ID LYAR_RAT Reviewed; 386 AA.
AC Q6AYK5;
DT 19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 13-SEP-2004, sequence version 1.
DT 27-MAR-2024, entry version 123.
DE RecName: Full=Cell growth-regulating nucleolar protein;
GN Name=Lyar;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Testis;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [2]
RP TISSUE SPECIFICITY.
RX PubMed=24990247; DOI=10.1007/s11010-014-2128-x;
RA Yonezawa K., Sugihara Y., Oshima K., Matsuda T., Nadano D.;
RT "Lyar, a cell growth-regulating zinc finger protein, was identified to be
RT associated with cytoplasmic ribosomes in male germ and cancer cells.";
RL Mol. Cell. Biochem. 395:221-229(2014).
CC -!- FUNCTION: Plays a role in the maintenance of the appropriate processing
CC of 47S/45S pre-rRNA to 32S/30S pre-rRNAs and their subsequent
CC processing to produce 18S and 28S rRNAs. Also acts at the level of
CC transcription regulation. Along with PRMT5, binds embryonic globin
CC promoter (By similarity). Represses the expression of embryonic globin
CC Hbb-y gene (By similarity). In neuroblastoma cells, may also repress
CC the expression of oxidative stress genes, including CHAC1, HMOX1,
CC SLC7A11, ULBP1 and that encoding the small nucleolar RNA SNORD41.
CC Preferentially binds to a DNA motif containing 5'-GGTTAT-3' (By
CC similarity). Negatively regulates the antiviral innate immune response
CC by targeting IRF3 and impairing its DNA-binding activity (By
CC similarity). In addition, inhibits NF-kappa-B-mediated expression of
CC pro-inflammatory cytokines (By similarity). Stimulates phagocytosis of
CC photoreceptor outer segments by retinal pigment epithelial cells.
CC Prevents NCL self-cleavage, maintaining a normal steady-state level of
CC NCL protein in undifferentiated embryonic stem cells (ESCs), which in
CC turn is essential for ESC self-renewal (By similarity).
CC {ECO:0000250|UniProtKB:Q08288, ECO:0000250|UniProtKB:Q9NX58}.
CC -!- SUBUNIT: Interacts with PRMT5; this interaction is direct. Interacts
CC with GNL2 and RPL23A (By similarity). Interacts with nucleolin/NCL;
CC this interaction is direct (By similarity). Interacts with
CC phosphorylated IRF3; this interaction impairs IRF3 DNA-binding activity
CC (By similarity). {ECO:0000250|UniProtKB:Q08288,
CC ECO:0000250|UniProtKB:Q9NX58}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus
CC {ECO:0000250|UniProtKB:Q08288}. Cytoplasm
CC {ECO:0000269|PubMed:24990247}. Cell projection, cilium, photoreceptor
CC outer segment {ECO:0000250|UniProtKB:Q08288}. Note=Component of pre-
CC ribosomal particles, including pre-40S, pre-60S and pre-90S (By
CC similarity). Associated with cytoplasmic ribosomes, but not polysomes,
CC as a component of the 60S subunit (PubMed:24990247). In the retina,
CC predominantly expressed in photoreceptor outer segments. In the
CC nucleolus, colocalizes with nucleolin/NCL, therefore may reside in the
CC dense fibrillar component (DFC) (By similarity).
CC {ECO:0000250|UniProtKB:Q08288, ECO:0000250|UniProtKB:Q9NX58,
CC ECO:0000269|PubMed:24990247}.
CC -!- TISSUE SPECIFICITY: Expressed in testis (at protein level).
CC {ECO:0000269|PubMed:24990247}.
CC -!- DOMAIN: The N-terminal zinc-finger domains are required for the
CC appropriate production of 28S rRNA and the formation of pre-60S
CC particles. {ECO:0000250|UniProtKB:Q9NX58}.
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DR EMBL; BC079008; AAH79008.1; -; mRNA.
DR RefSeq; NP_001011911.1; NM_001011911.1.
DR RefSeq; XP_006251149.1; XM_006251087.1.
DR AlphaFoldDB; Q6AYK5; -.
DR SMR; Q6AYK5; -.
DR BioGRID; 252995; 1.
DR STRING; 10116.ENSRNOP00000073585; -.
DR PhosphoSitePlus; Q6AYK5; -.
DR jPOST; Q6AYK5; -.
DR PaxDb; 10116-ENSRNOP00000007154; -.
DR GeneID; 289707; -.
DR KEGG; rno:289707; -.
DR AGR; RGD:1305352; -.
DR CTD; 55646; -.
DR RGD; 1305352; Lyar.
DR VEuPathDB; HostDB:ENSRNOG00000005374; -.
DR eggNOG; KOG2186; Eukaryota.
