YBOX1_XENLA
ID YBOX1_XENLA Reviewed; 303 AA.
AC P21573;
DT 01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1991, sequence version 1.
DT 25-MAY-2022, entry version 102.
DE RecName: Full=Y-box-binding protein 1 {ECO:0000250|UniProtKB:P67809};
DE Short=YB-1 {ECO:0000250|UniProtKB:P67809};
DE AltName: Full=Y-box transcription factor;
GN Name=ybx1 {ECO:0000250|UniProtKB:P67809};
GN Synonyms=frgy1 {ECO:0000303|PubMed:2247479};
OS Xenopus laevis (African clawed frog).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus.
OX NCBI_TaxID=8355;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND FUNCTION.
RX PubMed=2247479; DOI=10.1073/pnas.87.22.9028;
RA Tafuri S.R., Wolffe A.P.;
RT "Xenopus Y-box transcription factors: molecular cloning, functional
RT analysis and developmental regulation.";
RL Proc. Natl. Acad. Sci. U.S.A. 87:9028-9032(1990).
CC -!- FUNCTION: DNA- and RNA-binding protein involved in various processes,
CC such as translational repression, RNA stabilization, mRNA splicing and
CC transcription regulation (By similarity). 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:2247479). Binds to promoters that
CC contain a Y-box (5'-CTGATTGGCCAA-3') (PubMed:2247479). 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:2247479}.
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-43 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; M59453; AAA49715.1; -; mRNA.
DR PIR; A38274; A38274.
DR AlphaFoldDB; P21573; -.
DR BMRB; P21573; -.
DR SMR; P21573; -.
DR Proteomes; UP000186698; Genome assembly.
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: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: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: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..303
FT /note="Y-box-binding protein 1"
FT /id="PRO_0000100223"
FT DOMAIN 39..103
FT /note="CSD"
FT REGION 1..28
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 43..48
FT /note="C5-methylcytosine binding"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT REGION 98..303
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..15
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 229..248
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 267..285
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 286..303
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 43
FT /note="Important for C5-methylcytosine-recognition"
FT /evidence="ECO:0000250|UniProtKB:P67809"
SQ SEQUENCE 303 AA; 34633 MW; 691E8AB4216137C4 CRC64;
MSSEVETQQQ QPDALEGKAG QEPAATVGDK KVIATKVLGT VKWFNVRNGY GFINRNDTKE
DVFVHQTAIK KNNPRKYLRS VGDGETVEFD VVEGEKGAEA ANVTGPEGVP VQGSKYAADR
NHYRRYPRRR GPPRNYQQNY QNNESGEKAE ENESAPEGDD SNQQRPYHRR RFPPYYSRRP
YGRRPQYSNA PVQGEEAEGA DSQGTDEQGR PARQNMYRGF RPRFRRGPPR QRQPREEGNE
EDKENQGDET QSQPPPQRRY RRNFNYRRRR PENPKSQDGK ETKAAETSAE NTSTPEAEQG
GAE
