YBOX1_RABIT
ID YBOX1_RABIT Reviewed; 324 AA.
AC Q28618;
DT 21-MAR-2006, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 25-MAY-2022, entry version 135.
DE RecName: Full=Y-box-binding protein 1 {ECO:0000303|PubMed:7852402};
DE Short=YB-1 {ECO:0000303|PubMed:7852402};
DE AltName: Full=Nuclease-sensitive element-binding protein 1;
DE AltName: Full=Y-box transcription factor;
DE AltName: Full=p50 {ECO:0000303|PubMed:7852402};
GN Name=YBX1 {ECO:0000250|UniProtKB:P67809};
GN Synonyms=YB1 {ECO:0000303|PubMed:7852402};
OS Oryctolagus cuniculus (Rabbit).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Lagomorpha; Leporidae; Oryctolagus.
OX NCBI_TaxID=9986;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND SUBCELLULAR LOCATION.
RC TISSUE=Bone marrow;
RX PubMed=7852402; DOI=10.1074/jbc.270.7.3186;
RA Evdokimova V.M., Wei C.L., Sitikov A.S., Simonenko P.N., Lazarev O.A.,
RA Vasilenko K.S., Ustinov V.A., Hershey J.W., Ovchinnikov L.P.;
RT "The major protein of messenger ribonucleoprotein particles in somatic
RT cells is a member of the Y-box binding transcription factor family.";
RL J. Biol. Chem. 270:3186-3192(1995).
RN [2]
RP PARTIAL PROTEIN SEQUENCE, PROTEOLYTIC CLEAVAGE BY 20S PROTEASOMAL PROTEASE,
RP AND SUBCELLULAR LOCATION.
RX PubMed=16193061; DOI=10.1038/sj.emboj.7600830;
RA Sorokin A.V., Selyutina A.A., Skabkin M.A., Guryanov S.G., Nazimov I.V.,
RA Richard C., Th'ng J., Yau J., Sorensen P.H.B., Ovchinnikov L.P.,
RA Evdokimova V.;
RT "Proteasome-mediated cleavage of the Y-box-binding protein 1 is linked to
RT DNA-damage stress response.";
RL EMBO J. 24:3602-3612(2005).
RN [3]
RP FUNCTION.
RX PubMed=11574481; DOI=10.1093/emboj/20.19.5491;
RA Evdokimova V., Ruzanov P., Imataka H., Raught B., Svitkin Y.,
RA Ovchinnikov L.P., Sonenberg N.;
RT "The major mRNA-associated protein YB-1 is a potent 5' cap-dependent mRNA
RT stabilizer.";
RL EMBO J. 20:5491-5502(2001).
RN [4]
RP FUNCTION, SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=12582179; DOI=10.1074/jbc.m209145200;
RA Nekrasov M.P., Ivshina M.P., Chernov K.G., Kovrigina E.A., Evdokimova V.M.,
RA Thomas A.A.M., Hershey J.W.B., Ovchinnikov L.P.;
RT "The mRNA-binding protein YB-1 (p50) prevents association of the eukaryotic
RT initiation factor eIF4G with mRNA and inhibits protein synthesis at the
RT initiation stage.";
RL J. Biol. Chem. 278:13936-13943(2003).
RN [5]
RP MUTAGENESIS OF SER-102, PHOSPHORYLATION AT SER-102, SUBCELLULAR LOCATION,
RP INTERACTION WITH AKT1, AND FUNCTION.
RX PubMed=16354698; DOI=10.1128/mcb.26.1.277-292.2006;
RA Evdokimova V., Ruzanov P., Anglesio M.S., Sorokin A.V., Ovchinnikov L.P.,
RA Buckley J., Triche T.J., Sonenberg N., Sorensen P.H.B.;
RT "Akt-mediated YB-1 phosphorylation activates translation of silent mRNA
RT species.";
RL Mol. Cell. Biol. 26:277-292(2006).
