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UniProtKB - Q9EPU0 (RENT1_MOUSE)

Protein

Regulator of nonsense transcripts 1

Gene

Upf1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) (located 50-55 or more nucleotides downstream from the termination codon) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Phosphorylated UPF1 is recognized by EST1B/SMG5, SMG6 and SMG7 which are thought to provide a link to the mRNA degradation machinery involving exonucleolytic and endonucleolytic pathways, and to serve as adapters to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation. UPF1 can also activate NMD without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJC indicative for alternative NMD pathways. Plays a role in replication-dependent histone mRNA degradation at the end of phase S; the function is independent of UPF2. For the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. The ATPase activity of UPF1 is required for disassembly of mRNPs undergoing NMD (By similarity). Essential for embryonic viability.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei481ATPBy similarity1
Binding sitei671ATPBy similarity1
Binding sitei708ATPBy similarity1
Binding sitei839ATPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri116 – 267UPF1-typeAdd BLAST152
Nucleotide bindingi501 – 505ATPBy similarity5

GO - Molecular functioni

View the complete GO annotation on QuickGO ...

GO - Biological processi

View the complete GO annotation on QuickGO ...

Keywordsi

Molecular functionHelicase, Hydrolase, RNA-binding
Biological processNonsense-mediated mRNA decay
LigandATP-binding, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)

Names & Taxonomyi

Protein namesi
Recommended name:
Regulator of nonsense transcripts 1 (EC:3.6.4.-)
Alternative name(s):
ATP-dependent helicase RENT1
Nonsense mRNA reducing factor 1
Short name:
NORF1
Up-frameshift suppressor 1 homolog
Short name:
mUpf1
Gene namesi
Name:Upf1
Synonyms:Rent1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Mus › Mus
Proteomesi
  • UP000000589 Componenti: Chromosome 8

Organism-specific databases

MGIiMGI:107995 Upf1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

Embryos are viable in pre-implantation period, show complete loss of NMD but are resorbed shortly after implantation.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000807171 – 1124Regulator of nonsense transcripts 1Add BLAST1124

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei10PhosphoserineBy similarity1
Modified residuei31PhosphoserineBy similarity1
Modified residuei560PhosphoserineBy similarity1
Modified residuei951PhosphoserineBy similarity1
Modified residuei1014Omega-N-methylarginineBy similarity1
Modified residuei1084PhosphoserineBy similarity1
Modified residuei1102PhosphoserineCombined sources1
Modified residuei1105PhosphoserineCombined sources1
Modified residuei1122PhosphoserineBy similarity1

Post-translational modificationi

Phosphorylated by SMG1; required for formation of mRNA surveillance complexes.By similarity

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

PaxDbiQ9EPU0
PeptideAtlasiQ9EPU0
PRIDEiQ9EPU0

PTM databases

iPTMnetiQ9EPU0
PhosphoSitePlusiQ9EPU0
SwissPalmiQ9EPU0

Expressioni

Gene expression databases

BgeeiENSMUSG00000058301 Expressed in 208 organ(s), highest expression level in skin of back
GenevisibleiQ9EPU0 MM

Interactioni

Subunit structurei

Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Associates with the exon junction complex (EJC). Associates with the SGM1C complex; is phosphorylated by the complex kinase component SGM1. Interacts with UPF2. Interacts with UPF3A and UPF3B. Interacts with EST1A. Interacts with SLBP. Interacts (when hyperphosphorylated) with PNRC2. Interacts with AGO1 and AGO2. Interacts with GSPT2. Interacts with isoform 1 and isoform 5 of ADAR/ADAR1. Interacts with SMG7. Interacts with ZC3H12A; this interaction occurs in a mRNA translationally active- and termination-dependent manner and is essential for ZC3H12A-mediated degradation of target mRNAs. Interacts with CPSF6.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
Eri1Q7TMF22EBI-6876715,EBI-16026214

Protein-protein interaction databases

BioGridi202860, 7 interactors
DIPiDIP-60114N
IntActiQ9EPU0, 10 interactors
MINTiQ9EPU0
STRINGi10090.ENSMUSP00000075089

Structurei

3D structure databases

ProteinModelPortaliQ9EPU0
SMRiQ9EPU0
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 410Sufficient for interaction with RENT2By similarityAdd BLAST410

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi1084 – 1085[ST]-Q motif 12
Motifi1102 – 1103[ST]-Q motif 22

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi47 – 75Ala/Gly/Pro-richAdd BLAST29
Compositional biasi1037 – 1124Gln/Ser-richAdd BLAST88

Domaini

The [ST]-Q motif constitutes a recognition sequence for kinases from the PI3/PI4-kinase family.By similarity

Sequence similaritiesi

Belongs to the DNA2/NAM7 helicase family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri116 – 267UPF1-typeAdd BLAST152

