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Protein

Nuclear cap-binding protein subunit 2

Gene

ncbp2

Organism
Xenopus laevis (African clawed frog)
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)DescriptionActionsGraphical viewLength
Binding sitei17mRNA capBy similarity1
Binding sitei40mRNA capBy similarity1

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

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
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

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)DescriptionActionsGraphical viewLength
ChainiPRO_00000815011 – 153Nuclear cap-binding protein subunit 2Add BLAST153

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

BioGridi1079029. 1 interactor.
IntActiP52299. 1 interactor.

Structurei

3D structure databases

ProteinModelPortaliP52299.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini37 – 115RRMPROSITE-ProRule annotationAdd BLAST79

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni109 – 113mRNA cap-bindingBy similarity5
Regioni120 – 124mRNA cap-bindingBy similarity5
Regioni130 – 131mRNA cap-bindingBy similarity2

Sequence similaritiesi

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

Phylogenomic databases

HOVERGENiHBG052581.
KOiK12883.

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.

P52299-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALSALRSDS YVDLSQYRDQ HFRGNRSDQE SLLKQSCTLY VGNLSFYTTE
60 70 80 90 100
EQIHELFSKS GDVKRIVMGL DKVKKTACGF CFVEYYTRAD AEQAMRFING
110 120 130 140 150
TRLDDRIVRT DWDAGFKEGR QYGRGKSGGQ VRDEYRQDYD AGRGGYGKVV

QSF
Length:153
Mass (Da):17,565
Last modified:September 22, 2009 - v2
Checksum:iEFC141AB5C247627
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti6 – 8LRS → ARG in CAA59259 (PubMed:7651522).Curated3
Sequence conflicti92 – 93EQ → GT in CAA59259 (PubMed:7651522).Curated2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC072902 mRNA. Translation: AAH72902.1.
X84788 mRNA. Translation: CAA59259.1.
PIRiI51602.
RefSeqiNP_001167476.1. NM_001174005.1.
UniGeneiXl.43439.
Xl.81730.

Genome annotation databases

GeneIDi100380998.
KEGGixla:100380998.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC072902 mRNA. Translation: AAH72902.1.
X84788 mRNA. Translation: CAA59259.1.
PIRiI51602.
RefSeqiNP_001167476.1. NM_001174005.1.
UniGeneiXl.43439.
Xl.81730.

3D structure databases

ProteinModelPortaliP52299.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi1079029. 1 interactor.
IntActiP52299. 1 interactor.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi100380998.
KEGGixla:100380998.

Organism-specific databases

CTDi22916.

Phylogenomic databases

HOVERGENiHBG052581.
KOiK12883.

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...

Entry informationi

Entry nameiNCBP2_XENLA
AccessioniPrimary (citable) accession number: P52299
Secondary accession number(s): Q6GQ46
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: September 22, 2009
Last modified: October 5, 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

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.