NCBP2_YEAST
ID NCBP2_YEAST Reviewed; 208 AA.
AC Q08920; D6W3J0;
DT 18-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 169.
DE RecName: Full=Nuclear cap-binding protein subunit 2;
DE AltName: Full=20 kDa nuclear cap-binding protein;
DE AltName: Full=NCBP 20 kDa subunit;
DE Short=CBP20;
GN Name=CBC2; Synonyms=CBP20, MUD13, SAE1; OrderedLocusNames=YPL178W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, IDENTIFICATION IN THE
RP CBC AND SRP1-CBC COMPLEXES, U SNRNA-BINDING, SUBCELLULAR LOCATION, AND
RP FUNCTION OF THE CBC AND SRP1-CBC COMPLEXES.
RX PubMed=8858145; DOI=10.1016/s0092-8674(00)81319-7;
RA Goerlich D., Kraft R., Kostka S., Vogel F., Hartmann E., Laskey R.A.,
RA Mattaj I.W., Izaurraide E.;
RT "Importin provides a link between nuclear protein import and U snRNA
RT export.";
RL Cell 87:21-32(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP FUNCTION, AND IDENTIFICATION IN THE CBC COMPLEX.
RX PubMed=8682299; DOI=10.1101/gad.10.13.1699;
RA Colot H.V., Stutz F., Rosbash M.;
RT "The yeast splicing factor Mud13p is a commitment complex component and
RT corresponds to CBP20, the small subunit of the nuclear cap-binding
RT complex.";
RL Genes Dev. 10:1699-1708(1996).
RN [6]
RP FUNCTION OF THE CBC COMPLEX.
RX PubMed=8811086; DOI=10.1093/nar/24.17.3332;
RA Lewis J.D., Goerlich D., Mattaj I.W.;
RT "A yeast cap binding protein complex (yCBC) acts at an early step in pre-
RT mRNA splicing.";
RL Nucleic Acids Res. 24:3332-3336(1996).
RN [7]
RP FUNCTION.
RX PubMed=9215889; DOI=10.1093/genetics/146.3.817;
RA McKee A.H.Z., Kleckner N.;
RT "Mutations in Saccharomyces cerevisiae that block meiotic prophase
RT chromosome metabolism and confer cell cycle arrest at pachytene identify
RT two new meiosis-specific genes SAE1 and SAE3.";
RL Genetics 146:817-834(1997).
RN [8]
RP INTERACTION WITH MUD2 AND SNU56, AND FUNCTION OF THE CBC COMPLEX.
RX PubMed=10490594; DOI=10.1128/mcb.19.10.6543;
RA Fortes P., Kufel J., Fornerod M., Polycarpou-Schwarz M., Lafontaine D.,
RA Tollervey D., Mattaj I.W.;
RT "Genetic and physical interactions involving the yeast nuclear cap-binding
RT complex.";
RL Mol. Cell. Biol. 19:6543-6553(1999).
RN [9]
RP IDENTIFICATION IN THE CBC COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY, AND
RP INTERACTION OF THE COMPLEX WITH CAPPED RNA.
RX PubMed=10504710; DOI=10.1038/13732;
RA Rigaut G., Shevchenko A., Rutz B., Wilm M., Mann M., Seraphin B.;
RT "A generic protein purification method for protein complex characterization
RT and proteome exploration.";
RL Nat. Biotechnol. 17:1030-1032(1999).
RN [10]
RP INTERACTION WITH NPL3, AND FUNCTION.
RX PubMed=10823828; DOI=10.1074/jbc.m002312200;
RA Shen E.C., Stage-Zimmermann T., Chui P., Silver P.A.;
RT "7The yeast mRNA-binding protein Npl3p interacts with the cap-binding
RT complex.";
RL J. Biol. Chem. 275:23718-23724(2000).
RN [11]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [12]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [13]
RP FUNCTION.
RX PubMed=14671320; DOI=10.1073/pnas.2536857100;
RA Kushner D.B., Lindenbach B.D., Grdzelishvili V.Z., Noueiry A.O., Paul S.M.,
RA Ahlquist P.;
RT "Systematic, genome-wide identification of host genes affecting replication
RT of a positive-strand RNA virus.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:15764-15769(2003).
RN [14]
RP FUNCTION OF THE CBC COMPLEX.
RX PubMed=12756324; DOI=10.1261/rna.5100903;
RA Baron-Benhamou J., Fortes P., Inada T., Preiss T., Hentze M.W.;
RT "The interaction of the cap-binding complex (CBC) with eIF4G is dispensable
RT for translation in yeast.";
RL RNA 9:654-662(2003).
RN [15]
RP FUNCTION.
RX PubMed=15753296; DOI=10.1073/pnas.0500684102;
RA Gao Q., Das B., Sherman F., Maquat L.E.;
RT "Cap-binding protein 1-mediated and eukaryotic translation initiation
RT factor 4E-mediated pioneer rounds of translation in yeast.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:4258-4263(2005).
