NMD2_YEAST
ID NMD2_YEAST Reviewed; 1089 AA.
AC P38798; D3DL27;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 2.
DT 03-AUG-2022, entry version 175.
DE RecName: Full=Nonsense-mediated mRNA decay protein 2;
DE AltName: Full=Up-frameshift suppressor 2;
GN Name=NMD2; Synonyms=IFS1, SUA1, UPF2; OrderedLocusNames=YHR077C;
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 [GENOMIC DNA].
RX PubMed=7883168; DOI=10.1101/gad.9.4.437;
RA He F., Jacobson A.;
RT "Identification of a novel component of the nonsense-mediated mRNA decay
RT pathway by use of an interacting protein screen.";
RL Genes Dev. 9:437-454(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=PLY136;
RX PubMed=7883167; DOI=10.1101/gad.9.4.423;
RA Cui Y., Hagan K.W., Zhang S., Peltz S.W.;
RT "Identification and characterization of genes that are required for the
RT accelerated degradation of mRNAs containing a premature translational
RT termination codon.";
RL Genes Dev. 9:423-436(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=7604038; DOI=10.1073/pnas.92.14.6587;
RA Lee S.I., Umen J.G., Varmus H.E.;
RT "A genetic screen identifies cellular factors involved in retroviral -1
RT frameshifting.";
RL Proc. Natl. Acad. Sci. U.S.A. 92:6587-6591(1995).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8091229; DOI=10.1126/science.8091229;
RA Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z.,
RA Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T.,
RA Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P., Louis E.J.,
RA Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L.,
RA St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P.,
RA Waterston R., Wilson R., Vaudin M.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
RT VIII.";
RL Science 265:2077-2082(1994).
RN [5]
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 [6]
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).
CC -!- FUNCTION: Involved in nonsense-mediated decay of mRNAs containing
CC premature stop codons. It interacts, via its C-terminus, with
CC NAM7/UPF1. Could be involved in determining the efficiency of
CC translational termination or reinitiation or factors involved in the
CC initial assembly of an initiation- and termination-competent mRNP.
CC -!- INTERACTION:
CC P38798; P48412: UPF3; NbExp=3; IntAct=EBI-12071, EBI-20117;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- MISCELLANEOUS: Present with 1280 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
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DR EMBL; U14974; AAA67724.1; -; Genomic_DNA.
DR EMBL; U12137; AAA66521.1; -; Genomic_DNA.
DR EMBL; U28158; AAA74948.1; -; Genomic_DNA.
DR EMBL; U10556; AAB68893.1; -; Genomic_DNA.
DR EMBL; BK006934; DAA06771.1; -; Genomic_DNA.
DR PIR; S48244; S48244.
DR RefSeq; NP_011944.2; NM_001179207.1.
DR PDB; 4LUN; X-ray; 1.64 A; U=1-310.
DR PDBsum; 4LUN; -.
DR AlphaFoldDB; P38798; -.
DR SMR; P38798; -.
DR BioGRID; 36511; 349.
DR ComplexPortal; CPX-1315; Nonsense-mediated decay complex.
DR DIP; DIP-2295N; -.
DR IntAct; P38798; 6.
DR MINT; P38798; -.
DR STRING; 4932.YHR077C; -.
DR iPTMnet; P38798; -.
DR MaxQB; P38798; -.
DR PaxDb; P38798; -.
DR PRIDE; P38798; -.
DR EnsemblFungi; YHR077C_mRNA; YHR077C; YHR077C.
DR GeneID; 856476; -.
DR KEGG; sce:YHR077C; -.
DR SGD; S000001119; NMD2.
DR VEuPathDB; FungiDB:YHR077C; -.
DR eggNOG; KOG2051; Eukaryota.
DR GeneTree; ENSGT00530000064318; -.
DR HOGENOM; CLU_002633_1_0_1; -.
DR InParanoid; P38798; -.
DR OMA; DFQHHQI; -.
DR BioCyc; YEAST:G3O-31124-MON; -.
DR Reactome; R-SCE-975957; Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
DR PRO; PR:P38798; -.
DR Proteomes; UP000002311; Chromosome VIII.
DR RNAct; P38798; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0035145; C:exon-exon junction complex; IBA:GO_Central.
