NCBP2_DANRE
ID NCBP2_DANRE Reviewed; 155 AA.
AC Q8JGR6; Q1MT38; Q5XIY9;
DT 22-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT 22-SEP-2009, sequence version 2.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=Nuclear cap-binding protein subunit 2;
DE AltName: Full=20 kDa nuclear cap-binding protein;
DE AltName: Full=NCBP 20 kDa subunit;
DE Short=CBP20;
GN Name=ncbp2; Synonyms=cbp20; ORFNames=ch211-258l4.5;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Embryo;
RX PubMed=12006978; DOI=10.1038/ng896;
RA Golling G., Amsterdam A., Sun Z., Antonelli M., Maldonado E., Chen W.,
RA Burgess S., Haldi M., Artzt K., Farrington S., Lin S.-Y., Nissen R.M.,
RA Hopkins N.;
RT "Insertional mutagenesis in zebrafish rapidly identifies genes essential
RT for early vertebrate development.";
RL Nat. Genet. 31:135-140(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Component of the cap-binding complex (CBC), which binds co-
CC transcriptionally to the 5' cap of pre-mRNAs and is involved in various
CC processes such as pre-mRNA splicing, translation regulation, nonsense-
CC mediated mRNA decay, RNA-mediated gene silencing (RNAi) by microRNAs
CC (miRNAs) and mRNA export. The CBC complex is involved in mRNA export
CC from the nucleus, leading to the recruitment of the mRNA export
CC machinery to the 5' end of mRNA and to mRNA export in a 5' to 3'
CC direction through the nuclear pore. The CBC complex is also involved in
CC mediating U snRNA and intronless mRNAs export from the nucleus. The CBC
CC complex is essential for a pioneer round of mRNA translation, before
CC steady state translation when the CBC complex is replaced by
CC cytoplasmic cap-binding protein eIF4E. The pioneer round of mRNA
CC translation mediated by the CBC complex plays a central role in
CC nonsense-mediated mRNA decay (NMD), NMD only taking place in mRNAs
CC bound to the CBC complex, but not on eIF4E-bound mRNAs. The CBC complex
CC enhances NMD in mRNAs containing at least one exon-junction complex
CC (EJC), promoting the interaction between upf1 and upf2. The CBC complex
CC is also involved in 'failsafe' NMD, which is independent of the EJC
CC complex, while it does not participate in Staufen-mediated mRNA decay
CC (SMD). During cell proliferation, the CBC complex is also involved in
CC microRNAs (miRNAs) biogenesis via its interaction with srrt/ars2,
CC thereby being required for miRNA-mediated RNA interference. The CBC
CC complex also acts as a negative regulator of parn, thereby acting as an
CC inhibitor of mRNA deadenylation. In the CBC complex, ncbp2/cbp20
CC recognizes and binds capped RNAs (m7GpppG-capped RNA) but requires
CC ncbp1/cbp80 to stabilize the movement of its N-terminal loop and lock
CC the CBC into a high affinity cap-binding state with the cap structure.
CC The conventional cap-binding complex with NCBP2 binds both small
CC nuclear RNA (snRNA) and messenger (mRNA) and is involved in their
CC export from the nucleus (By similarity).
CC {ECO:0000250|UniProtKB:P52298}.
CC -!- SUBUNIT: Component of the nuclear cap-binding complex (CBC), a
CC heterodimer composed of ncbp1/cbp80 and ncbp2/cbp20 that interacts with
CC m7GpppG-capped RNA. {ECO:0000250|UniProtKB:P52298}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P52298}. Cytoplasm
CC {ECO:0000250|UniProtKB:P52298}.
CC -!- SIMILARITY: Belongs to the RRM NCBP2 family. {ECO:0000305}.
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DR EMBL; AY099530; AAM28218.1; -; mRNA.
DR EMBL; AL953867; CAK04823.1; -; Genomic_DNA.
DR EMBL; BC083529; AAH83529.1; -; mRNA.
DR RefSeq; NP_775356.1; NM_173249.1.
DR AlphaFoldDB; Q8JGR6; -.
DR SMR; Q8JGR6; -.
DR STRING; 7955.ENSDARP00000020688; -.
DR PaxDb; Q8JGR6; -.
DR PRIDE; Q8JGR6; -.
DR Ensembl; ENSDART00000008365; ENSDARP00000020688; ENSDARG00000014898.
DR GeneID; 192325; -.
DR KEGG; dre:192325; -.
DR CTD; 22916; -.
DR ZFIN; ZDB-GENE-020419-31; ncbp2.
DR eggNOG; KOG0121; Eukaryota.
DR GeneTree; ENSGT00390000003197; -.
DR HOGENOM; CLU_070952_2_0_1; -.
DR InParanoid; Q8JGR6; -.
DR OMA; AENCMRY; -.
DR OrthoDB; 1421503at2759; -.
DR PhylomeDB; Q8JGR6; -.
DR TreeFam; TF313897; -.
