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5'-3' exoribonuclease

 
Known also as: DNA strand transfer protein beta, STP-beta, KAR(-)-enhancing mutation protein, Strand exchange protein 1

Known abbreviations: KEM1, DST2, RAR5, SEP1, SKI1, XRN1, G1645

FUNCTION: 

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.
 

COFACTOR:

Magnesium. 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.

ENZYME REGULATION:

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.

CELLULAR LOCALIZATION:

Cytoplasm. Cytoplasm, perinuclear region. Cytoplasm, P-body.




Activities in which 5'-3' exoribonuclease is involved: Pathways in which 5'-3' exoribonuclease is involved:

NCBI GI number(s): 125342
6321265
Species: Saccharomyces cerevisiae

Links to other databases:

Database ID Link
Uniprot P22147 P22147
BRENDA - -
KEGG sce:YGL173C sce:YGL173C
PFAM: PF03159
PF03159
InterPro: IPR016494
IPR004859
IPR016494
IPR004859
CATH: - -
SCOP: - -


Protein sequence:
MGIPKFFRYISERWPMILQLIEGTQIPEFDNLYLDMNSILHNCTHGNDDD
VTKRLTEEEVFAKICTYIDHLFQTIKPKKIFYMAIDGVAPRAKMNQQRAR
RFRTAMDAEKALKKAIENGDEIPKGEPFDSNSITPGTEFMAKLTKNLQYF
IHDKISNDSKWREVQIIFSGHEVPGEGEHKIMNFIRHLKSQKDFNQNTRH
CIYGLDADLIMLGLSTHGPHFALLREEVTFGRRNSEKKSLEHQNFYLLHL
SLLREYMELEFKEIADEMQFEYNFERILDDFILVMFVIGNDFLPNLPDLH
LNKGAFPVLLQTFKEALLHTDGYINEHGKINLKRLGVWLNYLSQFELLNF
EKDDIDVEWFNKQLENISLEGERKRQRVGKKLLVKQQKKLIGSIKPWLME
QLQEKLSPDLPDEEIPTLELPKDLDMKDHLEFLKEFAFDLGLFITHSKSK
GSYSLKMDLDSINPDETEEEFQNRVNSIRKTIKKYQNAIIVEDKEELETE
KTIYNERFERWKHEYYHDKLKFTTDSEEKVRDLAKDYVEGLQWVLYYYYR
GCPSWSWYYPHHYAPRISDLAKGLDQDIEFDLSKPFTPFQQLMAVLPERS
KNLIPPAFRPLMYDEQSPIHDFYPAEVQLDKNGKTADWEAVVLISFVDEK
RLIEAMQPYLRKLSPEEKTRNQFGKDLIYSFNPQVDNLYKSPLGGIFSDI
EHNHCVEKEYITIPLDSSEIRYGLLPNAKLGAEMLAGFPTLLSLPFTSSL
EYNETMVFQQPSKQQSMVLQITDIYKTNNVTLEDFSKRHLNKVIYTRWPY
LRESKLVSLTDGKTIYEYQESNDKKKFGFITKPAETQDKKLFNSLKNSML
RMYAKQKAVKIGPMEAIATVFPVTGLVRDSDGGYIKTFSPTPDYYPLQLV
VESVVNEDERYKERGPIPIEEEFPLNSKVIFLGDYAYGGETTIDGYSSDR
RLKITVEKKFLDSEPTIGKERLQMDHQAVKYYPSYIVSKNMHLHPLFLSK
ITSKFMITDATGKHINVGIPVKFEARHQKVLGYARRNPRGWEYSNLTLNL
LKEYRQTFPDFFFRLSKVGNDIPVLEDLFPDTSTKDAMNLLDGIKQWLKY
VSSKFIAVSLESDSLTKTSIAAVEDHIMKYAANIEGHERKQLAKVPREAV
LNPRSSFALLRSQKFDLGDRVVYIQDSGKVPIFSKGTVVGYTTLSSSLSI
QVLFDHEIVAGNNFGGRLRTNRGLGLDASFLLNITNRQFIYHSKASKKAL
EKKKQSNNRNNNTKTAHKTPSKQQSEEKLRKERAHDLLNFIKKDTNEKNS
ESVDNKSMGSQKDSKPAKKVLLKRPAQKSSENVQVDLANFEKAPLDNPTV
AGSIFNAVANQYSDGIGSNLNIPTPPHPMNVVGGPIPGANDVADVGLPYN
IPPGFMTHPNGLHPLHPHQMPYPNMNGMSIPPPAPHGFGQPISFPPPPPM
TNVSDQGSRIVVNEKESQDLKKFINGKQHSNGSTIGGETKNSRKGEIKPS
SGTNSTECQSPKSQSNAADRDNKKDEST

5'-3' exoribonuclease (Saccharomyces cerevisiae) is product of expression of KEM1 gene.

