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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: 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

GO - Biological processi

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

Enzyme and pathway databases

BioCyciYEAST:G3O-31124-MONOMER.
ReactomeiR-SCE-975957. 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
Proteomesi
  • UP000002311 Componenti: Chromosome VIII

Organism-specific databases

EuPathDBiFungiDB:YHR077C.
SGDiS000001119. NMD2.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • exon-exon junction complex Source: GO_Central
  • polysome Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000968731 – 1089Nonsense-mediated mRNA decay protein 2Add BLAST1089

Proteomic databases

MaxQBiP38798.
PRIDEiP38798.

PTM databases

iPTMnetiP38798.

Interactioni

Protein-protein interaction databases

BioGridi36511. 195 interactors.
DIPiDIP-2295N.
IntActiP38798. 5 interactors.
MINTiMINT-1521719.

Structurei

Secondary structure

11089
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 17Combined sources15
Helixi34 – 44Combined sources11
Helixi52 – 60Combined sources9
Helixi66 – 68Combined sources3
Helixi69 – 81Combined sources13
Helixi87 – 104Combined sources18
Helixi106 – 116Combined sources11
Helixi117 – 120Combined sources4
Helixi130 – 152Combined sources23
Helixi159 – 161Combined sources3
Helixi170 – 172Combined sources3
Helixi182 – 190Combined sources9
Helixi195 – 197Combined sources3
Helixi201 – 210Combined sources10
Helixi212 – 214Combined sources3
Helixi223 – 225Combined sources3
Helixi231 – 271Combined sources41
Helixi277 – 303Combined sources27

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LUNX-ray1.64U1-310[»]
ProteinModelPortaliP38798.
SMRiP38798.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi843 – 975Asp/Glu-rich (highly acidic)Add BLAST133

Phylogenomic databases

GeneTreeiENSGT00530000064318.
InParanoidiP38798.
KOiK14327.
OMAiLHWEESE.
OrthoDBiEOG092C0C42.

Family and domain databases

Gene3Di1.25.40.180. 2 hits.
InterProiIPR016024. ARM-type_fold.
IPR016021. MIF4-like.
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)DescriptionActionsGraphical viewLength
Sequence conflicti2D → YQQ (PubMed:7604038).Curated1
Sequence conflicti2D → YQQ (PubMed:8091229).Curated1

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.
PIRiS48244.
RefSeqiNP_011944.2. NM_001179207.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LUNX-ray1.64U1-310[»]
ProteinModelPortaliP38798.
SMRiP38798.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36511. 195 interactors.
DIPiDIP-2295N.
IntActiP38798. 5 interactors.
MINTiMINT-1521719.

PTM databases

iPTMnetiP38798.

Proteomic databases

MaxQBiP38798.
PRIDEiP38798.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YHR077C.
SGDiS000001119. NMD2.

Phylogenomic databases

GeneTreeiENSGT00530000064318.
InParanoidiP38798.
KOiK14327.
OMAiLHWEESE.
OrthoDBiEOG092C0C42.

Enzyme and pathway databases

BioCyciYEAST:G3O-31124-MONOMER.
ReactomeiR-SCE-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

PROiP38798.

Family and domain databases

Gene3Di1.25.40.180. 2 hits.
InterProiIPR016024. ARM-type_fold.
IPR016021. MIF4-like.
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.
ProtoNetiSearch...

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 30, 2016
This is version 137 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

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.