P38798 (NMD2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Nonsense-mediated mRNA decay protein 2

Alternative name(s):
Up-frameshift suppressor 2

Gene names

Name:	NMD2
Synonyms:	IFS1, SUA1, UPF2
Ordered Locus Names:	YHR077C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	1089 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Involved in nonsense-mediated decay of mRNAs containing premature stop codons. It interacts, via its C-terminus, with NAM7/UPF1. Could be involved in determining the efficiency of translational termination or reinitiation or factors involved in the initial assembly of an initiation- and termination-competent mRNP.
Subcellular location	Cytoplasm Potential.
Miscellaneous	Present with 1280 molecules/cell in log phase SD medium.

Ontologies

Keywords
Cellular component	Cytoplasm
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Inferred from genetic interaction PubMed 12881429. Source: SGD
Cellular_component	cytoplasm Inferred from direct assay PubMed 16043493. Source: SGD polysome Inferred from direct assay PubMed 9268361. Source: SGD
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro RNA binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1089	1089	Nonsense-mediated mRNA decay protein 2		PRO_0000096873
Regions
	Compositional bias	843 – 975	133	Asp/Glu-rich (highly acidic)
Experimental info
	Sequence conflict	2	1	D → YQQ Ref.3
	Sequence conflict	2	1	D → YQQ Ref.4

Sequences

	Sequence		Length	Mass (Da)
	P38798 [UniParc]. Last modified November 1, 1995. Version 2. Checksum: 13BBE725675CBF52	FASTA	1,089	126,747
	10 20 30 40 50 60 MDDGRKKELH DLNTRAWNGE EVFPLKSKKL DSSIKRNTGF IKKLKKGFVK GSESSLLKDL 70 80 90 100 110 120 SEASLEKYLS EIIVTVTECL LNVLNKNDDV IAAVEIISGL HQRFNGRFTS PLLGAFLQAF 130 140 150 160 170 180 ENPSVDIESE RDELQRITRV KGNLRVFTEL YLVGVFRTLD DIESKDAIPN FLQKKTGRKD 190 200 210 220 230 240 PLLFSILREI LNYKFKLGFT TTIATAFIKK FAPLFRDDDN SWDDLIYDSK LKGALQSLFK 250 260 270 280 290 300 NFIDATFARA TELHKKVNKL QREHQKCQIR TGKLRDEYVE EYDKLLPIFI RFKTSAITLG 310 320 330 340 350 360 EFFKLEIPEL EGASNDDLKE TASPMITNQI LPPNQRLWEN EDTRKFYEIL PDISKTVEES 370 380 390 400 410 420 QSSKTEKDSN VNSKNINLFF TDLEMADCKD IIDDLSNRYW SSYLDNKATR NRILKFFMET 430 440 450 460 470 480 QDWSKLPVYS RFIATNSKYM PEIVSEFINY LDNGFRSQLH SNKINVKNII FFSEMIKFQL 490 500 510 520 530 540 IPSFMIFHKI RTLIMYMQVP NNVEILTVLL EHSGKFLLNK PEYKELMEKM VQLIKDKKND 550 560 570 580 590 600 RQLNMNMKSA LENIITLLYP PSVKSLNVTV KTITPEQQFY RILIRSELSS LDFKHIVKLV 610 620 630 640 650 660 RKAHWDDVAI QKVLFSLFSK PHKISYQNIP LLTKVLGGLY SYRRDFVIRC IDQVLENIER 670 680 690 700 710 720 GLEINDYGQN MHRISNVRYL TEIFNFEMIK SDVLLDTIYH IIRFGHINNQ PNPFYLNYSD 730 740 750 760 770 780 PPDNYFRIQL VTTILLNINR TPAAFTKKCK LLLRFFEYYT FIKEQPLPKE TEFRVSSTFK 790 800 810 820 830 840 KYENIFGNTK FERSENLVES ASRLESLLKS LNAIKSKDDR VKGSSASIHN GKESAVPIES 850 860 870 880 890 900 ITEDDEDEDD ENDDGVDLLG EDEDAEISTP NTESAPGKHQ AKQDESEDED DEDDDEDDDD 910 920 930 940 950 960 DDDDDDDDGE EGDEDDDEDD DDEDDDDEEE EDSDSDLEYG GDLDADRDIE MKRMYEEYER 970 980 990 1000 1010 1020 KLKDEEERKA EEELERQFQK MMQESIDARK SEKVVASKIP VISKPVSVQK PLLLKKSEEP 1030 1040 1050 1060 1070 1080 SSSKETYEEL SKPKKIAFTF LTKSGKKTQS RILQLPTDVK FVSDVLEEEE KLKTERNKIK KIVLKRSFD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification of a novel component of the nonsense-mediated mRNA decay pathway by use of an interacting protein screen." He F., Jacobson A. Genes Dev. 9:437-454(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Identification and characterization of genes that are required for the accelerated degradation of mRNAs containing a premature translational termination codon." Cui Y., Hagan K.W., Zhang S., Peltz S.W. Genes Dev. 9:423-436(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: PLY136.
[3]	"A genetic screen identifies cellular factors involved in retroviral -1 frameshifting." Lee S.I., Umen J.G., Varmus H.E. Proc. Natl. Acad. Sci. U.S.A. 92:6587-6591(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII." Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P. , Louis E.J., Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L., St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P., Waterston R., Wilson R., Vaudin M. Science 265:2077-2082(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[5]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[6]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U14974 Genomic DNA. Translation: AAA67724.1. U12137 Genomic DNA. Translation: AAA66521.1. U28158 Genomic DNA. Translation: AAA74948.1. U10556 Genomic DNA. Translation: AAB68893.1. BK006934 Genomic DNA. Translation: DAA06771.1.
PIR	S48244.
RefSeq	NP_011944.2. NM_001179207.1.
3D structure databases
ProteinModelPortal	P38798.
SMR	P38798. Positions 575-780.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2295N.
IntAct	P38798. 4 interactions.
MINT	MINT-1521719.
STRING	4932.YHR077C.
Proteomic databases
PaxDb	P38798.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YHR077C; YHR077C; YHR077C.
GeneID	856476.
KEGG	sce:YHR077C.
Organism-specific databases
CYGD	YHR077c.
SGD	S000001119. NMD2.
Phylogenomic databases
eggNOG	NOG321770.
GeneTree	ENSGT00530000064318.
KO	K14327.
OMA	YLDNGFR.
OrthoDB	EOG4NW2TJ.
Gene expression databases
Genevestigator	P38798.
GermOnline	YHR077C. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	1.25.40.180. 2 hits.
InterPro	IPR016024. ARM-type_fold. IPR016021. MIF4-like_typ_1/2/3. IPR003890. MIF4G-like_typ-3. IPR007193. Up-fram_suppressor-2. [Graphical view]
Pfam	PF02854. MIF4G. 3 hits. PF04050. Upf2. 1 hit. [Graphical view]
SMART	SM00543. MIF4G. 3 hits. [Graphical view]
SUPFAM	SSF48371. ARM-type_fold. 2 hits.
ProtoNet	Search...
Other
NextBio	982152.

Entry information

Entry name

NMD2_YEAST

Accession

Primary (citable) accession number: P38798
Secondary accession number(s): D3DL27

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	November 1, 1995
Last modified:	May 1, 2013
This is version 104 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program