References:

Title Authors Journal Publication date (Issue) PubMed ID
Structural modifications of RNA influence the 5' exoribonucleolytic hydrolysis by XRN1 and HKE1 of Saccharomyces cerevisiae. Poole TL, Stevens A Biochem Biophys Res Commun 1997-06-27 (235) 9207242
Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome. Orban TI, Izaurralde E RNA 2005-04-01 (11) 15703439
The final step in the formation of 25S rRNA in Saccharomyces cerevisiae is performed by 5'-->3' exonucleases. Geerlings TH, Vos JC, Raue HA RNA 2000-12-01 (6) 11142370
RNase MRP cleaves the CLB2 mRNA to promote cell cycle progression: novel method of mRNA degradation. Gill T, Cai T, Aulds J, Wierzbicki S, Schmitt ME Mol Cell Biol 2004-01-01 (24) 14729943
The 3' to 5' degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3' to 5' exonucleases of the exosome complex. Anderson JS, Parker RP EMBO J 1998-03-02 (17) 9482746
The nucleotide sequence of Saccharomyces cerevisiae chromosome VII. Tettelin H, Agostoni Carbone ML, Albermann K, Albers M, Arroyo J, Backes U, Barreiros T, Bertani I, Bjourson AJ, Bruckner M, Bruschi CV, Carignani G, Castagnoli L, Cerdan E, Clemente ML, Coblenz A, Coglievina M, Coissac E, Defoor E, Del Bino S, Delius H, Delneri D, de Wergifosse P, Dujon B, Kleine K Nature 1997-05-01 (387) 9169869
Global analysis of protein expression in yeast. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS Nature 2003-10-16 (425) 14562106
A multidimensional chromatography technology for in-depth phosphoproteome analysis. Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H Mol Cell Proteomics 2008-07-01 (7) 18407956
Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. Smolka MB, Albuquerque CP, Chen SH, Zhou H Proc Natl Acad Sci U S A 2007-06-19 (104) 17563356
Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Sheth U, Parker R Science 2003-05-02 (300) 12730603
Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Gruhler A, Olsen JV, Mohammed S, Mortensen P, Faergeman NJ, Mann M, Jensen ON Mol Cell Proteomics 2005-03-01 (4) 15665377
Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JE, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF Proc Natl Acad Sci U S A 2007-01-13 (104) 17287358
kem mutations affect nuclear fusion in Saccharomyces cerevisiae. Kim J, Ljungdahl PO, Fink GR Genetics 1990-12-01 (126) 2076815
Molecular and genetic analysis of the gene encoding the Saccharomyces cerevisiae strand exchange protein Sep1. Tishkoff DX, Johnson AW, Kolodner RD Mol Cell Biol 1991-05-01 (11) 1840632
Cloning and characterization of DST2, the gene for DNA strand transfer protein beta from Saccharomyces cerevisiae. Dykstra CC, Kitada K, Clark AB, Hamatake RK, Sugino A Mol Cell Biol 1991-05-01 (11) 1850100
Disruption of the gene XRN1, coding for a 5'----3' exoribonuclease, restricts yeast cell growth. Larimer FW, Stevens A Gene 1990-10-01 (95) 1979303
rar mutations which increase artificial chromosome stability in Saccharomyces cerevisiae identify transcription and recombination proteins. Kipling D, Tambini C, Kearsey SE Nucleic Acids Res 1991-04-11 (19) 2027746
The sequence of an 11.1 kb fragment on the left arm of Saccharomyces cerevisiae chromosome VII reveals six open reading frames including NSP49, KEM1 and four putative new genes. Bertani I, Coglievina M, Zaccaria P, Klima R, Bruschi CV Yeast 1995-09-01 (11) 8619317
Strand exchange protein 1 from Saccharomyces cerevisiae. A novel multifunctional protein that contains DNA strand exchange and exonuclease activities. Johnson AW, Kolodner RD J Biol Chem 1991-07-25 (266) 1856231
Characterization of the XRN1 gene encoding a 5'-->3' exoribonuclease: sequence data and analysis of disparate protein and mRNA levels of gene-disrupted yeast cells. Larimer FW, Hsu CL, Maupin MK, Stevens A Gene 1992-10-12 (120) 1398123
