YBOX1_CHICK
ID YBOX1_CHICK Reviewed; 321 AA.
AC Q06066;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1994, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=Y-box-binding protein 1 {ECO:0000303|PubMed:8321222};
DE Short=YB-1 {ECO:0000303|PubMed:8321222};
DE AltName: Full=Y-box transcription factor;
GN Name=YBX1 {ECO:0000250|UniProtKB:P67809};
GN Synonyms=YB1 {ECO:0000303|PubMed:8321222};
OS Gallus gallus (Chicken).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae;
OC Phasianinae; Gallus.
OX NCBI_TaxID=9031;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND FUNCTION.
RC TISSUE=Embryonic liver;
RX PubMed=8321222; DOI=10.1128/mcb.13.7.4186-4196.1993;
RA Grant C.E., Deeley R.G.;
RT "Cloning and characterization of chicken YB-1: regulation of expression in
RT the liver.";
RL Mol. Cell. Biol. 13:4186-4196(1993).
CC -!- FUNCTION: DNA- and RNA-binding protein involved in various processes,
CC such as translational repression, RNA stabilization, mRNA splicing and
CC transcription regulation (PubMed:8321222). Binds preferentially to the
CC 5'-[CU]CUGCG-3' RNA motif and specifically recognizes mRNA transcripts
CC modified by C5-methylcytosine (m5C) (By similarity). Promotes mRNA
CC stabilization: acts by binding to m5C-containing mRNAs and preventing
CC mRNA decay (By similarity). Plays a role in the maternal-to-zygotic
CC transition in early embryo by binding to m5C-containing maternal mRNAs
CC and preventing their degradation (By similarity). Also promotes
CC maternal-to-zygotic transition in oocytes and embryos by promoting
CC translation repression; molecular mechanisms governing translation
CC repression are unknown (By similarity). Plays a key role in RNA
CC composition of extracellular exosomes by defining the sorting of small
CC non-coding RNAs, such as tRNAs, Y RNAs, Vault RNAs and miRNAs (By
CC similarity). Probably sorts RNAs in exosomes by recognizing and binding
CC C5-methylcytosine (m5C)-containing RNAs (By similarity). Acts as a key
CC effector of epidermal progenitors by preventing epidermal progenitor
CC senescence: acts by regulating the translation of a senescence-
CC associated subset of cytokine mRNAs, possibly by binding to m5C-
CC containing mRNAs (By similarity). Also involved in pre-mRNA alternative
CC splicing regulation: binds to splice sites in pre-mRNA and regulates
CC splice site selection (By similarity). Also able to bind DNA and
CC regulate transcription (PubMed:8321222). Binds to promoters that
CC contain a Y-box (5'-CTGATTGGCCAA-3') (By similarity). Promotes
CC separation of DNA strands that contain mismatches or are modified by
CC cisplatin (By similarity). Has endonucleolytic activity and can
CC introduce nicks or breaks into double-stranded DNA, suggesting a role
CC in DNA repair (By similarity). The secreted form acts as an
CC extracellular mitogen and stimulates cell migration and proliferation
CC (By similarity). {ECO:0000250|UniProtKB:B5DE31,
CC ECO:0000250|UniProtKB:P67809, ECO:0000269|PubMed:8321222}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P67809}. Nucleus
CC {ECO:0000250|UniProtKB:P67809}. Cytoplasmic granule
CC {ECO:0000250|UniProtKB:P67809}. Secreted
CC {ECO:0000250|UniProtKB:P67809}. Secreted, extracellular exosome
CC {ECO:0000250|UniProtKB:P67809}.
CC -!- DOMAIN: In the CSD domain, Trp-62 specifically recognizes C5-
CC methylcytosine (m5C) modification through its indole ring.
CC {ECO:0000250|UniProtKB:P67809}.
CC -!- SIMILARITY: Belongs to the YBX1 family. {ECO:0000305}.
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DR EMBL; L13032; AAA02573.1; -; mRNA.
DR PIR; A48136; A48136.
DR AlphaFoldDB; Q06066; -.
DR SMR; Q06066; -.
DR STRING; 9031.ENSGALP00000028616; -.
DR VEuPathDB; HostDB:geneid_386575; -.
DR eggNOG; KOG3070; Eukaryota.
DR HOGENOM; CLU_063071_1_0_1; -.
DR InParanoid; Q06066; -.
DR Proteomes; UP000000539; Unplaced.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0070062; C:extracellular exosome; ISS:UniProtKB.
DR GO; GO:0071204; C:histone pre-mRNA 3'end processing complex; ISS:UniProtKB.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0062153; F:C5-methylcytidine-containing RNA binding; ISS:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0035198; F:miRNA binding; ISS:UniProtKB.
DR GO; GO:0003676; F:nucleic acid binding; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; ISS:UniProtKB.
DR GO; GO:0048598; P:embryonic morphogenesis; ISS:UniProtKB.
DR GO; GO:0008544; P:epidermis development; ISS:UniProtKB.
DR GO; GO:1990428; P:miRNA transport; ISS:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0048255; P:mRNA stabilization; ISS:UniProtKB.
DR GO; GO:2000773; P:negative regulation of cellular senescence; ISS:UniProtKB.
DR GO; GO:0017148; P:negative regulation of translation; ISS:UniProtKB.
DR GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central.
DR GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR GO; GO:0050658; P:RNA transport; ISS:UniProtKB.
DR GO; GO:0051031; P:tRNA transport; ISS:UniProtKB.
DR CDD; cd04458; CSP_CDS; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR011129; CSD.
DR InterPro; IPR019844; CSD_1.
DR InterPro; IPR002059; CSP_DNA-bd.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR Pfam; PF00313; CSD; 1.
DR PRINTS; PR00050; COLDSHOCK.
DR SMART; SM00357; CSP; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR PROSITE; PS00352; CSD_1; 1.
DR PROSITE; PS51857; CSD_2; 1.
PE 2: Evidence at transcript level;
KW Cytoplasm; DNA-binding; mRNA processing; mRNA splicing; Nucleus;
KW Reference proteome; Repressor; RNA-binding; Secreted; Transcription;
KW Transcription regulation.
FT CHAIN 1..321
FT /note="Y-box-binding protein 1"
FT /id="PRO_0000100222"
FT DOMAIN 58..122
FT /note="CSD"
FT REGION 1..47
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 15..68
FT /note="Interaction with ss-DNA"
FT /evidence="ECO:0000250"
FT REGION 62..67
FT /note="C5-methylcytosine binding"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT REGION 117..321
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 153..168
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 247..266
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 285..303
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 62
FT /note="Important for C5-methylcytosine-recognition"
FT /evidence="ECO:0000250|UniProtKB:P67809"
SQ SEQUENCE 321 AA; 35799 MW; 6496F306C1432274 CRC64;
MSSEAETQPP AAPVPAAPAA APADSKPNGG SGNGSSGLAS AAPPAGGDKK VIATKVLGTV
KWFNVRNGYG FINRNDTKED VFVHQTAIKK NNPRKYLRSV GDGETVEFDV VEGEKGAEAA
NVTGPGGVPV QGSKYAADRN HYRRYPRRRG PPRNYQQNYQ NSESGEKNEG AENIPEGQAQ
QRRPYRRRRY PPYYMRRPYG RRPQYSNPPV QGEIVEGADN QGAGEQGRPV RQNMYRGYRP
RFRRGPPRQR QPREDGNEED KENQGDETQG QQPPQRRYRR NFNYRRRRPE NPKPQDGKET
KTAEPPAENT SAPEAEQGGA E
