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Q92900

- RENT1_HUMAN

UniProt

Q92900 - RENT1_HUMAN

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Protein

Regulator of nonsense transcripts 1

Gene

UPF1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- 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 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.5 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei486 – 4861ATP
Binding sitei676 – 6761ATP
Binding sitei713 – 7131ATP
Binding sitei844 – 8441ATP

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri121 – 272152UPF1-typeAdd
BLAST
Nucleotide bindingi506 – 5105ATP

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. ATP-dependent RNA helicase activity Source: UniProtKB
  3. chromatin binding Source: HGNC
  4. DNA binding Source: InterPro
  5. helicase activity Source: UniProtKB
  6. poly(A) RNA binding Source: UniProtKB
  7. RNA binding Source: UniProtKB
  8. zinc ion binding Source: InterPro

GO - Biological processi

  1. ATP catabolic process Source: GOC
  2. DNA repair Source: HGNC
  3. DNA replication Source: HGNC
  4. dosage compensation by inactivation of X chromosome Source: Ensembl
  5. gene expression Source: Reactome
  6. histone mRNA catabolic process Source: UniProtKB
  7. mRNA export from nucleus Source: HGNC
  8. mRNA metabolic process Source: Reactome
  9. nuclear-transcribed mRNA catabolic process Source: UniProt
  10. nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: UniProtKB
  11. regulation of translational termination Source: UniProtKB
  12. RNA metabolic process Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

Nonsense-mediated mRNA decay

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, RNA-binding, Zinc

Enzyme and pathway databases

ReactomeiREACT_75768. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_75822. 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:
hUpf1
Gene namesi
Name:UPF1
Synonyms:KIAA0221, RENT1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 19

Organism-specific databases

HGNCiHGNC:9962. UPF1.

Subcellular locationi

Cytoplasm. CytoplasmP-body. Nucleus
Note: Hyperphosphorylated form is targeted to the P-body, while unphosphorylated protein is distributed throughout the cytoplasm.

GO - Cellular componenti

  1. chromatin Source: HGNC
  2. cytoplasm Source: UniProtKB
  3. cytosol Source: Reactome
  4. exon-exon junction complex Source: UniProtKB
  5. nucleus Source: UniProtKB
  6. supraspliceosomal complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi126 – 1261C → S: Abolishes ability to interact with UPF2/RENT2 and copurifies with greater amounts of SMG1, SMG8 and SMG9. 2 Publications
Mutagenesisi506 – 5083GTG → RTE: Prevents dephosphorylation and targets the protein to the P-body. 1 Publication
Mutagenesisi509 – 5091K → A: Inhibits histone mRNA degradation, ATPase activity and ATP binding. 3 Publications
Mutagenesisi610 – 6112KR → AA: Impairs RNA binding.
Mutagenesisi615 – 6151R → A: Impairs RNA binding. 1 Publication
Mutagenesisi647 – 6482DE → AA: Loss of ATPase activity and helicase activity. 2 Publications
Mutagenesisi676 – 6761Q → A: Impairs ATPase activity, no effect on ATP binding. 1 Publication
Mutagenesisi714 – 7141R → A: Impairs ATPase activity and ATP binding. 1 Publication
Mutagenesisi843 – 8431R → A: Inhibits histone mRNA degradation. 2 Publications
Mutagenesisi843 – 8431R → C: Abolishes NMD. 2 Publications
Mutagenesisi876 – 8761R → A: Impairs ATPase activity and ATP binding. 1 Publication
Mutagenesisi1084 – 10841S → A: Impairs association with UPF2, SMG1 and SMG7 and impairs phosphorylation; when associated with A-1089, A-1107 and A-1127. 1 Publication
Mutagenesisi1089 – 10891S → A: Impairs association with UPF2, SMG1 and SMG7 and impairs phosphorylation; when associated with A-1084, A-1107 and A-1127. 2 Publications
Mutagenesisi1089 – 10891S → A: Still phosphorylated but with less efficiency. 2 Publications
Mutagenesisi1107 – 11071S → A: Impairs association with UPF2, SMG1 and SMG7 and impairs phosphorylation; when associated with A-1084, A-1089 and A-1127. 2 Publications
Mutagenesisi1107 – 11071S → A: Impairs phosphorylation. 2 Publications
Mutagenesisi1108 – 11081Q → N: Impairs phosphorylation. 1 Publication
Mutagenesisi1127 – 11271S → A: Impairs association with UPF2, SMG1 and SMG7 and impairs phosphorylation; when associated with A-1084, A-1089 and A-1107. 1 Publication