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 (PubMed:11574481, PubMed:16354698,
CC PubMed:7852402). Predominantly acts as a RNA-binding protein: binds
CC preferentially to the 5'-[CU]CUGCG-3' RNA motif and specifically
CC recognizes mRNA transcripts modified by C5-methylcytosine (m5C) (By
CC similarity). Promotes mRNA stabilization: acts by binding to m5C-
CC containing mRNAs and recruiting the mRNA stability maintainer ELAVL1,
CC thereby preventing mRNA decay (By similarity). Component of the CRD-
CC mediated complex that promotes MYC mRNA stability (By similarity).
CC Contributes to the regulation of translation by modulating the
CC interaction between the mRNA and eukaryotic initiation factors
CC (PubMed:12582179). Plays a key role in RNA composition of extracellular
CC exosomes by defining the sorting of small non-coding RNAs, such as
CC tRNAs, Y RNAs, Vault RNAs and miRNAs (By similarity). Probably sorts
CC RNAs in exosomes by recognizing and binding C5-methylcytosine (m5C)-
CC containing RNAs (By similarity). Acts as a key effector of epidermal
CC progenitors by preventing epidermal progenitor senescence: acts by
CC regulating the translation of a senescence-associated subset of
CC cytokine mRNAs, possibly by binding to m5C-containing mRNAs (By
CC similarity). Also involved in pre-mRNA alternative splicing regulation:
CC binds to splice sites in pre-mRNA and regulates splice site selection
CC (By similarity). Also able to bind DNA: regulates transcription of the
CC multidrug resistance gene MDR1 is enhanced in presence of the APEX1
CC acetylated form at 'Lys-6' and 'Lys-7' (By similarity). Binds to
CC promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and
CC HLA class II genes (By similarity). Promotes separation of DNA strands
CC that contain mismatches or are modified by cisplatin (By similarity).
CC Has endonucleolytic activity and can introduce nicks or breaks into
CC double-stranded DNA, suggesting a role in DNA repair (By similarity).
CC The secreted form acts as an extracellular mitogen and stimulates cell
CC migration and proliferation (By similarity).
CC {ECO:0000250|UniProtKB:P67809, ECO:0000269|PubMed:11574481,
CC ECO:0000269|PubMed:12582179, ECO:0000269|PubMed:16354698,
CC ECO:0000269|PubMed:7852402}.
CC -!- SUBUNIT: Homodimer in the presence of ATP (PubMed:12582179). Component
CC of the coding region determinant (CRD)-mediated complex, composed of
CC DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1 (By similarity). Identified in
CC a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs
CC (By similarity). Component of the U11/U12 snRNPs that are part of the
CC U12-type spliceosome (By similarity). Identified in a histone pre-mRNA
CC complex, at least composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and
CC YBX1 (By similarity). Interacts with IGF2BP1 and RBBP6
CC (PubMed:16354698). Component of cytoplasmic messenger ribonucleoprotein
CC particles (mRNPs) (PubMed:16354698). Interacts with AKT1, MBNL1, SFRS9,
CC SFRS12, ALYREF/THOC4, MSH2, XRCC5, WRN and NCL (PubMed:16354698).
CC Interacts (via C-terminus) with APEX1 (via N-terminus); the interaction
CC is increased with APEX1 acetylated at 'Lys-6' and 'Lys-7' (By
CC similarity). Interacts with AGO1 and AGO2 (By similarity). Interacts
CC with ANKRD2 (By similarity). Interacts with DERA (By similarity).
CC Interacts with FMR1; this interaction occurs in association with
CC polyribosome (By similarity). Interacts with ZBTB7B (By similarity).
CC Interacts with HDGF (By similarity). Interacts with ELAVL1; leading to
CC ELAVL1 recruitment on C5-methylcytosine (m5C)-containing mRNAs and
CC subsequent mRNA stability (By similarity).
CC {ECO:0000250|UniProtKB:P62960, ECO:0000250|UniProtKB:P67809,
CC ECO:0000269|PubMed:12582179, ECO:0000269|PubMed:16354698}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:12582179,
CC ECO:0000269|PubMed:16193061, ECO:0000269|PubMed:16354698}. Nucleus
CC {ECO:0000269|PubMed:12582179, ECO:0000269|PubMed:16193061,
CC ECO:0000269|PubMed:16354698}. Cytoplasmic granule
CC {ECO:0000269|PubMed:7852402}. Secreted {ECO:0000250|UniProtKB:P67809}.
