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Protein

5'-3' exoribonuclease 1

Gene

XRN1

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

Functioni

Multifunctional protein that exhibits several independent functions at different levels of the cellular processes. 5'-3' exonuclease component of the nonsense-mediated mRNA decay (NMD) which is a highly conserved mRNA degradation pathway, an RNA surveillance system whose role is to identify and rid cells of mRNA with premature termination codons and thus prevents accumulation of potentially harmful truncated proteins. The NMD pathway has a second role regulating the decay of wild-type mRNAs, and especially mRNAs that are important for telomere functions. Participate in CTH2-mediated and VTS1-mediated mRNA turnover. Involved in the degradation of several hypomodified mature tRNA species and participates in the 5'-processing or the degradation of the snoRNA precursors and rRNA processing. Involved in defense against virus and suppresses viral RNA recombination by rapidly removing the 5'-truncated RNAs, the substrates of recombination, and thus reducing the chance for recombination to occur in the parental strain. Required for the assembly of the virus-like particles of the Ty3 retrotransposon and contributes to the efficient generation of narnavirus 20S RNA by playing a major role in the elimination of the non-viral upstream sequences from the primary transcripts. Degrades single-stranded DNA (ss-DNA) and can renature complementary ss-DNA as well as catalyzes the formation of heteroduplex DNA from circular ss-DNA and homologous linear ds-DNA in vitro. Acts as a microtubule-associated protein which interacts with cytoplasmic microtubules through beta-tubulin and promotes in vitro assembly of tubulin into microtubules. Associates with microtubule functions such as chromosome transmission, nuclear migration, and SPB duplication. Has also a role in G1 to S transition and is involved in nuclear fusion during karyogamy. Required for the expression of ROK1 at the post-transcriptional level and for the alpha-factor induction of the karyogamy genes KAR3 and KAR4. Plays a role in filamentous growth.35 Publications

Miscellaneous

Present with 11700 molecules/cell in log phase SD medium.1 Publication

Cofactori

Mg2+Note: Both strand exchange and nuclease activities require magnesium, for the strand exchange activity, calcium can replace magnesium when the linear ds-DNA has been first resected with an exogenous endonuclease.

Activity regulationi

3'-phosphoadenosine 5'-phosphate (pAp) is an inhibitor of KEM1. Sodium-induced GCN4 expression reduces pAp accumulation by activating HAL2 expression, and therefore maintains mRNA degradation capacity which is likely to be important for the accurate and rapid adaptation of gene expression to salt stress.1 Publication

GO - Molecular functioni

  • 5'-3' exoribonuclease activity Source: SGD
  • chromatin binding Source: SGD
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

Keywordsi

Molecular functionExonuclease, Hydrolase, Nuclease, RNA-binding
Biological processKaryogamy, Nonsense-mediated mRNA decay, rRNA processing
LigandMagnesium

Enzyme and pathway databases

BioCyciYEAST:G3O-30661-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
5'-3' exoribonuclease 1 (EC:3.1.13.-)
Alternative name(s):
DNA strand transfer protein beta
Short name:
STP-beta
KAR(-)-enhancing mutation protein
Strand exchange protein 1
p175
Gene namesi
Name:XRN1
Synonyms:DST2, KEM1, RAR5, SEP1, SKI1
Ordered Locus Names:YGL173C
ORF Names:G1645
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VII