Organism-specific databases

PharmGKBiPA34328.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11291129Regulator of nonsense transcripts 1PRO_0000080716Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1089 – 10891Phosphoserine2 Publications
Modified residuei1107 – 11071Phosphoserine7 Publications
Modified residuei1110 – 11101Phosphoserine2 Publications
Modified residuei1127 – 11271Phosphoserine1 Publication

Post-translational modificationi

Phosphorylated by SMG1; required for formation of mRNA surveillance complexes.10 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ92900.
PaxDbiQ92900.
PRIDEiQ92900.

PTM databases

PhosphoSiteiQ92900.

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

BgeeiQ92900.
CleanExiHS_UPF1.
ExpressionAtlasiQ92900. baseline and differential.
GenevestigatoriQ92900.

Organism-specific databases

HPAiHPA019587.
HPA020857.

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, UPF3A and UPF3B. Interacts with EST1A and SLBP. Interacts (when hyperphosphorylated) with PNRC2. Interacts with AGO1, AGO2 and GSPT2. Interacts with isoform 1 and isoform 5 of ADAR/ADAR1.14 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ACDQ96AP03EBI-373471,EBI-717666
DCP1AQ9NPI613EBI-373471,EBI-374238
DCP2Q8IU603EBI-373471,EBI-521577
EIF3AQ141525EBI-373492,EBI-366617
GSPT1P151702EBI-373471,EBI-948993
GSPT2Q8IYD13EBI-373471,EBI-3869637
L1RE1Q9UN816EBI-373471,EBI-722458
PNRC2Q9NPJ49EBI-373471,EBI-726549
SKI7Q084912EBI-373471,EBI-1389From a different organism.
SMG5Q9UPR32EBI-373492,EBI-3400861
SMG6Q86US82EBI-373492,EBI-3232100
STAU1O957935EBI-373471,EBI-358174
TERTO147463EBI-373471,EBI-1772203
UPF2Q9HAU525EBI-373471,EBI-372073
UPF3AQ9H1J14EBI-373471,EBI-521530
UPF3BQ9BZI78EBI-373471,EBI-372780

Protein-protein interaction databases

BioGridi111908. 104 interactions.
DIPiDIP-29875N.
IntActiQ92900. 79 interactions.
MINTiMINT-5005507.
STRINGi9606.ENSP00000262803.

