YBOX1_BOVIN
ID YBOX1_BOVIN Reviewed; 324 AA.
AC P67808; P16990; P16991; Q2KJF8;
DT 11-OCT-2004, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Y-box-binding protein 1 {ECO:0000303|PubMed:8444345};
DE Short=YB-1 {ECO:0000303|PubMed:8444345};
DE AltName: Full=DNA-binding protein B {ECO:0000303|PubMed:8444345};
DE Short=DBPB {ECO:0000303|PubMed:8444345};
DE AltName: Full=Enhancer factor I subunit A {ECO:0000303|PubMed:8444345};
DE Short=EFI-A {ECO:0000303|PubMed:8444345};
DE AltName: Full=Y-box transcription factor;
GN Name=YBX1 {ECO:0000250|UniProtKB:P67809};
GN Synonyms=YB1 {ECO:0000303|PubMed:8444345};
OS Bos taurus (Bovine).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae;
OC Bovinae; Bos.
OX NCBI_TaxID=9913;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Lung endothelial cell;
RX PubMed=8444345; DOI=10.1016/0378-1119(93)90397-l;
RA Ozer J., Chalkley R., Sealy L.;
RT "Isolation of the CCAAT transcription factor subunit EFIA cDNA and a
RT potentially functional EFIA processed pseudogene from Bos taurus: insights
RT into the evolution of the EFIA/dbpB/YB-1 gene family.";
RL Gene 124:223-230(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Hereford; TISSUE=Testis;
RG NIH - Mammalian Gene Collection (MGC) project;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: DNA- and RNA-binding protein involved in various processes,
CC such as translational repression, RNA stabilization, mRNA splicing, DNA
CC repair and transcription regulation. Predominantly acts as a RNA-
CC binding protein: binds preferentially to the 5'-[CU]CUGCG-3' RNA motif
CC and specifically recognizes mRNA transcripts modified by C5-
CC methylcytosine (m5C). Promotes mRNA stabilization: acts by binding to
CC m5C-containing mRNAs and recruiting the mRNA stability maintainer
CC ELAVL1, thereby preventing mRNA decay. Component of the CRD-mediated
CC complex that promotes MYC mRNA stability (By similarity). Contributes
CC to the regulation of translation by modulating the interaction between
CC the mRNA and eukaryotic initiation factors (By similarity). Plays a key
CC role in RNA composition of extracellular exosomes by defining the
CC sorting of small non-coding RNAs, such as tRNAs, Y RNAs, Vault RNAs and
CC miRNAs. Probably sorts RNAs in exosomes by recognizing and binding C5-
CC methylcytosine (m5C)-containing RNAs. Acts as a key effector of
CC epidermal progenitors by preventing epidermal progenitor senescence:
CC acts by regulating the translation of a senescence-associated subset of
CC cytokine mRNAs, possibly by binding to m5C-containing mRNAs. Also
CC involved in pre-mRNA alternative splicing regulation: binds to splice
CC sites in pre-mRNA and regulates splice site selection. Also able to
CC bind DNA: regulates transcription of the multidrug resistance gene MDR1
CC is enhanced in presence of the APEX1 acetylated form at 'Lys-6' and
CC 'Lys-7'. Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'),
CC such as MDR1 and HLA class II genes. Promotes separation of DNA strands
CC that contain mismatches or are modified by cisplatin. Has
CC endonucleolytic activity and can introduce nicks or breaks into double-
CC stranded DNA, suggesting a role in DNA repair. The secreted form acts
CC as an extracellular mitogen and stimulates cell migration and
CC proliferation (By similarity). {ECO:0000250|UniProtKB:P67809,
CC ECO:0000250|UniProtKB:Q28618}.
CC -!- SUBUNIT: Homodimer in the presence of ATP. Component of the coding
CC region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU,
CC IGF2BP1, SYNCRIP and YBX1. Identified in a IGF2BP1-dependent mRNP
CC granule complex containing untranslated mRNAs. Component of the U11/U12
CC snRNPs that are part of the U12-type spliceosome (By similarity).
CC Identified in a histone pre-mRNA complex, at least composed of ERI1,
CC LSM11, SLBP, SNRPB, SYNCRIP and YBX1 (By similarity). Interacts with
CC IGF2BP1 and RBBP6. Component of cytoplasmic messenger ribonucleoprotein
CC particles (mRNPs). Interacts with AKT1, MBNL1, SFRS9, SFRS12,
CC ALYREF/THOC4, MSH2, XRCC5, WRN and NCL. Interacts (via C-terminus) with
CC APEX1 (via N-terminus); the interaction is increased with APEX1
CC acetylated at 'Lys-6' and 'Lys-7'. Interacts with AGO1 and AGO2.
CC Interacts with ANKRD2. Interacts with DERA (By similarity). Interacts
CC with FMR1; this interaction occurs in association with polyribosome.
CC Interacts with ZBTB7B (By similarity). Interacts with HDGF. Interacts
CC with ELAVL1; leading to ELAVL1 recruitment on C5-methylcytosine (m5C)-
CC containing mRNAs and subsequent mRNA stability (By similarity).
CC {ECO:0000250|UniProtKB:P62960, ECO:0000250|UniProtKB:P67809}.
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}. Note=Predominantly cytoplasmic in
CC proliferating cells. Cytotoxic stress and DNA damage enhance
CC translocation to the nucleus. Localized in cytoplasmic mRNP granules
CC containing untranslated mRNAs. Shuttles between nucleus and cytoplasm.