DR Reactome; R-DRE-113418; Formation of the Early Elongation Complex.
DR Reactome; R-DRE-159236; Transport of Mature mRNA derived from an Intron-Containing Transcript.
DR Reactome; R-DRE-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-DRE-6803529; FGFR2 alternative splicing.
DR Reactome; R-DRE-6807505; RNA polymerase II transcribes snRNA genes.
DR Reactome; R-DRE-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-DRE-72165; mRNA Splicing - Minor Pathway.
DR Reactome; R-DRE-72187; mRNA 3'-end processing.
DR Reactome; R-DRE-72203; Processing of Capped Intron-Containing Pre-mRNA.
DR Reactome; R-DRE-73856; RNA Polymerase II Transcription Termination.
DR Reactome; R-DRE-77595; Processing of Intronless Pre-mRNAs.
DR Reactome; R-DRE-975956; Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
DR Reactome; R-DRE-975957; Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
DR PRO; PR:Q8JGR6; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 22.
DR Bgee; ENSDARG00000014898; Expressed in mature ovarian follicle and 29 other tissues.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005846; C:nuclear cap binding complex; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003729; F:mRNA binding; ISS:UniProtKB.
DR GO; GO:0000340; F:RNA 7-methylguanosine cap binding; ISS:UniProtKB.
DR GO; GO:0000339; F:RNA cap binding; IBA:GO_Central.
DR GO; GO:0017069; F:snRNA binding; ISS:UniProtKB.
DR GO; GO:0031047; P:gene silencing by RNA; IEA:UniProtKB-KW.
DR GO; GO:0045292; P:mRNA cis splicing, via spliceosome; ISS:UniProtKB.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IBA:GO_Central.
DR GO; GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IEA:UniProtKB-KW.
DR GO; GO:0046833; P:positive regulation of RNA export from nucleus; ISS:UniProtKB.
DR GO; GO:0006417; P:regulation of translation; IEA:UniProtKB-KW.
DR GO; GO:0008380; P:RNA splicing; ISS:UniProtKB.
DR GO; GO:0006408; P:snRNA export from nucleus; ISS:UniProtKB.
DR CDD; cd12240; RRM_NCBP2; 1.
DR Gene3D; 3.30.70.330; -; 1.
DR InterPro; IPR027157; NCBP2.
DR InterPro; IPR034148; NCBP2_RRM.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR000504; RRM_dom.
DR PANTHER; PTHR18847; PTHR18847; 1.
DR Pfam; PF00076; RRM_1; 1.
DR SMART; SM00360; RRM; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
DR PROSITE; PS50102; RRM; 1.
PE 2: Evidence at transcript level;
KW Cytoplasm; mRNA processing; mRNA splicing; mRNA transport;
KW Nonsense-mediated mRNA decay; Nucleus; Reference proteome; RNA-binding;
KW RNA-mediated gene silencing; Translation regulation; Transport.
FT CHAIN 1..155
FT /note="Nuclear cap-binding protein subunit 2"
FT /id="PRO_0000385251"
FT DOMAIN 39..117
FT /note="RRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 121..155
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 129..143
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 19
FT /ligand="mRNA"
FT /ligand_id="ChEBI:CHEBI:33699"
FT /ligand_part="mRNA cap"
FT /evidence="ECO:0000250"
FT BINDING 42
FT /ligand="mRNA"
FT /ligand_id="ChEBI:CHEBI:33699"
FT /ligand_part="mRNA cap"
FT /evidence="ECO:0000250"
FT BINDING 111..115
FT /ligand="mRNA"
FT /ligand_id="ChEBI:CHEBI:33699"
FT /ligand_part="mRNA cap"
FT /evidence="ECO:0000250"
FT BINDING 122..126
FT /ligand="mRNA"
FT /ligand_id="ChEBI:CHEBI:33699"
FT /ligand_part="mRNA cap"
FT /evidence="ECO:0000250"
FT BINDING 132..133
FT /ligand="mRNA"
FT /ligand_id="ChEBI:CHEBI:33699"
FT /ligand_part="mRNA cap"
FT /evidence="ECO:0000250"
FT CONFLICT 12
FT /note="S -> F (in Ref. 1; AAM28218)"
FT /evidence="ECO:0000305"
FT CONFLICT 57
FT /note="E -> V (in Ref. 1; AAM28218)"
FT /evidence="ECO:0000305"
FT CONFLICT 126
FT /note="R -> W (in Ref. 3; AAH83529)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 155 AA; 17932 MW; A548E56498E98E3F CRC64;
MSIKLNALFS DSYVDVSQYR DQHFKGNRYE QEKLLKQSAT LYVGNLSFYT TEEQVHELFA
KCGDVKRIII GLDKIKKTAC GFCFVEYYTR ADAENAMRFV NGTRLDDRII RTDWDAGFKE
GRQYGRGKSG GQVRDEYRQD YDPARGGYGK MVQKS