Structurei

Secondary structure

1
1129
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni124 – 1263Combined sources
Helixi131 – 1333Combined sources
Beta strandi134 – 1374Combined sources
Turni138 – 1414Combined sources
Beta strandi142 – 1465Combined sources
Beta strandi151 – 1533Combined sources
Helixi155 – 1639Combined sources
Beta strandi168 – 1703Combined sources
Beta strandi174 – 1763Combined sources
Turni184 – 1863Combined sources
Turni191 – 1933Combined sources
Beta strandi195 – 1973Combined sources
Beta strandi200 – 2023Combined sources
Beta strandi204 – 2096Combined sources
Turni210 – 2134Combined sources
Turni216 – 2183Combined sources
Turni220 – 2223Combined sources
Helixi226 – 2283Combined sources
Beta strandi230 – 2334Combined sources
Beta strandi235 – 2384Combined sources
Turni240 – 2423Combined sources
Helixi248 – 2536Combined sources
Helixi259 – 26911Combined sources
Helixi299 – 32123Combined sources
Beta strandi326 – 3294Combined sources
Beta strandi332 – 3354Combined sources
Turni337 – 3393Combined sources
Beta strandi341 – 3455Combined sources
Helixi364 – 3663Combined sources
Beta strandi372 – 3776Combined sources
Beta strandi379 – 3824Combined sources
Beta strandi385 – 3939Combined sources
Beta strandi396 – 3983Combined sources
Beta strandi402 – 4076Combined sources
Beta strandi410 – 4123Combined sources
Beta strandi418 – 4258Combined sources
Helixi429 – 44315Combined sources
Helixi450 – 4567Combined sources
Helixi484 – 49310Combined sources
Beta strandi497 – 5026Combined sources
Helixi509 – 52214Combined sources
Beta strandi523 – 5253Combined sources
Beta strandi528 – 5347Combined sources
Helixi535 – 54713Combined sources
Beta strandi552 – 5543Combined sources
Helixi558 – 5603Combined sources
Helixi568 – 5703Combined sources
Helixi572 – 5776Combined sources
Helixi582 – 59110Combined sources
Turni593 – 5953Combined sources
Helixi600 – 62021Combined sources
Beta strandi622 – 6276Combined sources
Helixi630 – 6323Combined sources
Helixi634 – 6363Combined sources
Beta strandi642 – 6465Combined sources
Helixi649 – 6513Combined sources
Helixi654 – 6618Combined sources
Turni662 – 6643Combined sources
Beta strandi665 – 6728Combined sources
Helixi684 – 6885Combined sources
Turni689 – 6924Combined sources
Helixi695 – 7028Combined sources
Helixi717 – 72711Combined sources
Beta strandi733 – 7364Combined sources
Helixi739 – 7413Combined sources
Beta strandi751 – 7544Combined sources
Beta strandi757 – 7615Combined sources
Beta strandi766 – 7683Combined sources
Beta strandi770 – 7734Combined sources
Beta strandi775 – 7773Combined sources
Helixi778 – 79417Combined sources
Helixi798 – 8003Combined sources
Beta strandi801 – 8066Combined sources
Helixi808 – 81912Combined sources
Helixi826 – 8305Combined sources
Beta strandi832 – 8365Combined sources
Turni837 – 8426Combined sources
Beta strandi845 – 8517Combined sources
Beta strandi857 – 8593Combined sources
Helixi862 – 8654Combined sources
Helixi867 – 8748Combined sources
Beta strandi875 – 88511Combined sources
Helixi887 – 8904Combined sources
Helixi894 – 90512Combined sources
Beta strandi909 – 9124Combined sources
Helixi914 – 9163Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2GJKX-ray2.60A295-925[»]
2GK6X-ray2.40A/B295-925[»]
2GK7X-ray2.80A295-925[»]
2IYKX-ray2.95A/B115-272[»]
2WJVX-ray2.85A/B115-925[»]
2WJYX-ray2.50A115-925[»]
2XZOX-ray2.40A295-925[»]
2XZPX-ray2.72A295-925[»]
ProteinModelPortaliQ92900.
SMRiQ92900. Positions 116-925.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ92900.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 415415Sufficient for interaction with RENT2Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi1089 – 10902[ST]-Q motif 1
Motifi1107 – 11082[ST]-Q motif 2

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi47 – 8034Ala/Gly/Pro-richAdd
BLAST
Compositional biasi1042 – 112988Gln/Ser-richAdd
BLAST