CC Localized with DDX1, MBNL1 and TIAL1 in stress granules upon stress.
CC Secreted by mesangial and monocytic cells after inflammatory
CC challenges. {ECO:0000250|UniProtKB:P67809}.
CC -!- DOMAIN: In the CSD domain, Trp-65 specifically recognizes C5-
CC methylcytosine (m5C) modification through its indole ring.
CC {ECO:0000250|UniProtKB:P67809}.
CC -!- PTM: Ubiquitinated by RBBP6; leading to a decrease of YBX1
CC transcactivational ability. {ECO:0000250|UniProtKB:P67809}.
CC -!- PTM: In the absence of phosphorylation the protein is retained in the
CC cytoplasm. {ECO:0000250|UniProtKB:P67809}.
CC -!- PTM: Cleaved by a 20S proteasomal protease in response to agents that
CC damage DNA. Cleavage takes place in the absence of ubiquitination and
CC ATP. The resulting N-terminal fragment accumulates in the nucleus (By
CC similarity). {ECO:0000250|UniProtKB:Q28618}.
CC -!- SIMILARITY: Belongs to the YBX1 family. {ECO:0000305}.
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DR EMBL; M95793; AAA30497.1; -; mRNA.
DR EMBL; BC105363; AAI05364.1; -; mRNA.
DR PIR; I39382; I39382.
DR PIR; JQ2292; JQ2292.
DR RefSeq; NP_777240.1; NM_174815.2.
DR AlphaFoldDB; P67808; -.
DR BMRB; P67808; -.
DR SMR; P67808; -.
DR STRING; 9913.ENSBTAP00000023094; -.
DR PaxDb; P67808; -.
DR PeptideAtlas; P67808; -.
DR PRIDE; P67808; -.
DR Ensembl; ENSBTAT00000023094; ENSBTAP00000023094; ENSBTAG00000017368.
DR GeneID; 287023; -.
DR KEGG; bta:287023; -.
DR CTD; 4904; -.
DR VEuPathDB; HostDB:ENSBTAG00000017368; -.
DR VGNC; VGNC:50233; YBX1.
DR eggNOG; KOG3070; Eukaryota.
DR GeneTree; ENSGT00940000153341; -.
DR InParanoid; P67808; -.
DR OMA; GDKKVIX; -.
DR OrthoDB; 1431946at2759; -.
DR Proteomes; UP000009136; Chromosome 3.
DR Bgee; ENSBTAG00000017368; Expressed in omental fat pad and 104 other tissues.
DR ExpressionAtlas; P67808; baseline and differential.
DR GO; GO:0010494; C:cytoplasmic stress granule; ISS:UniProtKB.
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:1990124; C:messenger ribonucleoprotein complex; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0031090; C:organelle membrane; IEA:UniProt.
DR GO; GO:1990904; C:ribonucleoprotein complex; ISS:UniProtKB.
DR GO; GO:0062153; F:C5-methylcytidine-containing RNA binding; ISS:UniProtKB.
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:0003697; F:single-stranded DNA binding; ISS:AgBase.
DR GO; GO:0070934; P:CRD-mediated mRNA stabilization; 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:0051781; P:positive regulation of cell division; IEA:UniProtKB-KW.
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 Acetylation; Activator; Cytoplasm; DNA-binding; Isopeptide bond; Mitogen;
KW mRNA processing; mRNA splicing; Nucleus; Phosphoprotein;
KW Reference proteome; Repressor; RNA-binding; Secreted; Transcription;
KW Transcription regulation; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT CHAIN 2..324
FT /note="Y-box-binding protein 1"
FT /id="PRO_0000100218"
FT DOMAIN 61..125
FT /note="CSD"
FT REGION 1..49
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 15..71
FT /note="Interaction with ss-DNA"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT REGION 65..70
FT /note="C5-methylcytosine binding"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT REGION 120..324
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 156..181
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 250..269
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 288..306
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 65
FT /note="Important for C5-methylcytosine-recognition"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT SITE 219..220
FT /note="Cleavage; by 20S proteasomal protease"
FT /evidence="ECO:0000250|UniProtKB:Q28618"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 102
FT /note="Phosphoserine; by PKB/AKT1"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 162
FT /note="Phosphotyrosine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 165
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 167
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 174
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 176
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 301
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 304
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 314
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT CROSSLNK 26
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT CROSSLNK 137
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000250|UniProtKB:P67809"
SQ SEQUENCE 324 AA; 35924 MW; DF0114BF974AEDB8 CRC64;
MSSEAETQQP PAAPPAAPAL SAADTKPGTT GSGAGSGGPG GLTSAAPAGG DKKVIATKVL
GTVKWFNVRN GYGFINRNDT KEDVFVHQTA IKKNNPRKYL RSVGDGETVE FDVVEGEKGA
EAANVTGPGG VPVQGSKYAA DRNHYRRYPR RRGPPRNYQQ NYQNSESGEK NEGSESAPEG
QAQQRRPYRR RRFPPYYMRR PYGRRPQYSN PPVQGEVMEG ADNQGAGEQG RPVRQNMYRG
YRPRFRRGPP RQRQPREDGN EEDKENQGDE TQGQQPPQRR YRRNFNYRRR RPENPKPQDG
KETKAADPPA ENSSAPEAEQ GGAE