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1802 Eukaryota
COG1112 LUCA
GeneTreeiENSGT00800000124068
HOGENOMiHOG000205990
HOVERGENiHBG061556
InParanoidiQ9EPU0
KOiK14326
OMAiQPCAAQN
OrthoDBiEOG091G01B6
PhylomeDBiQ9EPU0
TreeFamiTF300554

Family and domain databases

InterProiView protein in InterPro
IPR006935 Helicase/UvrB_N
IPR027417 P-loop_NTPase
IPR018999 RNA-helicase_UPF1_UPF2-interct
PfamiView protein in Pfam
PF04851 ResIII, 1 hit
PF09416 UPF1_Zn_bind, 1 hit
SUPFAMiSSF52540 SSF52540, 1 hit

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket
Isoform 1 (identifier: Q9EPU0-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MSVEAYGPSS QTLTFLDTEE AELLGADTQG SEFEFTDFTL PSQTQTPPGG 
        60         70         80         90        100
PGGAGGPGGA GAGGAAGQLD AQVGPEGILQ NGAVDDSVAK TSQLLAELNF 
       110        120        130        140        150
EEDEEDTYYT KDLPVHACSY CGIHDPACVV YCNTSKKWFC NGRGNTSGSH 
       160        170        180        190        200
IVNHLVRAKC KEVTLHKDGP LGETVLECYN CGCRNVFLLG FIPAKADSVV 
       210        220        230        240        250
VLLCRQPCAS QSSLKDINWD SSQWQPLIQD RCFLSWLVKI PSEQEQLRAR 
       260        270        280        290        300
QITAQQINKL EELWKENPSA TLEDLEKPGV DEEPQHVLLR YEDAYQYQNI 
       310        320        330        340        350
FGPLVKLEAD YDKKLKESQT QDNITVRWDL GLNKKRIAFF TLPKTDSGNE 
       360        370        380        390        400
DLVIIWLRDM RLMQGDEICL RYKGDLAPLW KGIGHVIKVP DNYGDEIAIE 
       410        420        430        440        450
LRSSVGAPVE VTHNFQVDFV WKSTSFDRMQ SALKTFAVDE TSVSGYIYHK 
       460        470        480        490        500
LLGHEVEDVV IKCQLPKRFT AQGLPDLNHS QVYAVKTVLQ RPLSLIQGPP 
       510        520        530        540        550
GTGKTVTSAT IVYHLARQGN GPVLVCAPSN IAVDQLTEKI HQTGLKVVRL 
       560        570        580        590        600
CAKSREAIDS PVSFLALHNQ IRNMDSMPEL QKLQQLKDET GELSSADEKR 
       610        620        630        640        650
YRALKRTAER ELLMNADVIC CTCVGAGDPR LAKMQFRSIL IDESTQATEP 
       660        670        680        690        700
ECMVPVVLGA KQLILVGDHC QLGPVVMCKK AAKAGLSQSL FERLVVLGIR 
       710        720        730        740        750
PIRLQVQYRM HPALSAFPSN IFYEGSLQNG VTAADRVKKG FDFQWPQPDK 
       760        770        780        790        800
PMFFYVTQGQ EEIASSGTSY LNRTEAANVE KITTKLLKAG AKPDQIGIIT 
       810        820        830        840        850
PYEGQRSYLV QYMQFSGSLH TKLYQEVEIA SVDAFQGREK DFIILSCVRA 
       860        870        880        890        900
NEHQGIGFLN DPRRLNVALT RARYGVIIVG NPKALSKQPL WNHLLSYYKE 
       910        920        930        940        950
QKALVEGPLN NLRESLMQFS KPRKLVNTVN PGARFMTTAM YDAREAIIPG 
       960        970        980        990       1000
SVYDRSSQGR PSNMYFQTHD QISMISAGPS HVAAMNIPIP FNLVMPPMPP 
      1010       1020       1030       1040       1050
PGYFGQANGP AAGRGTPKTK TGRGGRQKNR FGLPGPSQTT LPNSQASQDV 
      1060       1070       1080       1090       1100
ASQPFSQGAL TQGYVSMSQP SQMSQPGLSQ PELSQDSYLG DEFKSQIDVA 
      1110       1120 
LSQDSTYQGE RAYQHGGVTG LSQY
Length:1,124
Mass (Da):123,967
Last modified:May 29, 2007 - v2
Checksum:i5F1B0ED50F63C52E
GO
Isoform 2 (identifier: Q9EPU0-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     348-358: Missing.