Domaini

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

Sequence similaritiesi

Belongs to the DNA2/NAM7 helicase family.Curated
Contains 1 UPF1-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri121 – 272152UPF1-typeAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG1112.
GeneTreeiENSGT00550000074391.
HOGENOMiHOG000205990.
HOVERGENiHBG061556.
InParanoidiQ92900.
KOiK14326.
OMAiFLALHEQ.
OrthoDBiEOG76QFGF.
PhylomeDBiQ92900.
TreeFamiTF300554.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR027417. P-loop_NTPase.
IPR018999. RNA-helicase_UPF1_UPF2-interct.
[Graphical view]
PfamiPF09416. UPF1_Zn_bind. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q92900-1) [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
PGGPGGGGAG GPGGAGAGAA AGQLDAQVGP EGILQNGAVD DSVAKTSQLL
110 120 130 140 150
AELNFEEDEE DTYYTKDLPI HACSYCGIHD PACVVYCNTS KKWFCNGRGN
160 170 180 190 200
TSGSHIVNHL VRAKCKEVTL HKDGPLGETV LECYNCGCRN VFLLGFIPAK
210 220 230 240 250
ADSVVVLLCR QPCASQSSLK DINWDSSQWQ PLIQDRCFLS WLVKIPSEQE
260 270 280 290 300
QLRARQITAQ QINKLEELWK ENPSATLEDL EKPGVDEEPQ HVLLRYEDAY
310 320 330 340 350
QYQNIFGPLV KLEADYDKKL KESQTQDNIT VRWDLGLNKK RIAYFTLPKT
360 370 380 390 400
DSGNEDLVII WLRDMRLMQG DEICLRYKGD LAPLWKGIGH VIKVPDNYGD
410 420 430 440 450
EIAIELRSSV GAPVEVTHNF QVDFVWKSTS FDRMQSALKT FAVDETSVSG
460 470 480 490 500
YIYHKLLGHE VEDVIIKCQL PKRFTAQGLP DLNHSQVYAV KTVLQRPLSL
510 520 530 540 550
IQGPPGTGKT VTSATIVYHL ARQGNGPVLV CAPSNIAVDQ LTEKIHQTGL
560 570 580 590 600
KVVRLCAKSR EAIDSPVSFL ALHNQIRNMD SMPELQKLQQ LKDETGELSS
610 620 630 640 650
ADEKRYRALK RTAERELLMN ADVICCTCVG AGDPRLAKMQ FRSILIDEST
660 670 680 690 700
QATEPECMVP VVLGAKQLIL VGDHCQLGPV VMCKKAAKAG LSQSLFERLV
710 720 730 740 750
VLGIRPIRLQ VQYRMHPALS AFPSNIFYEG SLQNGVTAAD RVKKGFDFQW
760 770 780 790 800
PQPDKPMFFY VTQGQEEIAS SGTSYLNRTE AANVEKITTK LLKAGAKPDQ
810 820 830 840 850
IGIITPYEGQ RSYLVQYMQF SGSLHTKLYQ EVEIASVDAF QGREKDFIIL
860 870 880 890 900
SCVRANEHQG IGFLNDPRRL NVALTRARYG VIIVGNPKAL SKQPLWNHLL
910 920 930 940 950
NYYKEQKVLV EGPLNNLRES LMQFSKPRKL VNTINPGARF MTTAMYDARE
960 970 980 990 1000
AIIPGSVYDR SSQGRPSSMY FQTHDQIGMI SAGPSHVAAM NIPIPFNLVM
1010 1020 1030 1040 1050
PPMPPPGYFG QANGPAAGRG TPKGKTGRGG RQKNRFGLPG PSQTNLPNSQ
1060 1070 1080 1090 1100
ASQDVASQPF SQGALTQGYI SMSQPSQMSQ PGLSQPELSQ DSYLGDEFKS
1110 1120
QIDVALSQDS TYQGERAYQH GGVTGLSQY
Length:1,129
Mass (Da):124,345
Last modified:October 18, 2001 - v2
Checksum:i6CCA6FE42B15BA28
GO
Isoform 2 (identifier: Q92900-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     353-363: Missing.

Show »
Length:1,118
Mass (Da):123,036
Checksum:iA485D3ED52C39D06
GO

Sequence cautioni

The sequence BAA19664.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti61 – 611G → S in AAC51140. (PubMed:9064659)Curated
Sequence conflicti466 – 4661I → T in AAC51140. (PubMed:9064659)Curated
Sequence conflicti478 – 4781G → A in AAC50771. (PubMed:8855285)Curated
Sequence conflicti524 – 5241G → D in AAC50771. (PubMed:8855285)Curated
Sequence conflicti557 – 5571A → P in AAC50771. (PubMed:8855285)Curated
Sequence conflicti901 – 9022NY → IF in AAC50771. (PubMed:8855285)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti69 – 691A → S.1 Publication
Corresponds to variant rs17339451 [ dbSNP | Ensembl ].
VAR_056207

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei353 – 36311Missing in isoform 2. 4 PublicationsVSP_003393Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U65533 mRNA. Translation: AAC50771.1.
U59323 mRNA. Translation: AAC51140.1.
D86988 mRNA. Translation: BAA19664.2. Different initiation.
AF074016 mRNA. Translation: AAC26788.1.
AC003972 Genomic DNA. Translation: AAB94785.1.
BC039817 mRNA. Translation: AAH39817.1.
CCDSiCCDS12386.1. [Q92900-2]
CCDS74315.1. [Q92900-1]
RefSeqiNP_001284478.1. NM_001297549.1. [Q92900-1]
NP_002902.2. NM_002911.3. [Q92900-2]
UniGeneiHs.515266.

