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Protein

Nuclear cap-binding protein subunit 2

Gene

ncbp2

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
Binding sitei19mRNA capBy similarity1
Binding sitei42mRNA capBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionRNA-binding
Biological processmRNA processing, mRNA splicing, mRNA transport, Nonsense-mediated mRNA decay, RNA-mediated gene silencing, Translation regulation, Transport

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-6803529 FGFR2 alternative splicing
R-DRE-6807505 RNA polymerase II transcribes snRNA genes
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

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003852511 – 155Nuclear cap-binding protein subunit 2Add BLAST155

Proteomic databases

PaxDbiQ8JGR6
PRIDEiQ8JGR6

Expressioni

Gene expression databases

BgeeiENSDARG00000014898

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
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini39 – 117RRMPROSITE-ProRule annotationAdd BLAST79

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni111 – 115mRNA cap-bindingBy similarity5
Regioni122 – 126mRNA cap-bindingBy similarity5
Regioni132 – 133mRNA cap-bindingBy similarity2

Sequence similaritiesi

Belongs to the RRM NCBP2 family.Curated

Phylogenomic databases

eggNOGiKOG0121 Eukaryota
ENOG4111FJQ LUCA
GeneTreeiENSGT00390000003197
HOGENOMiHOG000217589
InParanoidiQ8JGR6
KOiK12883
OMAiCMKYIGG
OrthoDBiEOG091G0RKX
PhylomeDBiQ8JGR6
TreeFamiTF313897

Family and domain databases

CDDicd12240 RRM_NCBP2, 1 hit
Gene3Di3.30.70.330, 1 hit
InterProiView protein in InterPro
IPR027157 NCBP2
IPR034148 NCBP2_RRM
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR000504 RRM_dom
PANTHERiPTHR18847 PTHR18847, 1 hit
PfamiView protein in Pfam
PF00076 RRM_1, 1 hit
SMARTiView protein in SMART
SM00360 RRM, 1 hit
SUPFAMiSSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS50102 RRM, 1 hit

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)DescriptionActionsGraphical viewLength
Sequence conflicti12S → F in AAM28218 (PubMed:12006978).Curated1
Sequence conflicti57E → V in AAM28218 (PubMed:12006978).Curated1
Sequence conflicti126R → W in AAH83529 (Ref. 3) Curated1

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

Similar proteinsi

Entry informationi

Entry nameiNCBP2_DANRE
AccessioniPrimary (citable) accession number: Q8JGR6
Secondary accession number(s): Q1MT38, Q5XIY9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: September 22, 2009
Last modified: March 28, 2018
This is version 99 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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