RN [16]
RP FUNCTION.
RX PubMed=16166263; DOI=10.1073/pnas.0506518102;
RA Kuai L., Das B., Sherman F.;
RT "A nuclear degradation pathway controls the abundance of normal mRNAs in
RT Saccharomyces cerevisiae.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:13962-13967(2005).
RN [17]
RP IDENTIFICATION IN THE CBC COMPLEX, INTERACTION WITH SRP1, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=16729021; DOI=10.1038/sj.embor.7400702;
RA Hernandez H., Dziembowski A., Taverner T., Seraphin B., Robinson C.V.;
RT "Subunit architecture of multimeric complexes isolated directly from
RT cells.";
RL EMBO Rep. 7:605-610(2006).
RN [18]
RP IDENTIFICATION IN NRD1 COMPLEX, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=16427013; DOI=10.1016/j.molcel.2005.11.028;
RA Vasiljeva L., Buratowski S.;
RT "Nrd1 interacts with the nuclear exosome for 3' processing of RNA
RT polymerase II transcripts.";
RL Mol. Cell 21:239-248(2006).
RN [19]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC -!- FUNCTION: Component of the CBC complex, which binds co-
CC transcriptionally to the cap of pre-mRNAs and is involved in
CC maturation, export and degradation of nuclear mRNAs. The CBC complex is
CC required for efficient pre-mRNA splicing through efficient commitment
CC complex and spliceosome formation. Together with NPL3, the CBC complex
CC is required for export of mRNAs out of the nucleus. The CBC complex is
CC also involved in nuclear mRNA degradation, probably by directing the
CC mRNAs to the sites of degradation. Affects replication of the positive-
CC strand RNA virus BMV. {ECO:0000269|PubMed:10490594,
CC ECO:0000269|PubMed:10823828, ECO:0000269|PubMed:12756324,
CC ECO:0000269|PubMed:14671320, ECO:0000269|PubMed:15753296,
CC ECO:0000269|PubMed:16166263, ECO:0000269|PubMed:8682299,
CC ECO:0000269|PubMed:8811086, ECO:0000269|PubMed:8858145,
CC ECO:0000269|PubMed:9215889}.
CC -!- SUBUNIT: Component of the nuclear cap-binding complex (CBC), a
CC heterodimer composed of STO1/CBC1 and CBC2 that interacts with capped
CC RNAs. The complex interacts strongly with the importin subunit alpha
CC SRP1. The SRP1-CBC trimer also binds to capped RNAs, but formation of
CC the importin alpha/beta heterodimer upon binding of KAP95 to SRP1 in
CC the cytoplasm causes dissociation of CBC from the RNA. The CBC complex
CC is part of the commitment complex 1 (CC1), binding to the cap of pre-
CC mRNA and interacting with U1 snRNP subunits MUD2 and SNU56. The CBC
CC complex is part of the NRD1 complex, composed of CBC2, NAB1, NRD1, SEN1
CC and STO1/CBC2. The CBC complex also interacts with NPL3 and eIF4G
CC (TIF4631 and TIF4632). {ECO:0000269|PubMed:10490594,
CC ECO:0000269|PubMed:10504710, ECO:0000269|PubMed:10823828,
CC ECO:0000269|PubMed:16427013, ECO:0000269|PubMed:16729021,
CC ECO:0000269|PubMed:8682299, ECO:0000269|PubMed:8858145}.
CC -!- INTERACTION:
CC Q08920; Q02821: SRP1; NbExp=3; IntAct=EBI-33556, EBI-1797;
CC Q08920; P34160: STO1; NbExp=5; IntAct=EBI-33556, EBI-745;
CC -!- SUBCELLULAR LOCATION: Nucleus. Cytoplasm, perinuclear region.
CC Note=Predominantly nuclear, is able to exit the nucleus in an RNA-
CC dependent manner.
CC -!- MISCELLANEOUS: In contrast to metazoans, where the CBC complex is
CC involved in the nuclear export of capped U snRNAs, it is believed that
CC in yeast, U snRNAs are not exported from the nucleus and U snRNPs are
CC assembled in the nucleus from RNAs and imported proteins.
CC -!- MISCELLANEOUS: Present with 6200 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the RRM NCBP2 family. {ECO:0000305}.
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DR EMBL; U39665; AAF21454.1; -; mRNA.
DR EMBL; Z73534; CAA97885.1; -; Genomic_DNA.
DR EMBL; AY692949; AAT92968.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11256.1; -; Genomic_DNA.
DR PIR; S65190; S65190.
DR RefSeq; NP_015147.1; NM_001183992.1.
DR PDB; 6N7P; EM; 3.60 A; Y=1-208.
DR PDBsum; 6N7P; -.
DR AlphaFoldDB; Q08920; -.
DR SMR; Q08920; -.
DR BioGRID; 36005; 678.
DR ComplexPortal; CPX-1657; Nuclear cap-binding complex.