CC Secreted, extracellular exosome {ECO:0000250|UniProtKB:P67809}.
CC Note=Predominantly cytoplasmic in proliferating cells (By similarity).
CC Cytotoxic stress and DNA damage enhance translocation to the nucleus
CC (By similarity). Localized in cytoplasmic mRNP granules containing
CC untranslated mRNAs (By similarity). Shuttles between nucleus and
CC cytoplasm (PubMed:12582179). Localized with DDX1, MBNL1 and TIAL1 in
CC stress granules upon stress (By similarity). Secreted by mesangial and
CC monocytic cells after inflammatory challenges (By similarity).
CC {ECO:0000250|UniProtKB:P67809, ECO:0000269|PubMed:12582179}.
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:P62960}.
CC -!- PTM: In the absence of phosphorylation the protein is retained in the
CC cytoplasm (By similarity). Phosphorylation by PKB/AKT1 reduces
CC interaction with cytoplasmic mRNA (PubMed:16354698).
CC {ECO:0000250|UniProtKB:P62960, ECO:0000269|PubMed:16354698}.
CC -!- PTM: Cleaved by a 20S proteasomal protease in response to agents that
CC damage DNA (PubMed:16193061). Cleavage takes place in the absence of
CC ubiquitination and ATP. The resulting N-terminal fragment accumulates
CC in the nucleus (PubMed:16193061). {ECO:0000269|PubMed:16193061}.
CC -!- SIMILARITY: Belongs to the YBX1 family. {ECO:0000305}.
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DR EMBL; U16821; AAA66069.1; -; mRNA.
DR PIR; A55971; A55971.
DR RefSeq; NP_001076254.1; NM_001082785.1.
DR AlphaFoldDB; Q28618; -.
DR SMR; Q28618; -.
DR BioGRID; 1172602; 2.
DR STRING; 9986.ENSOCUP00000023346; -.
DR iPTMnet; Q28618; -.
DR GeneID; 100009583; -.
DR KEGG; ocu:100009583; -.
DR CTD; 4904; -.
DR eggNOG; KOG3070; Eukaryota.
DR InParanoid; Q28618; -.
DR OrthoDB; 1431946at2759; -.
DR Proteomes; UP000001811; Unplaced.
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:1990904; C:ribonucleoprotein 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: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: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 1: Evidence at protein level;
KW Acetylation; Activator; Cytoplasm; Direct protein sequencing; DNA-binding;
KW Isopeptide bond; Mitogen; mRNA processing; mRNA splicing; Nucleus;
KW Phosphoprotein; Reference proteome; Repressor; RNA-binding; Secreted;
KW Transcription; 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_0000227814"
FT DOMAIN 58..128
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:0000269|PubMed:16193061"
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:0000269|PubMed:16354698"
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"
FT MUTAGEN 102
FT /note="S->A: Abolishes phosphorylation by PKB/AKT1."
FT /evidence="ECO:0000269|PubMed:16354698"
SQ SEQUENCE 324 AA; 35824 MW; B2700FD2E61BF8B9 CRC64;
MSSEAETQQP PAAPPAAPAL SAAETKPGTT GSGAGSGGPG GLTSAAPAGG DKKVIATKVL
GTVKWFNVRN GYGFINRNDT KEDVFVHQTA IKKNNPRKYL RSVGDGETVE FDVVEGEKGA
EAANVTGPGG VPVQGSKYAA DRNHYRRYPR RRGPPRNYQQ NYQNSESGEK NEGSESAPEG
QAQQRRPYRR RRFPPYYMRR PYGRRPQYSN PPVQGEVMEG ADNQGAGEQG RPVRQNMYRG
YRPRFRRGPP RQRQPREDGN EEDKENQGDE TQGQQPPPSR YRRNFNYRRR RPDNPKPQDG
KETKAADPPA ENSSAPEAEQ GGAE