Show »
Length:1,113
Mass (Da):122,657
Checksum:iBFE8D50AD49DAA54
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti56G → S in AAT46119 (Ref. 3) Curated1
Sequence conflicti58G → A in BAE28409 (PubMed:16141072).Curated1
Sequence conflicti60A → P in AAT46119 (Ref. 3) Curated1
Sequence conflicti71A → S in AAT46119 (Ref. 3) Curated1
Sequence conflicti428R → K in AAT46119 (Ref. 3) Curated1
Sequence conflicti439D → E in AAT46119 (Ref. 3) Curated1
Sequence conflicti460V → F in AAT46119 (Ref. 3) Curated1
Sequence conflicti495L → F in AAT46119 (Ref. 3) Curated1
Sequence conflicti633K → E in BAE28409 (PubMed:16141072).Curated1
Sequence conflicti820H → Y in BAE28409 (PubMed:16141072).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_025764348 – 358Missing in isoform 2. 4 PublicationsAdd BLAST11

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF322655 mRNA Translation: AAG42830.1
AY597039, AY597038 Genomic DNA Translation: AAT46119.1
AK148196 mRNA Translation: BAE28409.1
BC030916 mRNA Translation: AAH30916.1
BC052149 mRNA Translation: AAH52149.1
BC056442 mRNA Translation: AAH56442.1
AF182947 mRNA Translation: AAK08652.1
CCDSiCCDS52572.1 [Q9EPU0-1]
RefSeqiNP_001116301.1, NM_001122829.2 [Q9EPU0-1]
NP_109605.2, NM_030680.3 [Q9EPU0-2]
XP_006509667.1, XM_006509604.3 [Q9EPU0-1]
XP_006509668.1, XM_006509605.3 [Q9EPU0-1]
UniGeneiMm.258280
Mm.390048

Genome annotation databases

EnsembliENSMUST00000075666; ENSMUSP00000075089; ENSMUSG00000058301 [Q9EPU0-1]
ENSMUST00000215817; ENSMUSP00000148927; ENSMUSG00000058301 [Q9EPU0-2]
GeneIDi19704
KEGGimmu:19704
UCSCiuc009mab.2 mouse [Q9EPU0-1]
uc012gfa.1 mouse [Q9EPU0-2]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF322655 mRNA Translation: AAG42830.1
AY597039, AY597038 Genomic DNA Translation: AAT46119.1
AK148196 mRNA Translation: BAE28409.1
BC030916 mRNA Translation: AAH30916.1
BC052149 mRNA Translation: AAH52149.1
BC056442 mRNA Translation: AAH56442.1
AF182947 mRNA Translation: AAK08652.1
CCDSiCCDS52572.1 [Q9EPU0-1]
RefSeqiNP_001116301.1, NM_001122829.2 [Q9EPU0-1]
NP_109605.2, NM_030680.3 [Q9EPU0-2]
XP_006509667.1, XM_006509604.3 [Q9EPU0-1]
XP_006509668.1, XM_006509605.3 [Q9EPU0-1]
UniGeneiMm.258280
Mm.390048

3D structure databases

ProteinModelPortaliQ9EPU0
SMRiQ9EPU0
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi202860, 7 interactors
DIPiDIP-60114N
IntActiQ9EPU0, 10 interactors
MINTiQ9EPU0
STRINGi10090.ENSMUSP00000075089

PTM databases

iPTMnetiQ9EPU0
PhosphoSitePlusiQ9EPU0
SwissPalmiQ9EPU0

Proteomic databases

PaxDbiQ9EPU0
PeptideAtlasiQ9EPU0
PRIDEiQ9EPU0

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000075666; ENSMUSP00000075089; ENSMUSG00000058301 [Q9EPU0-1]
ENSMUST00000215817; ENSMUSP00000148927; ENSMUSG00000058301 [Q9EPU0-2]
GeneIDi19704
KEGGimmu:19704
UCSCiuc009mab.2 mouse [Q9EPU0-1]
uc012gfa.1 mouse [Q9EPU0-2]

Organism-specific databases

CTDi5976
MGIiMGI:107995 Upf1

Phylogenomic databases

eggNOGiKOG1802 Eukaryota
COG1112 LUCA
GeneTreeiENSGT00800000124068
HOGENOMiHOG000205990
HOVERGENiHBG061556
InParanoidiQ9EPU0
KOiK14326
OMAiQPCAAQN
OrthoDBiEOG091G01B6
PhylomeDBiQ9EPU0
TreeFamiTF300554

Enzyme and pathway databases

ReactomeiR-MMU-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)

Miscellaneous databases

ChiTaRSiUpf1 mouse
PROiPR:Q9EPU0
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000058301 Expressed in 208 organ(s), highest expression level in skin of back
GenevisibleiQ9EPU0 MM

Family and domain databases

InterProiView protein in InterPro
IPR006935 Helicase/UvrB_N
IPR027417 P-loop_NTPase
IPR018999 RNA-helicase_UPF1_UPF2-interct
PfamiView protein in Pfam
PF04851 ResIII, 1 hit
PF09416 UPF1_Zn_bind, 1 hit
SUPFAMiSSF52540 SSF52540, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRENT1_MOUSE
AccessioniPrimary (citable) accession number: Q9EPU0
Secondary accession number(s): Q3UG00
, Q6GYP5, Q6PHQ5, Q8K0N4, Q99PR4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 18, 2001
Last sequence update: May 29, 2007
Last modified: November 7, 2018
This is version 158 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
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