Genome annotation databases

EnsembliENST00000262803; ENSP00000262803; ENSG00000005007. [Q92900-2]
ENST00000599848; ENSP00000470142; ENSG00000005007. [Q92900-1]
GeneIDi5976.
KEGGihsa:5976.
UCSCiuc002nkf.3. human. [Q92900-2]
uc002nkg.3. human. [Q92900-1]

Polymorphism databases

DMDMi17380291.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U65533 mRNA. Translation: AAC50771.1 .
U59323 mRNA. Translation: AAC51140.1 .
D86988 mRNA. Translation: BAA19664.2 . Different initiation.
AF074016 mRNA. Translation: AAC26788.1 .
AC003972 Genomic DNA. Translation: AAB94785.1 .
BC039817 mRNA. Translation: AAH39817.1 .
CCDSi CCDS12386.1. [Q92900-2 ]
CCDS74315.1. [Q92900-1 ]
RefSeqi NP_001284478.1. NM_001297549.1. [Q92900-1 ]
NP_002902.2. NM_002911.3. [Q92900-2 ]
UniGenei Hs.515266.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2GJK X-ray 2.60 A 295-925 [» ]
2GK6 X-ray 2.40 A/B 295-925 [» ]
2GK7 X-ray 2.80 A 295-925 [» ]
2IYK X-ray 2.95 A/B 115-272 [» ]
2WJV X-ray 2.85 A/B 115-925 [» ]
2WJY X-ray 2.50 A 115-925 [» ]
2XZO X-ray 2.40 A 295-925 [» ]
2XZP X-ray 2.72 A 295-925 [» ]
ProteinModelPortali Q92900.
SMRi Q92900. Positions 116-925.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 111908. 104 interactions.
DIPi DIP-29875N.
IntActi Q92900. 79 interactions.
MINTi MINT-5005507.
STRINGi 9606.ENSP00000262803.

PTM databases

PhosphoSitei Q92900.

Polymorphism databases

DMDMi 17380291.

Proteomic databases

MaxQBi Q92900.
PaxDbi Q92900.
PRIDEi Q92900.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000262803 ; ENSP00000262803 ; ENSG00000005007 . [Q92900-2 ]
ENST00000599848 ; ENSP00000470142 ; ENSG00000005007 . [Q92900-1 ]
GeneIDi 5976.
KEGGi hsa:5976.
UCSCi uc002nkf.3. human. [Q92900-2 ]
uc002nkg.3. human. [Q92900-1 ]

Organism-specific databases

CTDi 5976.
GeneCardsi GC19P018942.
HGNCi HGNC:9962. UPF1.
HPAi HPA019587.
HPA020857.
MIMi 601430. gene.
neXtProti NX_Q92900.
PharmGKBi PA34328.
HUGEi Search...
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG1112.
GeneTreei ENSGT00550000074391.
HOGENOMi HOG000205990.
HOVERGENi HBG061556.
InParanoidi Q92900.
KOi K14326.
OMAi FLALHEQ.
OrthoDBi EOG76QFGF.
PhylomeDBi Q92900.
TreeFami TF300554.

Enzyme and pathway databases

Reactomei REACT_75768. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_75822. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

ChiTaRSi UPF1. human.
EvolutionaryTracei Q92900.
GeneWikii UPF1.
GenomeRNAii 5976.
NextBioi 23259.
PROi Q92900.
SOURCEi Search...

Gene expression databases

Bgeei Q92900.
CleanExi HS_UPF1.
ExpressionAtlasi Q92900. baseline and differential.
Genevestigatori Q92900.