DR DIP; DIP-1117N; -.
DR IntAct; Q08920; 27.
DR MINT; Q08920; -.
DR STRING; 4932.YPL178W; -.
DR iPTMnet; Q08920; -.
DR MaxQB; Q08920; -.
DR PaxDb; Q08920; -.
DR PRIDE; Q08920; -.
DR EnsemblFungi; YPL178W_mRNA; YPL178W; YPL178W.
DR GeneID; 855925; -.
DR KEGG; sce:YPL178W; -.
DR SGD; S000006099; CBC2.
DR VEuPathDB; FungiDB:YPL178W; -.
DR eggNOG; KOG0121; Eukaryota.
DR GeneTree; ENSGT00390000003197; -.
DR HOGENOM; CLU_070952_1_0_1; -.
DR InParanoid; Q08920; -.
DR OMA; AENCMRY; -.
DR BioCyc; YEAST:G3O-34073-MON; -.
DR Reactome; R-SCE-113418; Formation of the Early Elongation Complex.
DR Reactome; R-SCE-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-SCE-72086; mRNA Capping.
DR Reactome; R-SCE-77595; Processing of Intronless Pre-mRNAs.
DR Reactome; R-SCE-975956; Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
DR Reactome; R-SCE-975957; Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
DR PRO; PR:Q08920; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q08920; protein.
DR GO; GO:0000243; C:commitment complex; IDA:SGD.
DR GO; GO:0005845; C:mRNA cap binding complex; IPI:ComplexPortal.
DR GO; GO:0005846; C:nuclear cap binding complex; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:ComplexPortal.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0000339; F:RNA cap binding; IDA:SGD.
DR GO; GO:0031124; P:mRNA 3'-end processing; IMP:ComplexPortal.
DR GO; GO:0045292; P:mRNA cis splicing, via spliceosome; IEA:InterPro.
DR GO; GO:0006406; P:mRNA export from nucleus; IDA:ComplexPortal.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IDA:ComplexPortal.
DR GO; GO:0042789; P:mRNA transcription by RNA polymerase II; IMP:ComplexPortal.
DR GO; GO:0000956; P:nuclear-transcribed mRNA catabolic process; IMP:ComplexPortal.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IEA:UniProtKB-KW.
DR GO; GO:0031053; P:primary miRNA processing; IC:ComplexPortal.
DR GO; GO:0006970; P:response to osmotic stress; IDA:ComplexPortal.
DR CDD; cd12240; RRM_NCBP2; 1.
DR Gene3D; 3.30.70.330; -; 1.
DR InterPro; IPR027157; NCBP2.
DR InterPro; IPR034148; NCBP2_RRM.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR000504; RRM_dom.
DR PANTHER; PTHR18847; PTHR18847; 1.
DR Pfam; PF00076; RRM_1; 1.
DR SMART; SM00360; RRM; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
DR PROSITE; PS50102; RRM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; mRNA processing;
KW mRNA splicing; mRNA transport; Nonsense-mediated mRNA decay; Nucleus;
KW Reference proteome; RNA-binding; Transport.
FT CHAIN 1..208
FT /note="Nuclear cap-binding protein subunit 2"
FT /id="PRO_0000232990"
FT DOMAIN 46..124
FT /note="RRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 168..208
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 168..185
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 193..208
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 24
FT /ligand="mRNA"
FT /ligand_id="ChEBI:CHEBI:33699"
FT /ligand_part="mRNA cap"
FT /evidence="ECO:0000250"
FT BINDING 49
FT /ligand="mRNA"
FT /ligand_id="ChEBI:CHEBI:33699"
FT /ligand_part="mRNA cap"
FT /evidence="ECO:0000250"
FT BINDING 118..122
FT /ligand="mRNA"
FT /ligand_id="ChEBI:CHEBI:33699"
FT /ligand_part="mRNA cap"
FT /evidence="ECO:0000250"
FT BINDING 129..133
FT /ligand="mRNA"
FT /ligand_id="ChEBI:CHEBI:33699"
FT /ligand_part="mRNA cap"
FT /evidence="ECO:0000250"
FT BINDING 139..140
FT /ligand="mRNA"
FT /ligand_id="ChEBI:CHEBI:33699"
FT /ligand_part="mRNA cap"
FT /evidence="ECO:0000250"
SQ SEQUENCE 208 AA; 23774 MW; B77E93BDDC429160 CRC64;
MSLEEFDEVK YDHSTKRLDT PSRYLLRKAR RNPNGLQELR ESMKSSTIYV GNLSFYTSEE
QIYELFSKCG TIKRIIMGLD RFKFTPCGFC FIIYSCPDEA LNALKYLSDT KLDEKTITID
LDPGFEDGRQ FGRGKSGGQV SDELRFDFDA SRGGFAIPFA ERVGVPHSRF DNSSSQSNTN
NYIPPPDAMG TFRPGFDEER EDDNYVPQ