Organism-specific databases

EuPathDBiFungiDB:YGL173C
SGDiS000003141 XRN1

Subcellular locationi

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

Keywords - Cellular componenti

Cytoplasm, Microtubule

Pathology & Biotechi

Disruption phenotypei

Mutations affect nuclear fusion, leed to reduced chromosome stability and defects in spindle pole body duplication and/or separation as well as loss of viability under conditions of nitrogen starvation. Homozygous diploids are unable to sporulate. Leads also to arrest in pachytene and deficiency in meiotic recombination and sensitivity to oleate.3 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi37N → D: Reduces strongly exonuclease activity. 1 Publication1
Mutagenesisi41H → R or D: Reduces strongly exonuclease activity. 1 Publication1
Mutagenesisi86D → G: Reduces strongly exonuclease activity. 1 Publication1
Mutagenesisi87G → D: Reduces strongly exonuclease activity. 1 Publication1
Mutagenesisi93K → M: Reduces strongly exonuclease activity. 1 Publication1
Mutagenesisi97Q → E or R: Reduces strongly exonuclease activity. 1 Publication1
Mutagenesisi101R → G: Reduces strongly exonuclease activity. 1 Publication1
Mutagenesisi176E → G: Reduces strongly exonuclease activity. 1
Mutagenesisi178E → D or G: Reduces strongly exonuclease activity. 1 Publication1
Mutagenesisi201C → Y or R: Reduces strongly exonuclease activity. 1 Publication1
Mutagenesisi206D → A: Abolishes exonuclease activity in vitro. 1 Publication1
Mutagenesisi208D → A: Abolishes exonuclease activity in vitro. 1 Publication1
Mutagenesisi592L → P: Reduces strongly exonuclease activity; when associated with Y-710. 1 Publication1
Mutagenesisi710Y → C: Reduces strongly exonuclease activity; when associated with P-592. 1 Publication1
Mutagenesisi798W → R: Reduces strongly exonuclease activity; when associated with D-1024; F-1043 and P-1197. 1 Publication1
Mutagenesisi1024E → D: Reduces strongly exonuclease activity; when associated with R-798; F-1043 and P-1197. 1 Publication1
Mutagenesisi1043Y → F: Reduces strongly exonuclease activity; when associated with R-798; D-1024 and P-1197. 1 Publication1
Mutagenesisi1197S → P: Reduces strongly exonuclease activity; when associated with R-798; D-1024 and F-1043. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000713951 – 15285'-3' exoribonuclease 1Add BLAST1528

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1506PhosphothreonineCombined sources1
Modified residuei1510PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP22147
PaxDbiP22147
PRIDEiP22147

PTM databases

iPTMnetiP22147

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
LSM4P400703EBI-9642,EBI-188

Protein-protein interaction databases

BioGridi33080, 815 interactors
DIPiDIP-656N
IntActiP22147, 116 interactors
MINTiP22147
STRINGi4932.YGL173C

Structurei

3D structure databases

ProteinModelPortaliP22147
SMRiP22147
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the 5'-3' exonuclease family.Curated

Phylogenomic databases

GeneTreeiENSGT00670000098080
HOGENOMiHOG000160331
KOiK12618
OMAiWVLMGFM
OrthoDBiEOG092C068M

Family and domain databases

Gene3Di2.30.30.30, 1 hit
InterProiView protein in InterPro
IPR027073 5_3_exoribonuclease
IPR016494 5_3_exoribonuclease_1
IPR004859 Put_53exo
IPR014722 Rib_L2_dom2
PANTHERiPTHR12341 PTHR12341, 1 hit
PfamiView protein in Pfam
PF03159 XRN_N, 1 hit
PIRSFiPIRSF006743 Exonuclease_Xnr1, 1 hit

Sequencei

Sequence statusi: Complete.