Family and domain databases

Gene3Di 3.40.50.300. 2 hits.
InterProi IPR027417. P-loop_NTPase.
IPR018999. RNA-helicase_UPF1_UPF2-interct.
[Graphical view ]
Pfami PF09416. UPF1_Zn_bind. 1 hit.
[Graphical view ]
SUPFAMi SSF52540. SSF52540. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Mammalian orthologues of a yeast regulator of nonsense transcript stability."
    Perlick H.A., Medghalchi S.M., Spencer F.A., Kendzior R.J. Jr., Dietz H.C.
    Proc. Natl. Acad. Sci. U.S.A. 93:10928-10932(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
    Tissue: Heart.
  2. "Cloning and characterization of HUPF1, a human homolog of the Saccharomyces cerevisiae nonsense mRNA-reducing UPF1 protein."
    Applequist S.E., Selg M., Raman C., Jaeck H.-M.
    Nucleic Acids Res. 25:814-821(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), CHARACTERIZATION.
  3. "Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain."
    Nagase T., Seki N., Ishikawa K., Ohira M., Kawarabayasi Y., Ohara O., Tanaka A., Kotani H., Miyajima N., Nomura N.
    DNA Res. 3:321-329(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT SER-69.
    Tissue: Bone marrow.
  4. "SMG-2 is a phosphorylated protein required for mRNA surveillance in Caenorhabditis elegans and related to Upf1p of yeast."
    Page M.F., Carr B., Anders K.R., Grimson A., Anderson P.
    Mol. Cell. Biol. 19:5943-5951(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
  5. "The DNA sequence and biology of human chromosome 19."
    Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V.
    , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M.
    Nature 428:529-535(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Uterus.
  7. "Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon."
    Lykke-Andersen J., Shu M.-D., Steitz J.A.
    Cell 103:1121-1131(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN NONSENSE-MEDIATED MRNA DECAY, INTERACTION WITH WITH UPF2; UPF3A AND UPF3B, SUBCELLULAR LOCATION, MUTAGENESIS OF ARG-843.
  8. "Novel Upf2p orthologues suggest a functional link between translation initiation and nonsense surveillance complexes."
    Mendell J.T., Medghalchi S.M., Lake R.G., Noensie E.N., Dietz H.C.
    Mol. Cell. Biol. 20:8944-8957(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH UPF2.
  9. "Characterization of the biochemical properties of the human Upf1 gene product that is involved in nonsense-mediated mRNA decay."
    Bhattacharya A., Czaplinski K., Trifillis P., He F., Jacobson A., Peltz S.W.
    RNA 6:1226-1235(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME ACTIVITY, RNA-BINDING, MUTAGENESIS OF 647-ASP-GLU-648.
  10. "Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay."
    Yamashita A., Ohnishi T., Kashima I., Taya Y., Ohno S.
    Genes Dev. 15:2215-2228(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-1089 AND SER-1107, MUTAGENESIS OF SER-1089; SER-1107 AND GLN-1108.
  11. "Cloning of a novel phosphatidylinositol kinase-related kinase: characterization of the human SMG-1 RNA surveillance protein."
    Denning G., Jamieson L., Maquat L.E., Thompson E.A., Fields A.P.
    J. Biol. Chem. 276:22709-22714(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION.
  12. "Identification and characterization of human orthologues to Saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4)."
    Serin G., Gersappe A., Black J.D., Aronoff R., Maquat L.E.
    Mol. Cell. Biol. 21:209-223(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH UPF2, SUBCELLULAR LOCATION.
  13. "Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1."
    Lykke-Andersen J., Shu M.-D., Steitz J.A.
    Science 293:1836-1839(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN A POST-SPLICING MRNP COMPLEX, ASSOCIATION WITH THE EJC COMPLEX.
  14. "Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7."
    Ohnishi T., Yamashita A., Kashima I., Schell T., Anders K.R., Grimson A., Hachiya T., Hentze M.W., Anderson P., Ohno S.
    Mol. Cell 12:1187-1200(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION.
  15. "Characterization of human Smg5/7a: a protein with similarities to Caenorhabditis elegans SMG5 and SMG7 that functions in the dephosphorylation of Upf1."
    Chiu S.-Y., Serin G., Ohara O., Maquat L.E.
    RNA 9:77-87(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH EST1A.
  16. "SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway."
    Fukuhara N., Ebert J., Unterholzner L., Lindner D., Izaurralde E., Conti E.
    Mol. Cell 17:537-547(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SMG7.
  17. "Regulated degradation of replication-dependent histone mRNAs requires both ATR and Upf1."
    Kaygun H., Marzluff W.F.
    Nat. Struct. Mol. Biol. 12:794-800(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH SLBP, MUTAGENESIS OF LYS-509 AND ARG-843.
