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P38798

- NMD2_YEAST

UniProt

P38798 - NMD2_YEAST

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Protein

Nonsense-mediated mRNA decay protein 2

Gene

NMD2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli

Functioni

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.

GO - Molecular functioni

  1. RNA binding Source: InterPro

GO - Biological processi

  1. DNA recombination Source: SGD
  2. nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Source: SGD
  3. nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: SGD
Complete GO annotation...

Enzyme and pathway databases

BioCyciYEAST:G3O-31124-MONOMER.
ReactomeiREACT_189050. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Names & Taxonomyi

Protein namesi
Recommended name:
Nonsense-mediated mRNA decay protein 2
Alternative name(s):
Up-frameshift suppressor 2
Gene namesi
Name:NMD2
Synonyms:IFS1, SUA1, UPF2
Ordered Locus Names:YHR077C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome VIII

Organism-specific databases

CYGDiYHR077c.
SGDiS000001119. NMD2.

Subcellular locationi

Cytoplasm Curated

GO - Cellular componenti

  1. cytoplasm Source: SGD
  2. polysome Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10891089Nonsense-mediated mRNA decay protein 2PRO_0000096873Add
BLAST

Proteomic databases

MaxQBiP38798.
PaxDbiP38798.

Expressioni

Gene expression databases

GenevestigatoriP38798.

Interactioni

Protein-protein interaction databases

BioGridi36511. 161 interactions.
DIPiDIP-2295N.
IntActiP38798. 4 interactions.
MINTiMINT-1521719.
STRINGi4932.YHR077C.

Structurei

Secondary structure

1
1089
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1715Combined sources
Helixi34 – 4411Combined sources
Helixi52 – 609Combined sources
Helixi66 – 683Combined sources
Helixi69 – 8113Combined sources
Helixi87 – 10418Combined sources
Helixi106 – 11611Combined sources
Helixi117 – 1204Combined sources
Helixi130 – 15223Combined sources
Helixi159 – 1613Combined sources
Helixi170 – 1723Combined sources
Helixi182 – 1909Combined sources
Helixi195 – 1973Combined sources
Helixi201 – 21010Combined sources
Helixi212 – 2143Combined sources
Helixi223 – 2253Combined sources
Helixi231 – 27141Combined sources
Helixi277 – 30327Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4LUNX-ray1.64U1-310[»]
ProteinModelPortaliP38798.
SMRiP38798. Positions 1-310, 575-780.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi843 – 975133Asp/Glu-rich (highly acidic)Add
BLAST

Phylogenomic databases

eggNOGiNOG321770.
GeneTreeiENSGT00530000064318.
InParanoidiP38798.
KOiK14327.
OMAiIRKLHWE.
OrthoDBiEOG7TJ3S6.

Family and domain databases

Gene3Di1.25.40.180. 2 hits.
InterProiIPR016024. ARM-type_fold.
IPR016021. MIF4-like_typ_1/2/3.
IPR003890. MIF4G-like_typ-3.
IPR007193. Up-fram_suppressor-2.
[Graphical view]
PfamiPF02854. MIF4G. 3 hits.
PF04050. Upf2. 1 hit.
[Graphical view]
SMARTiSM00543. MIF4G. 3 hits.
[Graphical view]
SUPFAMiSSF48371. SSF48371. 2 hits.

Sequencei

Sequence statusi: Complete.

