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Protein

Nuclear cap-binding protein subunit 2

Gene

ncbp2

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Component of the cap-binding complex (CBC), which binds co-transcriptionally to the 5' cap of pre-mRNAs and is involved in various processes such as pre-mRNA splicing, translation regulation, nonsense-mediated mRNA decay, RNA-mediated gene silencing (RNAi) by microRNAs (miRNAs) and mRNA export. The CBC complex is involved in mRNA export from the nucleus, leading to the recruitment of the mRNA export machinery to the 5' end of mRNA and to mRNA export in a 5' to 3' direction through the nuclear pore. The CBC complex is also involved in mediating U snRNA and intronless mRNAs export from the nucleus. The CBC complex is essential for a pioneer round of mRNA translation, before steady state translation when the CBC complex is replaced by cytoplasmic cap-binding protein eIF4E. The pioneer round of mRNA translation mediated by the CBC complex plays a central role in nonsense-mediated mRNA decay (NMD), NMD only taking place in mRNAs bound to the CBC complex, but not on eIF4E-bound mRNAs. The CBC complex enhances NMD in mRNAs containing at least one exon-junction complex (EJC), promoting the interaction between upf1 and upf2. The CBC complex is also involved in 'failsafe' NMD, which is independent of the EJC complex, while it does not participate in Staufen-mediated mRNA decay (SMD). During cell proliferation, the CBC complex is also involved in microRNAs (miRNAs) biogenesis via its interaction with srrt/ars2, thereby being required for miRNA-mediated RNA interference. The CBC complex also acts as a negative regulator of parn, thereby acting as an inhibitor of mRNA deadenylation. In the CBC complex, ncbp2/cbp20 recognizes and binds capped RNAs (m7GpppG-capped RNA) but requires ncbp1/cbp80 to stabilize the movement of its N-terminal loop and lock the CBC into a high affinity cap-binding state with the cap structure. The conventional cap-binding complex with NCBP2 binds both small nuclear RNA (snRNA) and messenger (mRNA) and is involved in their export from the nucleus (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei19 – 191mRNA capBy similarity
Binding sitei42 – 421mRNA capBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

mRNA capping, mRNA processing, mRNA splicing, mRNA transport, Nonsense-mediated mRNA decay, RNA-mediated gene silencing, Translation regulation, Transport

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-DRE-113418. Formation of the Early Elongation Complex.
R-DRE-159236. Transport of Mature mRNA derived from an Intron-Containing Transcript.
R-DRE-674695. RNA Polymerase II Pre-transcription Events.
R-DRE-72163. mRNA Splicing - Major Pathway.
R-DRE-72165. mRNA Splicing - Minor Pathway.
R-DRE-72187. mRNA 3'-end processing.
R-DRE-72203. Processing of Capped Intron-Containing Pre-mRNA.
R-DRE-77595. Processing of Intronless Pre-mRNAs.
R-DRE-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-DRE-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Names & Taxonomyi

Protein namesi
Recommended name:
Nuclear cap-binding protein subunit 2
Alternative name(s):
20 kDa nuclear cap-binding protein
NCBP 20 kDa subunit
Short name:
CBP20
Gene namesi
Name:ncbp2
Synonyms:cbp20
ORF Names:ch211-258l4.5
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Chromosome 22

Organism-specific databases

ZFINiZDB-GENE-020419-31. ncbp2.

Subcellular locationi

  • Nucleus By similarity
  • Cytoplasm By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 155155Nuclear cap-binding protein subunit 2PRO_0000385251Add
BLAST

Proteomic databases

PaxDbiQ8JGR6.

Expressioni

Gene expression databases

BgeeiQ8JGR6.

Interactioni

Subunit structurei

Component of the nuclear cap-binding complex (CBC), a heterodimer composed of ncbp1/cbp80 and ncbp2/cbp20 that interacts with m7GpppG-capped RNA.By similarity

Protein-protein interaction databases

STRINGi7955.ENSDARP00000020688.