DR GO; GO:0005844; C:polysome; IDA:SGD.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0071026; P:cytoplasmic RNA surveillance; IC:ComplexPortal.
DR GO; GO:0006310; P:DNA recombination; IMP:SGD.
DR GO; GO:0070478; P:nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay; IGI:SGD.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IMP:SGD.
DR InterPro; IPR016024; ARM-type_fold.
DR InterPro; IPR003890; MIF4G-like_typ-3.
DR InterPro; IPR039762; Nmd2/UPF2.
DR InterPro; IPR007193; Upf2/Nmd2_C.
DR PANTHER; PTHR12839; PTHR12839; 2.
DR Pfam; PF02854; MIF4G; 3.
DR Pfam; PF04050; Upf2; 1.
DR SMART; SM00543; MIF4G; 3.
DR SUPFAM; SSF48371; SSF48371; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Reference proteome.
FT CHAIN 1..1089
FT /note="Nonsense-mediated mRNA decay protein 2"
FT /id="PRO_0000096873"
FT REGION 819..951
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 840..868
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 886..939
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 2
FT /note="D -> YQQ (in Ref. 3 and 4)"
FT /evidence="ECO:0000305"
FT HELIX 3..17
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 34..44
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 52..60
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 66..68
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 69..81
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 87..104
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 106..116
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 117..120
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 130..152
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 159..161
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 182..190
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 195..197
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 201..210
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 212..214
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 223..225
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 231..271
FT /evidence="ECO:0007829|PDB:4LUN"
FT HELIX 277..303
FT /evidence="ECO:0007829|PDB:4LUN"
SQ SEQUENCE 1089 AA; 126747 MW; 13BBE725675CBF52 CRC64;
MDDGRKKELH DLNTRAWNGE EVFPLKSKKL DSSIKRNTGF IKKLKKGFVK GSESSLLKDL
SEASLEKYLS EIIVTVTECL LNVLNKNDDV IAAVEIISGL HQRFNGRFTS PLLGAFLQAF
ENPSVDIESE RDELQRITRV KGNLRVFTEL YLVGVFRTLD DIESKDAIPN FLQKKTGRKD
PLLFSILREI LNYKFKLGFT TTIATAFIKK FAPLFRDDDN SWDDLIYDSK LKGALQSLFK
NFIDATFARA TELHKKVNKL QREHQKCQIR TGKLRDEYVE EYDKLLPIFI RFKTSAITLG
EFFKLEIPEL EGASNDDLKE TASPMITNQI LPPNQRLWEN EDTRKFYEIL PDISKTVEES
QSSKTEKDSN VNSKNINLFF TDLEMADCKD IIDDLSNRYW SSYLDNKATR NRILKFFMET
QDWSKLPVYS RFIATNSKYM PEIVSEFINY LDNGFRSQLH SNKINVKNII FFSEMIKFQL
IPSFMIFHKI RTLIMYMQVP NNVEILTVLL EHSGKFLLNK PEYKELMEKM VQLIKDKKND
RQLNMNMKSA LENIITLLYP PSVKSLNVTV KTITPEQQFY RILIRSELSS LDFKHIVKLV
RKAHWDDVAI QKVLFSLFSK PHKISYQNIP LLTKVLGGLY SYRRDFVIRC IDQVLENIER
GLEINDYGQN MHRISNVRYL TEIFNFEMIK SDVLLDTIYH IIRFGHINNQ PNPFYLNYSD
PPDNYFRIQL VTTILLNINR TPAAFTKKCK LLLRFFEYYT FIKEQPLPKE TEFRVSSTFK
KYENIFGNTK FERSENLVES ASRLESLLKS LNAIKSKDDR VKGSSASIHN GKESAVPIES
ITEDDEDEDD ENDDGVDLLG EDEDAEISTP NTESAPGKHQ AKQDESEDED DEDDDEDDDD
DDDDDDDDGE EGDEDDDEDD DDEDDDDEEE EDSDSDLEYG GDLDADRDIE MKRMYEEYER
KLKDEEERKA EEELERQFQK MMQESIDARK SEKVVASKIP VISKPVSVQK PLLLKKSEEP
SSSKETYEEL SKPKKIAFTF LTKSGKKTQS RILQLPTDVK FVSDVLEEEE KLKTERNKIK
KIVLKRSFD