DR HOGENOM; CLU_057137_0_1_1; -.
DR InParanoid; Q6AYK5; -.
DR OrthoDB; 5490568at2759; -.
DR PhylomeDB; Q6AYK5; -.
DR TreeFam; TF314925; -.
DR PRO; PR:Q6AYK5; -.
DR Proteomes; UP000002494; Chromosome 14.
DR Bgee; ENSRNOG00000005374; Expressed in testis and 19 other cell types or tissues.
DR ExpressionAtlas; Q6AYK5; baseline and differential.
DR Genevisible; Q6AYK5; RN.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005730; C:nucleolus; ISS:UniProtKB.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0001750; C:photoreceptor outer segment; ISS:UniProtKB.
DR GO; GO:0003677; F:DNA binding; ISS:UniProtKB.
DR GO; GO:0140297; F:DNA-binding transcription factor binding; ISO:RGD.
DR GO; GO:0042802; F:identical protein binding; ISO:RGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0140416; F:transcription regulator inhibitor activity; ISO:RGD.
DR GO; GO:0048821; P:erythrocyte development; ISS:UniProtKB.
DR GO; GO:0045087; P:innate immune response; IEA:UniProtKB-KW.
DR GO; GO:0045824; P:negative regulation of innate immune response; ISO:RGD.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; ISS:UniProtKB.
DR GO; GO:0050766; P:positive regulation of phagocytosis; ISS:UniProtKB.
DR GO; GO:0045943; P:positive regulation of transcription by RNA polymerase I; ISO:RGD.
DR GO; GO:0006364; P:rRNA processing; ISS:UniProtKB.
DR Gene3D; 1.10.10.2100; -; 1.
DR Gene3D; 3.30.1490.490; -; 1.
DR InterPro; IPR039999; LYAR.
DR InterPro; IPR041010; Znf-ACC.
DR InterPro; IPR014898; Znf_C2H2_LYAR.
DR InterPro; IPR036236; Znf_C2H2_sf.
DR PANTHER; PTHR13100:SF10; CELL GROWTH-REGULATING NUCLEOLAR PROTEIN; 1.
DR PANTHER; PTHR13100; CELL GROWTH-REGULATING NUCLEOLAR PROTEIN LYAR; 1.
DR Pfam; PF17848; zf-ACC; 1.
DR Pfam; PF08790; zf-LYAR; 1.
DR SUPFAM; SSF57667; beta-beta-alpha zinc fingers; 2.
DR PROSITE; PS00059; ADH_ZINC; 1.
DR PROSITE; PS51804; ZF_C2HC_LYAR; 2.
PE 1: Evidence at protein level;
KW Cell projection; Coiled coil; Cytoplasm; Immunity; Innate immunity;
KW Isopeptide bond; Metal-binding; Nucleus; Reference proteome; Repeat;
KW Ubl conjugation; Zinc; Zinc-finger.
FT CHAIN 1..386
FT /note="Cell growth-regulating nucleolar protein"
FT /id="PRO_0000084530"
FT ZN_FING 1..26
FT /note="C2HC LYAR-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01145"
FT ZN_FING 28..52
FT /note="C2HC LYAR-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01145"
FT REGION 141..316
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 172..214
FT /evidence="ECO:0000255"
FT COMPBIAS 141..173
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 174..211
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 220..314
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 6
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01145"
FT BINDING 9
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01145"
FT BINDING 21
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01145"
FT BINDING 25
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01145"
FT BINDING 33
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01145"
FT BINDING 36
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01145"
FT BINDING 48
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01145"
FT BINDING 51
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01145"
FT CROSSLNK 14
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q9NX58"
FT CROSSLNK 202
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q9NX58"
SQ SEQUENCE 386 AA; 43680 MW; 4CCA06474390EA04 CRC64;
MVFFTCNACG ESVKKIQVEK HVSICRNCEC LSCIDCGKDF WGDDYKNHVK CISEDQKYGG
KGYEAKTHKG DVKQQAWIQK INELIKKPNV SPKVRELLQQ ISAFDNVPRK KAKFQNWMRN
SLKVHSDSVL EQVWNIFSEA ASSEQDQQPP SHMAKPNTEV PTKVPSTKTN GTTEEQTEAK
KNKRERKEER QKSRKKEKKE LKLENHQENL KGQKPKKRKK GQEAGHEAGG EDAAEANGAP
EKKRARDAQA SEEGADRNGG PAEDADEGPT KTAAGKRKRQ KHSEVESDNK KKKMKLPGQP
EEGEPEDHEA PSKGKFNWKG TIKAVLKQAP DNEISVKKLK KKVIAQYHAV MSDHHTSEEE
LLAIFNKKIS RNPTFKVLKD KVKLLK
//