Structurei

3D structure databases

ProteinModelPortaliQ8JGR6.
SMRiQ8JGR6. Positions 5-151.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini39 – 11779RRMPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni111 – 1155mRNA cap-bindingBy similarity
Regioni122 – 1265mRNA cap-bindingBy similarity
Regioni132 – 1332mRNA cap-bindingBy similarity

Sequence similaritiesi

Belongs to the RRM NCBP2 family.Curated
Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0121. Eukaryota.
ENOG4111FJQ. LUCA.
GeneTreeiENSGT00390000003197.
HOGENOMiHOG000217589.
InParanoidiQ8JGR6.
KOiK12883.
OMAiGNRYEQE.
OrthoDBiEOG7PP58M.
PhylomeDBiQ8JGR6.
TreeFamiTF313897.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR027157. NCBP2.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PANTHERiPTHR18847. PTHR18847. 1 hit.
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8JGR6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSIKLNALFS DSYVDVSQYR DQHFKGNRYE QEKLLKQSAT LYVGNLSFYT
60 70 80 90 100
TEEQVHELFA KCGDVKRIII GLDKIKKTAC GFCFVEYYTR ADAENAMRFV
110 120 130 140 150
NGTRLDDRII RTDWDAGFKE GRQYGRGKSG GQVRDEYRQD YDPARGGYGK

MVQKS
Length:155
Mass (Da):17,932
Last modified:September 22, 2009 - v2
Checksum:iA548E56498E98E3F
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti12 – 121S → F in AAM28218 (PubMed:12006978).Curated
Sequence conflicti57 – 571E → V in AAM28218 (PubMed:12006978).Curated
Sequence conflicti126 – 1261R → W in AAH83529 (Ref. 3) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY099530 mRNA. Translation: AAM28218.1.
AL953867 Genomic DNA. Translation: CAK04823.1.
BC083529 mRNA. Translation: AAH83529.1.
RefSeqiNP_775356.1. NM_173249.1.
UniGeneiDr.83993.

Genome annotation databases

EnsembliENSDART00000008365; ENSDARP00000020688; ENSDARG00000014898.
GeneIDi192325.
KEGGidre:192325.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY099530 mRNA. Translation: AAM28218.1.
AL953867 Genomic DNA. Translation: CAK04823.1.
BC083529 mRNA. Translation: AAH83529.1.
RefSeqiNP_775356.1. NM_173249.1.
UniGeneiDr.83993.

3D structure databases

ProteinModelPortaliQ8JGR6.
SMRiQ8JGR6. Positions 5-151.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000020688.

Proteomic databases

PaxDbiQ8JGR6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000008365; ENSDARP00000020688; ENSDARG00000014898.
GeneIDi192325.
KEGGidre:192325.

Organism-specific databases

CTDi22916.
ZFINiZDB-GENE-020419-31. ncbp2.

Phylogenomic databases

eggNOGiKOG0121. Eukaryota.
ENOG4111FJQ. LUCA.
GeneTreeiENSGT00390000003197.
HOGENOMiHOG000217589.
InParanoidiQ8JGR6.
KOiK12883.
OMAiGNRYEQE.
OrthoDBiEOG7PP58M.
PhylomeDBiQ8JGR6.
TreeFamiTF313897.

Enzyme and pathway databases

ReactomeiR-DRE-113418. Formation of the Early Elongation Complex.
R-DRE-159236. Transport of Mature mRNA derived from an Intron-Containing Transcript.
R-DRE-674695. RNA Polymerase II Pre-transcription Events.
R-DRE-72163. mRNA Splicing - Major Pathway.
R-DRE-72165. mRNA Splicing - Minor Pathway.
R-DRE-72187. mRNA 3'-end processing.
R-DRE-72203. Processing of Capped Intron-Containing Pre-mRNA.
R-DRE-77595. Processing of Intronless Pre-mRNAs.
R-DRE-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-DRE-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

NextBioi20797161.
PROiQ8JGR6.

Gene expression databases

BgeeiQ8JGR6.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR027157. NCBP2.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PANTHERiPTHR18847. PTHR18847. 1 hit.
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Insertional mutagenesis in zebrafish rapidly identifies genes essential for early vertebrate development."
    Golling G., Amsterdam A., Sun Z., Antonelli M., Maldonado E., Chen W., Burgess S., Haldi M., Artzt K., Farrington S., Lin S.-Y., Nissen R.M., Hopkins N.
    Nat. Genet. 31:135-140(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Embryo.
  2. "The zebrafish reference genome sequence and its relationship to the human genome."
    Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
    , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
    Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Tuebingen.
  3. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].

Entry informationi

Entry nameiNCBP2_DANRE
AccessioniPrimary (citable) accession number: Q8JGR6
Secondary accession number(s): Q1MT38, Q5XIY9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: September 22, 2009
Last modified: May 11, 2016
This is version 88 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.