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Protein

Nuclear cap-binding protein subunit 2

Gene

CBP20

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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 and RNA-mediated gene silencing (RNAi) by microRNAs (miRNAs). The CBC complex is involved in miRNA-mediated RNA interference and is required for primary miRNA processing. In the CBC complex, CBP20 recognizes and binds capped RNAs (m7GpppG-capped RNA) but requires ABH1/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. CBP20 also plays a role in stabilization of ABH1/CBP80 and ABH1/CBP80 localization to the nucleus. Involved in flowering regulation via its interaction with FRIGIDA.3 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei14 – 141mRNA capBy similarity
Binding sitei37 – 371mRNA capBy similarity

GO - Molecular functioni

  • nucleotide binding Source: InterPro
  • RNA cap binding Source: TAIR

GO - Biological processi

  • 7-methylguanosine mRNA capping Source: UniProtKB-KW
  • mRNA cis splicing, via spliceosome Source: InterPro
  • mRNA splicing, via spliceosome Source: GO_Central
  • primary miRNA processing Source: TAIR
  • RNA metabolic process Source: TAIR
  • RNA splicing, via endonucleolytic cleavage and ligation Source: TAIR
Complete GO annotation...

Keywords - Biological processi

mRNA capping, mRNA processing, mRNA splicing, RNA-mediated gene silencing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-ATH-112382. Formation of RNA Pol II elongation complex.
R-ATH-113418. Formation of the Early Elongation Complex.
R-ATH-674695. RNA Polymerase II Pre-transcription Events.
R-ATH-72086. mRNA Capping.
R-ATH-72163. mRNA Splicing - Major Pathway.
R-ATH-72165. mRNA Splicing - Minor Pathway.
R-ATH-72187. mRNA 3'-end processing.
R-ATH-72203. Processing of Capped Intron-Containing Pre-mRNA.
R-ATH-77595. Processing of Intronless Pre-mRNAs.
R-ATH-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-ATH-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:
AtCBP20
Gene namesi
Name:CBP20
Ordered Locus Names:At5g44200
ORF Names:MLN1.12
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G44200.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • mRNA cap binding complex Source: TAIR
  • nuclear cap binding complex Source: GO_Central
  • nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

Hypersensitivity to abscisic acid during germination, significant reduction of stomatal conductance and greatly enhanced tolerance to drought. Plants also display mild developmental abnormalities, such as serrated rosette leaves, delayed development and slightly reduced stature.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 257257Nuclear cap-binding protein subunit 2PRO_0000385277Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei245 – 2451PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ9XFD1.
PRIDEiQ9XFD1.

PTM databases

iPTMnetiQ9XFD1.

Expressioni

Tissue specificityi

Expressed in all tissues analyzed, including roots, stems, leaves and flowers.2 Publications

Gene expression databases

GenevisibleiQ9XFD1. AT.

Interactioni

Subunit structurei

Component of the nuclear cap-binding complex (CBC), a heterodimer composed of ABH1/CBP80 and CBP20 that interacts with m7GpppG-capped RNA. Interacts with FRIGIDA; the interaction is direct.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ABH1Q9SIU27EBI-2354070,EBI-2359412
FRIQ9FDW02EBI-2354070,EBI-2126171

Protein-protein interaction databases

BioGridi19693. 7 interactions.
IntActiQ9XFD1. 2 interactions.
STRINGi3702.AT5G44200.1.

Structurei

3D structure databases

ProteinModelPortaliQ9XFD1.
SMRiQ9XFD1. Positions 10-146.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini34 – 11279RRMPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni106 – 1105mRNA cap-bindingBy similarity
Regioni117 – 1215mRNA cap-bindingBy similarity
Regioni127 – 1282mRNA cap-bindingBy similarity

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi201 – 2077Nuclear localization signalSequence analysis
Motifi254 – 2574Nuclear localization signalSequence analysis

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.
HOGENOMiHOG000217589.
InParanoidiQ9XFD1.
KOiK12883.
OMAiAPPQYDR.
PhylomeDBiQ9XFD1.

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.

Q9XFD1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASLFKEQAK LSAYRDRRFS GTQEEFDEAL RASTTVYIGN VSFYTTEEQL
60 70 80 90 100
YELFSRAGEI KKIIMGLDKN TKTPCGFCFV LFYSREDTED AVKYISGTIL
110 120 130 140 150
DDRPIRVDFD WGFQEGRQWG RGRSGGQVRD EYRTDYDPAR GGYGKLVQKE
160 170 180 190 200
LEAQRQLVDY GTGSLGAYPQ AAPTNYGNGR RGGGNYGQGG QNRHGRGDYH
210 220 230 240 250
RKRQRDDDRY GRDNSRRNTD HESRRDTDSD MRPEKNPRFR ESGDSDDDGE

DDRKRRS
Length:257
Mass (Da):29,609
Last modified:November 1, 1999 - v1
Checksum:iDD8B12A0639E1D58
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF140219 mRNA. Translation: AAD29697.1.
AB005239 Genomic DNA. Translation: BAB10987.1.
CP002688 Genomic DNA. Translation: AED95073.1.
CP002688 Genomic DNA. Translation: AED95074.1.
BT004813 mRNA. Translation: AAO44079.1.
AK227850 mRNA. Translation: BAE99827.1.
RefSeqiNP_001078705.1. NM_001085236.1.
NP_199233.1. NM_123787.3.
UniGeneiAt.23549.