  18. "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
    Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
    Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  19. "Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay."
    Kashima I., Yamashita A., Izumi N., Kataoka N., Morishita R., Hoshino S., Ohno M., Dreyfuss G., Ohno S.
    Genes Dev. 20:355-367(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE SURF COMPLEX, PHOSPHORYLATION AT SER-1089 AND SER-1107, MUTAGENESIS OF CYS-126; LYS-509; SER-1084; SER-1089; SER-1107 AND SER-1127.
  20. "Proteomic and functional analysis of Argonaute-containing mRNA-protein complexes in human cells."
    Hoeck J., Weinmann L., Ender C., Ruedel S., Kremmer E., Raabe M., Urlaub H., Meister G.
    EMBO Rep. 8:1052-1060(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH AGO1 AND AGO2.
  21. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1107, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic kidney.
  22. "Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'."
    Mullen T.E., Marzluff W.F.
    Genes Dev. 22:50-65(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN HISTONE MRNA DEGRADATION ACTIVITY.
  23. "A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay."
    Singh G., Rebbapragada I., Lykke-Andersen J.
    PLoS Biol. 6:E111-E111(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH GSPT2.
  24. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1107, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  25. "The editing enzyme ADAR1 and the mRNA surveillance protein hUpf1 interact in the cell nucleus."
    Agranat L., Raitskin O., Sperling J., Sperling R.
    Proc. Natl. Acad. Sci. U.S.A. 105:5028-5033(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH ADAR, SUBCELLULAR LOCATION.
  26. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  27. "SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay."
    Yamashita A., Izumi N., Kashima I., Ohnishi T., Saari B., Katsuhata Y., Muramatsu R., Morita T., Iwamatsu A., Hachiya T., Kurata R., Hirano H., Anderson P., Ohno S.
    Genes Dev. 23:1091-1105(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ASSOCIATION WITH THE SMG1C COMPLEX, MUTAGENESIS OF CYS-126.
  28. "Human proline-rich nuclear receptor coregulatory protein 2 mediates an interaction between mRNA surveillance machinery and decapping complex."
    Cho H., Kim K.M., Kim Y.K.
    Mol. Cell 33:75-86(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, PHOSPHORYLATION, INTERACTION WITH PNRC2, MUTAGENESIS OF 506-GLY--GLY-508.
  29. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
    Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
    Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1107, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  30. "Upf1 ATPase-dependent mRNP disassembly is required for completion of nonsense- mediated mRNA decay."
    Franks T.M., Singh G., Lykke-Andersen J.
    Cell 143:938-950(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN MRNP DISASSEMBLY.
  31. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1107; SER-1110 AND SER-1127, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  32. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  33. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1107 AND SER-1110, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  34. "Structural and functional insights into the human Upf1 helicase core."
    Cheng Z., Muhlrad D., Lim M.K., Parker R., Song H.
    EMBO J. 26:253-264(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 295-914, MUTAGENESIS OF LYS-509; 610-LYS--ARG-612; ARG-615; 647-ASP-GLU-648; GLN-676; ARG-714 AND ARG-876.
  35. "Unusual bipartite mode of interaction between the nonsense-mediated decay factors, UPF1 and UPF2."
    Clerici M., Mourao A., Gutsche I., Gehring N.H., Hentze M.W., Kulozik A., Kadlec J., Sattler M., Cusack S.
    EMBO J. 28:2293-2306(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 115-914 IN COMPLEX WITH UPF2.
  36. "Molecular mechanisms for the RNA-dependent ATPase activity of Upf1 and its regulation by Upf2."
    Chakrabarti S., Jayachandran U., Bonneau F., Fiorini F., Basquin C., Domcke S., Le Hir H., Conti E.
    Mol. Cell 41:693-703(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 295-925 IN COMPLEX WITH ATP ANALOG AND RNA, FUNCTION.

Entry informationi

Entry nameiRENT1_HUMAN
AccessioniPrimary (citable) accession number: Q92900
Secondary accession number(s): O00239
, O43343, Q86Z25, Q92842
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 18, 2001
Last sequence update: October 18, 2001
Last modified: November 26, 2014
This is version 151 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3