CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-018869
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Regulator of nonsense transcripts 1 
Protein Synonyms/Alias
 ATP-dependent helicase RENT1; Nonsense mRNA reducing factor 1; NORF1; Up-frameshift suppressor 1 homolog; hUpf1 
Gene Name
 UPF1 
Gene Synonyms/Alias
 KIAA0221; RENT1 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
428DRMQSALKTFAVDETubiquitination[1]
576DSMPELQKLQQLKDEubiquitination[1]
593ELSSADEKRYRALKRubiquitination[1]
782KITTKLLKAGAKPDQubiquitination[1]
Reference
 [1] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661] 
Functional Description
 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 and allowing the recycling of NMD factors. 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. Essential for embryonic viability. 
Sequence Annotation
 ZN_FING 121 272 UPF1-type.
 NP_BIND 506 510 ATP.
 REGION 1 415 Sufficient for interaction with RENT2.
 MOTIF 1089 1090 [ST]-Q motif 1.
 MOTIF 1107 1108 [ST]-Q motif 2.
 BINDING 486 486 ATP.
 BINDING 676 676 ATP.
 BINDING 713 713 ATP.
 BINDING 844 844 ATP.
 MOD_RES 1089 1089 Phosphoserine.
 MOD_RES 1107 1107 Phosphoserine.
 MOD_RES 1110 1110 Phosphoserine.
 MOD_RES 1127 1127 Phosphoserine.  
Keyword
 3D-structure; Alternative splicing; ATP-binding; Complete proteome; Cytoplasm; Helicase; Hydrolase; Metal-binding; Nonsense-mediated mRNA decay; Nucleotide-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repeat; RNA-binding; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1129 AA 
Protein Sequence
MSVEAYGPSS QTLTFLDTEE AELLGADTQG SEFEFTDFTL PSQTQTPPGG PGGPGGGGAG 60
GPGGAGAGAA AGQLDAQVGP EGILQNGAVD DSVAKTSQLL AELNFEEDEE DTYYTKDLPI 120
HACSYCGIHD PACVVYCNTS KKWFCNGRGN TSGSHIVNHL VRAKCKEVTL HKDGPLGETV 180
LECYNCGCRN VFLLGFIPAK ADSVVVLLCR QPCASQSSLK DINWDSSQWQ PLIQDRCFLS 240
WLVKIPSEQE QLRARQITAQ QINKLEELWK ENPSATLEDL EKPGVDEEPQ HVLLRYEDAY 300
QYQNIFGPLV KLEADYDKKL KESQTQDNIT VRWDLGLNKK RIAYFTLPKT DSDMRLMQGD 360
EICLRYKGDL APLWKGIGHV IKVPDNYGDE IAIELRSSVG APVEVTHNFQ VDFVWKSTSF 420
DRMQSALKTF AVDETSVSGY IYHKLLGHEV EDVIIKCQLP KRFTAQGLPD LNHSQVYAVK 480
TVLQRPLSLI QGPPGTGKTV TSATIVYHLA RQGNGPVLVC APSNIAVDQL TEKIHQTGLK 540
VVRLCAKSRE AIDSPVSFLA LHNQIRNMDS MPELQKLQQL KDETGELSSA DEKRYRALKR 600
TAERELLMNA DVICCTCVGA GDPRLAKMQF RSILIDESTQ ATEPECMVPV VLGAKQLILV 660
GDHCQLGPVV MCKKAAKAGL SQSLFERLVV LGIRPIRLQV QYRMHPALSA FPSNIFYEGS 720
LQNGVTAADR VKKGFDFQWP QPDKPMFFYV TQGQEEIASS GTSYLNRTEA ANVEKITTKL 780
LKAGAKPDQI GIITPYEGQR SYLVQYMQFS GSLHTKLYQE VEIASVDAFQ GREKDFIILS 840
CVRANEHQGI GFLNDPRRLN VALTRARYGV IIVGNPKALS KQPLWNHLLN YYKEQKVLVE 900
GPLNNLRESL MQFSKPRKLV NTINPGARFM TTAMYDAREA IIPGSVYDRS SQGRPSSMYF 960
QTHDQIGMIS AGPSHVAAMN IPIPFNLVMP PMPPPGYFGQ ANGPAAGRGT PKGKTGRGGR 1020
QKNRFGLPGP SQTNLPNSQA SQDVASQPFS QGALTQGYIS MSQPSQMSQP GLSQPELSQD 1080
SYLGDEFKSQ IDVALSQDST YQGERAYQHG GVTGLSQY 1118 
Gene Ontology
 GO:0000785; C:chromatin; IDA:HGNC.
 GO:0000932; C:cytoplasmic mRNA processing body; IEA:UniProtKB-SubCell.
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0035145; C:exon-exon junction complex; IDA:UniProtKB.
 GO:0044530; C:supraspliceosomal complex; IDA:UniProtKB.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0004004; F:ATP-dependent RNA helicase activity; IDA:UniProtKB.
 GO:0003682; F:chromatin binding; IDA:HGNC.
 GO:0003677; F:DNA binding; IEA:InterPro.
 GO:0003723; F:RNA binding; NAS:UniProtKB.
 GO:0008270; F:zinc ion binding; IEA:InterPro.
 GO:0007049; P:cell cycle; IMP:HGNC.
 GO:0006281; P:DNA repair; IDA:HGNC.
 GO:0006260; P:DNA replication; IMP:HGNC.
 GO:0009048; P:dosage compensation by inactivation of X chromosome; IEA:Compara.
 GO:0010467; P:gene expression; TAS:Reactome.
 GO:0071044; P:histone mRNA catabolic process; IMP:UniProtKB.
 GO:0006406; P:mRNA export from nucleus; TAS:HGNC.
 GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IDA:UniProtKB.
 GO:0006449; P:regulation of translational termination; IMP:UniProtKB. 
Interpro
 IPR027417; P-loop_NTPase.
 IPR018999; RNA-helicase_UPF1_UPF2-interct. 
Pfam
 PF09416; UPF1_Zn_bind 
SMART
  
PROSITE
  
PRINTS