Genome annotation databases

EnsemblPlantsiAT5G44200.1; AT5G44200.1; AT5G44200.
AT5G44200.2; AT5G44200.2; AT5G44200.
GeneIDi834443.
GrameneiAT5G44200.1; AT5G44200.1; AT5G44200.
AT5G44200.2; AT5G44200.2; AT5G44200.
KEGGiath:AT5G44200.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF140219 mRNA. Translation: AAD29697.1.
AB005239 Genomic DNA. Translation: BAB10987.1.
CP002688 Genomic DNA. Translation: AED95073.1.
CP002688 Genomic DNA. Translation: AED95074.1.
BT004813 mRNA. Translation: AAO44079.1.
AK227850 mRNA. Translation: BAE99827.1.
RefSeqiNP_001078705.1. NM_001085236.1.
NP_199233.1. NM_123787.3.
UniGeneiAt.23549.

3D structure databases

ProteinModelPortaliQ9XFD1.
SMRiQ9XFD1. Positions 10-146.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi19693. 7 interactions.
IntActiQ9XFD1. 2 interactions.
STRINGi3702.AT5G44200.1.

PTM databases

iPTMnetiQ9XFD1.

Proteomic databases

PaxDbiQ9XFD1.
PRIDEiQ9XFD1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G44200.1; AT5G44200.1; AT5G44200.
AT5G44200.2; AT5G44200.2; AT5G44200.
GeneIDi834443.
GrameneiAT5G44200.1; AT5G44200.1; AT5G44200.
AT5G44200.2; AT5G44200.2; AT5G44200.
KEGGiath:AT5G44200.

Organism-specific databases

TAIRiAT5G44200.

Phylogenomic databases

eggNOGiKOG0121. Eukaryota.
ENOG4111FJQ. LUCA.
HOGENOMiHOG000217589.
InParanoidiQ9XFD1.
KOiK12883.
OMAiAPPQYDR.
PhylomeDBiQ9XFD1.

Enzyme and pathway databases

ReactomeiR-ATH-112382. Formation of RNA Pol II elongation complex.
R-ATH-113418. Formation of the Early Elongation Complex.
R-ATH-674695. RNA Polymerase II Pre-transcription Events.
R-ATH-72086. mRNA Capping.
R-ATH-72163. mRNA Splicing - Major Pathway.
R-ATH-72165. mRNA Splicing - Minor Pathway.
R-ATH-72187. mRNA 3'-end processing.
R-ATH-72203. Processing of Capped Intron-Containing Pre-mRNA.
R-ATH-77595. Processing of Intronless Pre-mRNAs.
R-ATH-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-ATH-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

PROiQ9XFD1.

Gene expression databases

GenevisibleiQ9XFD1. AT.

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

« Hide 'large scale' publications
  1. "Cloning and characterization of two subunits of Arabidopsis thaliana nuclear cap-binding complex."
    Kmieciak M., Simpson C.G., Lewandowska D., Brown J.W.S., Jarmolowski A.
    Gene 283:171-183(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
  2. "Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones."
    Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M., Miyajima N., Tabata S.
    DNA Res. 4:215-230(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
    , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
    Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  6. "An mRNA cap binding protein, ABH1, modulates early abscisic acid signal transduction in Arabidopsis."
    Hugouvieux V., Kwak J.M., Schroeder J.I.
    Cell 106:477-487(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH ABH1.
  7. "Localization, ion channel regulation, and genetic interactions during abscisic acid signaling of the nuclear mRNA cap-binding protein, ABH1."
    Hugouvieux V., Murata Y., Young J.J., Kwak J.M., Mackesy D.Z., Schroeder J.I.
    Plant Physiol. 130:1276-1287(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY.
  8. "A mutation in the cap binding protein 20 gene confers drought tolerance to Arabidopsis."
    Papp I., Mur L.A., Dalmadi A., Dulai S., Koncz C.
    Plant Mol. Biol. 55:679-686(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
  9. "The nuclear cap-binding protein complex is not essential for nonsense-mediated mRNA decay (NMD) in plants."
    Dzikiewicz-Krawczyk A., Piontek P., Szweykowska-Kulinska Z., Jarmolowski A.
    Acta Biochim. Pol. 55:825-828(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: LACK OF FUNCTION IN NMD.
  10. "Two cap-binding proteins CBP20 and CBP80 are involved in processing primary MicroRNAs."
    Kim S., Yang J.-Y., Xu J., Jang I.-C., Prigge M.J., Chua N.-H.
    Plant Cell Physiol. 49:1634-1644(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  11. "Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana."
    Laubinger S., Sachsenberg T., Zeller G., Busch W., Lohmann J.U., Raetsch G., Weigel D.
    Proc. Natl. Acad. Sci. U.S.A. 105:8795-8800(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  12. "The Arabidopsis CBP20 targets the cap-binding complex to the nucleus, and is stabilized by CBP80."
    Kierzkowski D., Kmieciak M., Piontek P., Wojtaszek P., Szweykowska-Kulinska Z., Jarmolowski A.
    Plant J. 59:814-825(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, INTERACTION WITH ABH1.
  13. "FRIGIDA delays flowering in Arabidopsis via a cotranscriptional mechanism involving direct interaction with the nuclear cap-binding complex."
    Geraldo N., Baeurle I., Kidou S., Hu X., Dean C.
    Plant Physiol. 150:1611-1618(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH FRIGIDA.
  14. "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks."
    Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S.
    Plant Physiol. 150:889-903(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-245, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiNCBP2_ARATH
AccessioniPrimary (citable) accession number: Q9XFD1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: November 1, 1999
Last modified: March 16, 2016
This is version 111 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

In contrast to other organisms, the CBC complex is apparently not essential for nonsense-mediated mRNA decay (NMD) in Arabidopsis.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. 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.