P38798-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MDDGRKKELH DLNTRAWNGE EVFPLKSKKL DSSIKRNTGF IKKLKKGFVK
60 70 80 90 100
GSESSLLKDL SEASLEKYLS EIIVTVTECL LNVLNKNDDV IAAVEIISGL
110 120 130 140 150
HQRFNGRFTS PLLGAFLQAF ENPSVDIESE RDELQRITRV KGNLRVFTEL
160 170 180 190 200
YLVGVFRTLD DIESKDAIPN FLQKKTGRKD PLLFSILREI LNYKFKLGFT
210 220 230 240 250
TTIATAFIKK FAPLFRDDDN SWDDLIYDSK LKGALQSLFK NFIDATFARA
260 270 280 290 300
TELHKKVNKL QREHQKCQIR TGKLRDEYVE EYDKLLPIFI RFKTSAITLG
310 320 330 340 350
EFFKLEIPEL EGASNDDLKE TASPMITNQI LPPNQRLWEN EDTRKFYEIL
360 370 380 390 400
PDISKTVEES QSSKTEKDSN VNSKNINLFF TDLEMADCKD IIDDLSNRYW
410 420 430 440 450
SSYLDNKATR NRILKFFMET QDWSKLPVYS RFIATNSKYM PEIVSEFINY
460 470 480 490 500
LDNGFRSQLH SNKINVKNII FFSEMIKFQL IPSFMIFHKI RTLIMYMQVP
510 520 530 540 550
NNVEILTVLL EHSGKFLLNK PEYKELMEKM VQLIKDKKND RQLNMNMKSA
560 570 580 590 600
LENIITLLYP PSVKSLNVTV KTITPEQQFY RILIRSELSS LDFKHIVKLV
610 620 630 640 650
RKAHWDDVAI QKVLFSLFSK PHKISYQNIP LLTKVLGGLY SYRRDFVIRC
660 670 680 690 700
IDQVLENIER GLEINDYGQN MHRISNVRYL TEIFNFEMIK SDVLLDTIYH
710 720 730 740 750
IIRFGHINNQ PNPFYLNYSD PPDNYFRIQL VTTILLNINR TPAAFTKKCK
760 770 780 790 800
LLLRFFEYYT FIKEQPLPKE TEFRVSSTFK KYENIFGNTK FERSENLVES
810 820 830 840 850
ASRLESLLKS LNAIKSKDDR VKGSSASIHN GKESAVPIES ITEDDEDEDD
860 870 880 890 900
ENDDGVDLLG EDEDAEISTP NTESAPGKHQ AKQDESEDED DEDDDEDDDD
910 920 930 940 950
DDDDDDDDGE EGDEDDDEDD DDEDDDDEEE EDSDSDLEYG GDLDADRDIE
960 970 980 990 1000
MKRMYEEYER KLKDEEERKA EEELERQFQK MMQESIDARK SEKVVASKIP
1010 1020 1030 1040 1050
VISKPVSVQK PLLLKKSEEP SSSKETYEEL SKPKKIAFTF LTKSGKKTQS
1060 1070 1080
RILQLPTDVK FVSDVLEEEE KLKTERNKIK KIVLKRSFD
Length:1,089
Mass (Da):126,747
Last modified:November 1, 1995 - v2
Checksum:i13BBE725675CBF52
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti2 – 21D → YQQ(PubMed:7604038)Curated
Sequence conflicti2 – 21D → YQQ(PubMed:8091229)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiS48244.
RefSeqiNP_011944.2. NM_001179207.1.

Genome annotation databases

EnsemblFungiiYHR077C; YHR077C; YHR077C.
GeneIDi856476.
KEGGisce:YHR077C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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 .
PIRi S48244.
RefSeqi NP_011944.2. NM_001179207.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4LUN X-ray 1.64 U 1-310 [» ]
ProteinModelPortali P38798.
SMRi P38798. Positions 1-310, 575-780.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 36511. 161 interactions.
DIPi DIP-2295N.
IntActi P38798. 4 interactions.
MINTi MINT-1521719.
STRINGi 4932.YHR077C.

Proteomic databases

MaxQBi P38798.
PaxDbi P38798.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YHR077C ; YHR077C ; YHR077C .
GeneIDi 856476.
KEGGi sce:YHR077C.

Organism-specific databases

CYGDi YHR077c.
SGDi S000001119. NMD2.

Phylogenomic databases

eggNOGi NOG321770.
GeneTreei ENSGT00530000064318.
InParanoidi P38798.
KOi K14327.
OMAi IRKLHWE.
OrthoDBi EOG7TJ3S6.

Enzyme and pathway databases

BioCyci YEAST:G3O-31124-MONOMER.
Reactomei REACT_189050. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

NextBioi 982152.
PROi P38798.

Gene expression databases

Genevestigatori P38798.

Family and domain databases

Gene3Di 1.25.40.180. 2 hits.
InterProi IPR016024. ARM-type_fold.
IPR016021. MIF4-like_typ_1/2/3.
IPR003890. MIF4G-like_typ-3.
IPR007193. Up-fram_suppressor-2.
[Graphical view ]
Pfami PF02854. MIF4G. 3 hits.
PF04050. Upf2. 1 hit.
[Graphical view ]
SMARTi SM00543. MIF4G. 3 hits.
[Graphical view ]
SUPFAMi SSF48371. SSF48371. 2 hits.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiNMD2_YEAST
AccessioniPrimary (citable) accession number: P38798
Secondary accession number(s): D3DL27
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: November 1, 1995
Last modified: November 26, 2014
This is version 120 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 1280 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome VIII
    Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names

External Data

Dasty 3