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Protein

Nuclear cap-binding protein subunit 2

Gene

Ncbp2

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -Experimental evidence at protein 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 via its interaction with ALYREF/THOC4/ALY, 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) via its interaction with UPF1, 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 sitei20mRNA capBy similarity1
Binding sitei43mRNA capBy similarity1

GO - Molecular functioni

  • mRNA binding Source: UniProtKB
  • RNA 7-methylguanosine cap binding Source: RGD
  • snRNA binding Source: UniProtKB

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-RNO-109688 Cleavage of Growing Transcript in the Termination Region
R-RNO-111367 SLBP independent Processing of Histone Pre-mRNAs
R-RNO-112382 Formation of RNA Pol II elongation complex
R-RNO-113418 Formation of the Early Elongation Complex
R-RNO-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-RNO-191859 snRNP Assembly
R-RNO-674695 RNA Polymerase II Pre-transcription Events
R-RNO-6803529 FGFR2 alternative splicing
R-RNO-6807505 RNA polymerase II transcribes snRNA genes
R-RNO-72086 mRNA Capping
R-RNO-72163 mRNA Splicing - Major Pathway
R-RNO-72165 mRNA Splicing - Minor Pathway
R-RNO-72187 mRNA 3'-end processing
R-RNO-72203 Processing of Capped Intron-Containing Pre-mRNA
R-RNO-77588 SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs
R-RNO-77595 Processing of Intronless Pre-mRNAs
R-RNO-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
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 11

Organism-specific databases

RGDi1596188 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
Initiator methionineiRemovedBy similarity
ChainiPRO_00003852482 – 156Nuclear cap-binding protein subunit 2Add BLAST155

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineBy similarity1
Modified residuei13PhosphoserineCombined sources1
Modified residuei18PhosphoserineBy similarity1
Modified residuei146Omega-N-methylarginineBy similarity1

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

PaxDbiB1WC40
PeptideAtlasiB1WC40
PRIDEiB1WC40

PTM databases

iPTMnetiB1WC40
PhosphoSitePlusiB1WC40

Expressioni

Gene expression databases

BgeeiENSRNOG00000001746
GenevisibleiB1WC40 RN

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. Found in a U snRNA export complex with PHAX/RNUXA, NCBP1/CBP80, NCBP2/CBP20, RAN, XPO1 and m7G-capped RNA. Interacts with PHAX/RNUXA, EIF4G1, HNRNPF, HNRNPH1 and ALYREF/THOC4/ALY. Interacts with SRRT/ARS2 and KPNA3 (By similarity).By similarity

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000066677

Structurei

3D structure databases

ProteinModelPortaliB1WC40
SMRiB1WC40
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini40 – 118RRMPROSITE-ProRule annotationAdd BLAST79

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni112 – 116mRNA cap-bindingBy similarity5
Regioni123 – 127mRNA cap-bindingBy similarity5
Regioni133 – 134mRNA cap-bindingBy similarity2

Sequence similaritiesi

Belongs to the RRM NCBP2 family.Curated

Phylogenomic databases

eggNOGiKOG0121 Eukaryota
ENOG4111FJQ LUCA
GeneTreeiENSGT00390000003197
HOGENOMiHOG000217589
InParanoidiB1WC40
KOiK12883
OMAiCMKYIGG
OrthoDBiEOG091G0RKX
PhylomeDBiB1WC40
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.

Sequence processingi: The displayed sequence is further processed into a mature form.

B1WC40-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGGLLKALR SDSYVELSEY RDQHFRGDNE EQEKLLKKSC TLYVGNLSFY
60 70 80 90 100
TTEEQIYELF SKSGDIKKII MGLDKMKKTA CGFCFVEYYS RADAENAMRY
110 120 130 140 150
INGTRLDDRI IRTDWDAGFK EGRQYGRGRS GGQVRDEYRE DYDAGRGGYG

KLAQKQ
Length:156
Mass (Da):18,017
Last modified:May 20, 2008 - v1
Checksum:iC6DF61E0C6A2CC2C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC161994 mRNA Translation: AAI61994.1
RefSeqiNP_001102995.1, NM_001109525.1
UniGeneiRn.204538

Genome annotation databases

EnsembliENSRNOT00000002381; ENSRNOP00000002381; ENSRNOG00000001746
ENSRNOT00000071483; ENSRNOP00000066677; ENSRNOG00000048589
GeneIDi689116
KEGGirno:689116
UCSCiRGD:1596188 rat

Similar proteinsi

Entry informationi

Entry nameiNCBP2_RAT
AccessioniPrimary (citable) accession number: B1WC40
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: May 20, 2008
Last modified: May 23, 2018
This is version 77 of the entry and version 1 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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