| IED ID | IndEnz0002011781 |
| Enzyme Type ID | protease011781 |
| Protein Name |
Y-box-binding protein 1 YB-1 CCAAT-binding transcription factor I subunit A CBF-A DNA-binding protein B DBPB Enhancer factor I subunit A EFI-A Nuclease-sensitive element-binding protein 1 Y-box transcription factor |
| Gene Name | YBX1 NSEP1 YB1 |
| Organism | Homo sapiens (Human) |
| Taxonomic Lineage | cellular organisms Eukaryota Opisthokonta Metazoa Eumetazoa Bilateria Deuterostomia Chordata Craniata Vertebrata Gnathostomata (jawed vertebrates) Teleostomi Euteleostomi Sarcopterygii Dipnotetrapodomorpha Tetrapoda Amniota Mammalia Theria Eutheria Boreoeutheria Euarchontoglires Primates Haplorrhini Simiiformes Catarrhini Hominoidea (apes) Hominidae (great apes) Homininae Homo Homo sapiens (Human) |
| Enzyme Sequence | MSSEAETQQPPAAPPAAPALSAADTKPGTTGSGAGSGGPGGLTSAAPAGGDKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRPYRRRRFPPYYMRRPYGRRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQNMYRGYRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPPQRRYRRNFNYRRRRPENPKPQDGKETKAADPPAENSSAPEAEQGGAE |
| Enzyme Length | 324 |
| Uniprot Accession Number | P67809 |
| Absorption | |
| Active Site | |
| Activity Regulation | |
| Binding Site | |
| Calcium Binding | |
| catalytic Activity | |
| DNA Binding | |
| EC Number | |
| Enzyme Function | FUNCTION: DNA- and RNA-binding protein involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation (PubMed:8188694, PubMed:10817758, PubMed:11698476, PubMed:14718551, PubMed:18809583, PubMed:31358969). Predominantly acts as a RNA-binding protein: binds preferentially to the 5'-[CU]CUGCG-3' RNA motif and specifically recognizes mRNA transcripts modified by C5-methylcytosine (m5C) (PubMed:19561594, PubMed:31358969). Promotes mRNA stabilization: acts by binding to m5C-containing mRNAs and recruiting the mRNA stability maintainer ELAVL1, thereby preventing mRNA decay (PubMed:10817758, PubMed:11698476, PubMed:31358969). Component of the CRD-mediated complex that promotes MYC mRNA stability (PubMed:19029303). Contributes to the regulation of translation by modulating the interaction between the mRNA and eukaryotic initiation factors (By similarity). Plays a key role in RNA composition of extracellular exosomes by defining the sorting of small non-coding RNAs, such as tRNAs, Y RNAs, Vault RNAs and miRNAs (PubMed:27559612, PubMed:29073095). Probably sorts RNAs in exosomes by recognizing and binding C5-methylcytosine (m5C)-containing RNAs (PubMed:28341602, PubMed:29073095). Acts as a key effector of epidermal progenitors by preventing epidermal progenitor senescence: acts by regulating the translation of a senescence-associated subset of cytokine mRNAs, possibly by binding to m5C-containing mRNAs (PubMed:29712925). Also involved in pre-mRNA alternative splicing regulation: binds to splice sites in pre-mRNA and regulates splice site selection (PubMed:12604611). Also able to bind DNA: regulates transcription of the multidrug resistance gene MDR1 is enhanced in presence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7' (PubMed:18809583). Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes (PubMed:8188694, PubMed:18809583). Promotes separation of DNA strands that contain mismatches or are modified by cisplatin (PubMed:14718551). Has endonucleolytic activity and can introduce nicks or breaks into double-stranded DNA, suggesting a role in DNA repair (PubMed:14718551). The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation (PubMed:19483673). {ECO:0000250|UniProtKB:Q28618, ECO:0000269|PubMed:10817758, ECO:0000269|PubMed:11698476, ECO:0000269|PubMed:12604611, ECO:0000269|PubMed:14718551, ECO:0000269|PubMed:18809583, ECO:0000269|PubMed:19029303, ECO:0000269|PubMed:19483673, ECO:0000269|PubMed:19561594, ECO:0000269|PubMed:27559612, ECO:0000269|PubMed:28341602, ECO:0000269|PubMed:29073095, ECO:0000269|PubMed:29712925, ECO:0000269|PubMed:31358969, ECO:0000269|PubMed:8188694}. |
