazoa; JC8.6b.1; JC8.6b.1; WBGene00003037. [Q95QD7-2]
DR GeneID; 178280; -.
DR KEGG; cel:CELE_JC8.6; -.
DR UCSC; JC8.6a; c. elegans. [Q95QD7-1]
DR CTD; 178280; -.
DR WormBase; JC8.6a; CE17989; WBGene00003037; lin-54. [Q95QD7-1]
DR WormBase; JC8.6b; CE17990; WBGene00003037; lin-54. [Q95QD7-2]
DR eggNOG; KOG1171; Eukaryota.
DR GeneTree; ENSGT00940000168375; -.
DR InParanoid; Q95QD7; -.
DR OMA; KDCHNNI; -.
DR OrthoDB; 943786at2759; -.
DR PhylomeDB; Q95QD7; -.
DR Reactome; R-CEL-1538133; G0 and Early G1.
DR PRO; PR:Q95QD7; -.
DR Proteomes; UP000001940; Chromosome IV.
DR Bgee; WBGene00003037; Expressed in germ line (C elegans) and 4 other tissues.
DR ExpressionAtlas; Q95QD7; baseline and differential.
DR GO; GO:0030849; C:autosome; IDA:WormBase.
DR GO; GO:0000794; C:condensed nuclear chromosome; IDA:WormBase.
DR GO; GO:0070176; C:DRM complex; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:WormBase.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000977; F:RNA polymerase II transcription regulatory region sequence-specific DNA binding; IDA:WormBase.
DR GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR GO; GO:1903507; P:negative regulation of nucleic acid-templated transcription; IC:ComplexPortal.
DR GO; GO:0040027; P:negative regulation of vulval development; IDA:ComplexPortal.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; ISS:WormBase.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IBA:GO_Central.
DR InterPro; IPR005172; CRC.
DR InterPro; IPR028307; Lin-54_fam.
DR InterPro; IPR033467; Tesmin/TSO1-like_CXC.
DR PANTHER; PTHR12446; PTHR12446; 1.
DR Pfam; PF03638; TCR; 2.
DR SMART; SM01114; CXC; 2.
DR PROSITE; PS51634; CRC; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cell cycle; Chromosome; DNA-binding; Metal-binding;
KW Nucleus; Reference proteome; Repressor; Transcription;
KW Transcription regulation; Zinc.
FT CHAIN 1..435
FT /note="Protein lin-54"
FT /id="PRO_0000341395"
FT DOMAIN 173..288
FT /note="CRC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00971"
FT REGION 73..136
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 175..188
FT /note="DNA-binding"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT REGION 235..250
FT /note="Linker"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT REGION 253..266
FT /note="DNA-binding"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT REGION 415..435
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 98..128
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 177
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 177
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 179
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 184
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 184
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 189
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 191
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 198
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 198
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 201
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 203
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 206
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 253
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 253
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="5"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 255
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 260
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 260
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="6"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 265
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 267
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="5"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 274
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="5"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 274
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="6"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 278
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="5"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 280
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="6"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT BINDING 283
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="6"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT SITE 188
FT /note="Critical for interaction with target DNA"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT SITE 226
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT SITE 264
FT /note="Critical for interaction with target DNA"
FT /evidence="ECO:0000250|UniProtKB:Q6MZP7"
FT VAR_SEQ 43..45
FT /note="Missing (in isoform b)"
FT /evidence="ECO:0000305"
FT /id="VSP_034280"
FT VAR_SEQ 95..97
FT /note="Missing (in isoform b)"
FT /evidence="ECO:0000305"
FT /id="VSP_034281"
SQ SEQUENCE 435 AA; 49109 MW; 7629A5C749D25A5D CRC64;
MNQGEIVYQD DDDYYDESEI YDNYEEGAEF IEVNGQLVPH NPNLQAQQNR PGTSSMIQQH
NRSMEVNQGL VKDEPIDTSS HRVYVPPPRP VQRKLFQPGP STPGSSQYTV RNLSNLSGSP
SMYDRQPASL PRTVQPMGLE MGNSEQRKVY IDMKDHVSHI RLKTKKKVFA PGQRKPCNCT
KSQCLKLYCD CFANGEFCRD CNCKDCHNNI EYDSQRSKAI RQSLERNPNA FKPKIGIARG
GITDIERLHQ KGCHCKKSGC LKNYCECYEA KVPCTDRCKC KGCQNTETYR MTRYKNSGGA
VSNTNALMSL TNASSTATPD SGPGSVVTDE HGDDYEDMLL SHKPKVEMDP RRFPWYYMTD
EVVEAATMCM VAQAEEALNY EKVQTEDEKL INMEKLVLRE FGRCLEQMIT NTTELTQDLD
AAPTDDIPGP STSTS