P22147-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MGIPKFFRYI SERWPMILQL IEGTQIPEFD NLYLDMNSIL HNCTHGNDDD
60 70 80 90 100
VTKRLTEEEV FAKICTYIDH LFQTIKPKKI FYMAIDGVAP RAKMNQQRAR
110 120 130 140 150
RFRTAMDAEK ALKKAIENGD EIPKGEPFDS NSITPGTEFM AKLTKNLQYF
160 170 180 190 200
IHDKISNDSK WREVQIIFSG HEVPGEGEHK IMNFIRHLKS QKDFNQNTRH
210 220 230 240 250
CIYGLDADLI MLGLSTHGPH FALLREEVTF GRRNSEKKSL EHQNFYLLHL
260 270 280 290 300
SLLREYMELE FKEIADEMQF EYNFERILDD FILVMFVIGN DFLPNLPDLH
310 320 330 340 350
LNKGAFPVLL QTFKEALLHT DGYINEHGKI NLKRLGVWLN YLSQFELLNF
360 370 380 390 400
EKDDIDVEWF NKQLENISLE GERKRQRVGK KLLVKQQKKL IGSIKPWLME
410 420 430 440 450
QLQEKLSPDL PDEEIPTLEL PKDLDMKDHL EFLKEFAFDL GLFITHSKSK
460 470 480 490 500
GSYSLKMDLD SINPDETEEE FQNRVNSIRK TIKKYQNAII VEDKEELETE
510 520 530 540 550
KTIYNERFER WKHEYYHDKL KFTTDSEEKV RDLAKDYVEG LQWVLYYYYR
560 570 580 590 600
GCPSWSWYYP HHYAPRISDL AKGLDQDIEF DLSKPFTPFQ QLMAVLPERS
610 620 630 640 650
KNLIPPAFRP LMYDEQSPIH DFYPAEVQLD KNGKTADWEA VVLISFVDEK
660 670 680 690 700
RLIEAMQPYL RKLSPEEKTR NQFGKDLIYS FNPQVDNLYK SPLGGIFSDI
710 720 730 740 750
EHNHCVEKEY ITIPLDSSEI RYGLLPNAKL GAEMLAGFPT LLSLPFTSSL
760 770 780 790 800
EYNETMVFQQ PSKQQSMVLQ ITDIYKTNNV TLEDFSKRHL NKVIYTRWPY
810 820 830 840 850
LRESKLVSLT DGKTIYEYQE SNDKKKFGFI TKPAETQDKK LFNSLKNSML
860 870 880 890 900
RMYAKQKAVK IGPMEAIATV FPVTGLVRDS DGGYIKTFSP TPDYYPLQLV
910 920 930 940 950
VESVVNEDER YKERGPIPIE EEFPLNSKVI FLGDYAYGGE TTIDGYSSDR
960 970 980 990 1000
RLKITVEKKF LDSEPTIGKE RLQMDHQAVK YYPSYIVSKN MHLHPLFLSK
1010 1020 1030 1040 1050
ITSKFMITDA TGKHINVGIP VKFEARHQKV LGYARRNPRG WEYSNLTLNL
1060 1070 1080 1090 1100
LKEYRQTFPD FFFRLSKVGN DIPVLEDLFP DTSTKDAMNL LDGIKQWLKY
1110 1120 1130 1140 1150
VSSKFIAVSL ESDSLTKTSI AAVEDHIMKY AANIEGHERK QLAKVPREAV
1160 1170 1180 1190 1200
LNPRSSFALL RSQKFDLGDR VVYIQDSGKV PIFSKGTVVG YTTLSSSLSI
1210 1220 1230 1240 1250
QVLFDHEIVA GNNFGGRLRT NRGLGLDASF LLNITNRQFI YHSKASKKAL
1260 1270 1280 1290 1300
EKKKQSNNRN NNTKTAHKTP SKQQSEEKLR KERAHDLLNF IKKDTNEKNS
1310 1320 1330 1340 1350
ESVDNKSMGS QKDSKPAKKV LLKRPAQKSS ENVQVDLANF EKAPLDNPTV
1360 1370 1380 1390 1400
AGSIFNAVAN QYSDGIGSNL NIPTPPHPMN VVGGPIPGAN DVADVGLPYN
1410 1420 1430 1440 1450
IPPGFMTHPN GLHPLHPHQM PYPNMNGMSI PPPAPHGFGQ PISFPPPPPM
1460 1470 1480 1490 1500
TNVSDQGSRI VVNEKESQDL KKFINGKQHS NGSTIGGETK NSRKGEIKPS
1510 1520
SGTNSTECQS PKSQSNAADR DNKKDEST
Length:1,528
Mass (Da):175,460
Last modified:August 1, 1991 - v1
Checksum:i49C2EDAF73D3EB92
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M90097 Genomic DNA Translation: AAA35219.1
X54717 Genomic DNA Translation: CAA38520.1
M58367 Genomic DNA Translation: AAA35036.1
M36725 Genomic DNA Translation: AAA35125.1
X61181 Genomic DNA Translation: CAA43487.1
X84705 Genomic DNA Translation: CAA59180.1
Z72695 Genomic DNA Translation: CAA96885.1
BK006941 Genomic DNA Translation: DAA07940.1
PIRiS13743
RefSeqiNP_011342.1, NM_001181038.1

Genome annotation databases

EnsemblFungiiYGL173C; YGL173C; YGL173C
GeneIDi852702
KEGGisce:YGL173C

Similar proteinsi

Entry informationi

Entry nameiXRN1_YEAST
AccessioniPrimary (citable) accession number: P22147
Secondary accession number(s): D6VTX9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: August 1, 1991
Last modified: September 12, 2018
This is version 183 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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