| Temperature Dependency | |
| PH Dependency | |
| Pathway | |
| nucleotide Binding | |
| Features | Beta strand (5); Chain (1); Compositional bias (3); Cross-link (2); Domain (1); Erroneous initiation (1); Frameshift (2); Helix (1); Initiator methionine (1); Modified residue (10); Mutagenesis (5); Region (4); Sequence conflict (1); Site (2); Turn (2) |
| Keywords | 3D-structure;Acetylation;Activator;Cytoplasm;DNA-binding;Direct protein sequencing;Isopeptide bond;Mitogen;Nucleus;Phosphoprotein;RNA-binding;Reference proteome;Repressor;Secreted;Transcription;Transcription regulation;Ubl conjugation;mRNA processing;mRNA splicing |
| Interact With | Q07021; Q13616; Q08211; Q09472; Q7Z6M2; Q14103-4; P62310; Q99697; O15355; Q13148; P13693; Q08705; P19712 |
| Induction | |
| Subcellular Location | SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:12604611, ECO:0000269|PubMed:14718551, ECO:0000269|PubMed:15806160}. Nucleus {ECO:0000269|PubMed:12604611, ECO:0000269|PubMed:14718551, ECO:0000269|PubMed:15806160}. Cytoplasmic granule {ECO:0000269|PubMed:17289661, ECO:0000269|PubMed:18335541, ECO:0000269|PubMed:19029303, ECO:0000269|PubMed:25229427}. Secreted {ECO:0000269|PubMed:19483673}. Secreted, extracellular exosome {ECO:0000269|PubMed:27559612, ECO:0000269|PubMed:28341602}. Note=Predominantly cytoplasmic in proliferating cells (PubMed:12604611). Cytotoxic stress and DNA damage enhance translocation to the nucleus (PubMed:14718551). Localized in cytoplasmic mRNP granules containing untranslated mRNAs (PubMed:25229427). Shuttles between nucleus and cytoplasm (PubMed:25229427). Localized with DDX1, MBNL1 and TIAL1 in stress granules upon stress (PubMed:18335541). Secreted by mesangial and monocytic cells after inflammatory challenges (PubMed:19483673). {ECO:0000269|PubMed:12604611, ECO:0000269|PubMed:14718551, ECO:0000269|PubMed:18335541, ECO:0000269|PubMed:19483673, ECO:0000269|PubMed:25229427}. |
| Modified Residue | MOD_RES 2; /note="N-acetylserine"; /evidence="ECO:0000269|Ref.6, ECO:0007744|PubMed:19413330"; MOD_RES 102; /note="Phosphoserine; by PKB/AKT1"; /evidence="ECO:0000269|PubMed:15806160, ECO:0007744|PubMed:19690332"; MOD_RES 162; /note="Phosphotyrosine"; /evidence="ECO:0007744|PubMed:15592455"; MOD_RES 165; /note="Phosphoserine"; /evidence="ECO:0000269|Ref.6, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163"; MOD_RES 167; /note="Phosphoserine"; /evidence="ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:24275569"; MOD_RES 174; /note="Phosphoserine"; /evidence="ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569"; MOD_RES 176; /note="Phosphoserine"; /evidence="ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569"; MOD_RES 301; /note="N6-acetyllysine"; /evidence="ECO:0000269|PubMed:19483673"; MOD_RES 304; /note="N6-acetyllysine"; /evidence="ECO:0000269|PubMed:19483673"; MOD_RES 314; /note="Phosphoserine"; /evidence="ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163" |
| Post Translational Modification | PTM: Ubiquitinated by RBBP6; leading to a decrease of YBX1 transcactivational ability. {ECO:0000269|PubMed:18851979}.; PTM: In the absence of phosphorylation the protein is retained in the cytoplasm. {ECO:0000269|PubMed:15806160, ECO:0000269|Ref.6}.; PTM: Cleaved by a 20S proteasomal protease in response to agents that damage DNA. Cleavage takes place in the absence of ubiquitination and ATP. The resulting N-terminal fragment accumulates in the nucleus (By similarity). {ECO:0000250|UniProtKB:Q28618}. |
| Signal Peptide | |
| Structure 3D | NMR spectroscopy (3); X-ray crystallography (7) |
| Cross Reference PDB | 1H95; 5YTS; 5YTT; 5YTV; 5YTX; 6A6L; 6KTC; 6KUG; 6LMR; 6LMS; |
| Mapped Pubmed ID | 10207048; 11101529; 11118221; 11333026; 11532962; 11607023; 11731270; 11788582; 11907223; 11991638; 12080043; 12176931; 12379116; 12411573; 12414731; 12477934; 12565174; 12646178; 12674497; 12695516; 12743601; 12917425; 14604279; 14625303; 14743216; 14752049; 15024032; 15047060; 15123725; 15161933; 15166247; 15229244; 15327898; 15615704; 15702969; 15735691; 16093352; 16101161; 16198352; 16415342; 16797541; 16809785; 17332742; 17339575; 17418094; 17459055; 17572683; 17595327; 17620599; 17686777; 17822788; 17875215; 17940139; 17967494; 18075498; 18172301; 18258596; 18307537; 18316615; 18322460; 18377424; 18571458; 18800033; 18978732; 19036157; 19052544; 19098458; 19103666; 19135240; 19151767; 19156129; 19167051; 19174163; 19323802; 19343720; 19411069; 19517610; 19523114; 19549727; 19640841; 19713745; 19738201; 19805454; 19838214; 19901122; 19930682; 19996271; 20004191; 20011972; 20017303; 20190818; 20332234; 20360068; 20398058; 20423332; 20562859; 20596676; 20599698; 20711500; 20838384; 20844753; 20856196; 20929136; 20929326; 20972459; 20980672; 21067243; 21083641; 21138866; 21150319; 21170361; 21182205; 21245151; 21278420; 21282530; 21344396; 21392397; 21423216; 21518489; 21526149; 21565611; 21595987; 21630125; 21642987; 21652770; 21695211; 21730024; 21781495; 21849455; 21851590; 21909940; 21911578; 21968648; 21987172; 21988832; 22095225; 22095791; 22110043; 22113938; 22118625; 22134169; 22215526; 22280412; 22284440; 22339596; 22365833; 22417301; 22419818; 22519956; 22522808; 22590640; 22619371; 22623428; 22674792; 22730292; 22772059; 22787154; 22810585; 22843890; 22855482; 22959432; 22967496; 23084401; 23160378; 23178914; 23216250; 23285076; 23345524; 23395237; 23455153; 23462806; 23499936; 23589019; 23613305; 23658892; 23663784; 23672612; 23749898; 23775496; 23804301; 23822148; 23838318; 23851501; 23872051; 23902751; 23986595; 24044901; 24075827; 24103640; 24107631; 24165022; 24189400; 24211838; 24217978; 24260353; 24260892; 24335958; 24349210; 24378923; 24443788; 24461929; 24554780; 24648416; 24729449; 24770864; 24774443; 24796623; 24817634; 24833360; 24885403; 24947514; 24965446; 25078572; 25156912; 25201740; 2524422; 25270600; 25292190; 25354590; 25398005; 25402957; 25497084; 25539742; 25544376; 25605055; 25609649; 25639555; 25640309; 25645014; 25674237; 25720531; 25790262; 25797255; 25800057; 25877750; 25904138; 25920683; 25957686; 25959498; 25965573; 25993060; 26055210; 26093350; 26122241; 26147853; 26193840; 26240386; 26318844; 26343856; 26355086; 26420826; 26430912; 26453809; 26496610; 26498684; 26512918; 26725322; 26794392; 26805816; 26857528; 26931209; 26936129; 26939718; 27013200; 27044807; 27072400; 27080258; 27168020; 27174937; 27286449; 27322209; 27371774; 27384875; 27397581; 27510544; 27524241; 27544639; 27607350; 27699813; 27713156; 27751836; 27794479; 27821766; 27879270; 27911878; 27922666; 28009354; 28027578; 28035913; 28077578; 28107702; 28123588; 28302118; 28382490; 28400280; 28415756; 28428004; 28624808; 28708785; 28714514; 28782557; 29024700; 29113949; 29133115; 29187452; 29274785; 29289594; 29517281; 29529249; 2963332; 29669758; 29670170; 29737063; 29743296; 29995936; 30126195; 30221675; 30275756; 30278358; 30286788; 30321499; 30356079; 30419346; 30426615; 30470227; 30605522; 30864697; 30903644; 30905819; 31010234; 31113805; 31160337; 31180040; 31358880; 31481087; 31495785; 31672764; 31713447; 31879363; 31906126; 31944153; 32013098; 32015133; 32028981; 32047913; 32112110; 32178290; 32206124; 32209435; 32216017; 32423800; 32561752; 32585856; 32681926; 32710623; 32787509; 32882852; 32894437; 32929382; 32931865; 32947956; 32963329; 32973139; 33003386; 33054752; 33064355; 33239784; 33247987; 33361760; 33377748; 33379356; 33516877; 33556375; 33763698; 33767152; 33911076; 33934437; 34110104; 34218256; 34266873; 34281280; 34364882; 34366628; 34440660; 34469566; 34499772; 34643163; 34766549; 6088074; 6206566; 8835860; 9731529; |
| Motif | |
| Gene Encoded By | |
| Mass | 35,924 |
| Kinetics | |
| Metal Binding | |
| Rhea ID | |
| Cross Reference Brenda |