The Sep1 strand exchange protein from Saccharomyces cerevisiae promotes a paranemic joint between homologous DNA molecules. Chen J, Kanaar R, Cozzarelli NR Genes Dev 1994-06-01 (8) 7926736
The activity of the Saccharomyces cerevisiae strand exchange protein 1 intrinsic exonuclease during joint molecule formation. Johnson AW, Kolodner RD J Biol Chem 1994-01-04 (269) 8106411
Characterization of the interaction of Saccharomyces cerevisiae strand exchange protein 1 with DNA. Johnon AW, Kolodner RD J Biol Chem 1994-01-04 (269) 8106412
A multifunctional exonuclease from vegetative Schizosaccharomyces pombe cells exhibiting in vitro strand exchange activity. Kaslin E, Heyer WD J Biol Chem 1994-05-13 (269) 8188690
The yeast KEM1 gene encodes a nuclease specific for G4 tetraplex DNA: implication of in vivo functions for this novel DNA structure. Liu Z, Gilbert W Cell 1994-07-01 (77) 8020096
A role of Sep1 (= Kem1, Xrn1) as a microtubule-associated protein in Saccharomyces cerevisiae. Interthal H, Bellocq C, Bahler J, Bashkirov VI, Edelstein S, Heyer WD EMBO J 1995-03-15 (14) 7720696
The sep1 mutant of Saccharomyces cerevisiae arrests in pachytene and is deficient in meiotic recombination. Tishkoff DX, Rockmill B, Roeder GS, Kolodner RD Genetics 1995-01-01 (139) 7713413
Regulation and intracellular localization of Saccharomyces cerevisiae strand exchange protein 1 (Sep1/Xrn1/Kem1), a multifunctional exonuclease. Heyer WD, Johnson AW, Reinhart U, Kolodner RD Mol Cell Biol 1995-05-01 (15) 7739553
Gene disruption of a G4-DNA-dependent nuclease in yeast leads to cellular senescence and telomere shortening. Liu Z, Lee A, Gilbert W Proc Natl Acad Sci U S A 1995-06-20 (92) 7597069
Rat1p and Xrn1p are functionally interchangeable exoribonucleases that are restricted to and required in the nucleus and cytoplasm, respectively. Johnson AW Mol Cell Biol 1997-10-01 (17) 9315672
Processing of the precursors to small nucleolar RNAs and rRNAs requires common components. Petfalski E, Dandekar T, Henry Y, Tollervey D Mol Cell Biol 1998-03-01 (18) 9488433
Telomere length regulation and telomeric chromatin require the nonsense-mediated mRNA decay pathway. Lew JE, Enomoto S, Berman J Mol Cell Biol 1998-10-01 (18) 9742129
Mutational analysis of exoribonuclease I from Saccharomyces cerevisiae. Page AM, Davis K, Molineux C, Kolodner RD, Johnson AW Nucleic Acids Res 1998-08-15 (26) 9685486
Active-site mutations in the Xrn1p exoribonuclease of Saccharomyces cerevisiae reveal a specific role in meiosis. Solinger JA, Pascolini D, Heyer WD Mol Cell Biol 1999-09-01 (19) 10454540
Upf1p, Nmd2p, and Upf3p regulate the decapping and exonucleolytic degradation of both nonsense-containing mRNAs and wild-type mRNAs. He F, Jacobson A Mol Cell Biol 2001-03-01 (21) 11238889
KEM1 is involved in filamentous growth of Saccharomyces cerevisiae. Kim J, Kim J FEMS Microbiol Lett 2002-10-01 (216) 12423748
An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Frischmeyer PA, van Hoof A, O'Donnell K, Guerrerio AL, Parker R, Dietz HC Science 2002-03-22 (295) 11910109
Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast. He F, Li X, Spatrick P, Casillo R, Dong S, Jacobson A Mol Cell 2003-12-01 (12) 14690598
The Upf-dependent decay of wild-type PPR1 mRNA depends on its 5'-UTR and first 92 ORF nucleotides. Kebaara B, Nazarenus T, Taylor R, Forch A, Atkin AL Nucleic Acids Res 2003-06-15 (31) 12799443
Initiation-mediated mRNA decay in yeast affects heat-shock mRNAs, and works through decapping and 5'-to-3' hydrolysis. Heikkinen HL, Llewellyn SA, Barnes CA Nucleic Acids Res 2003-07-15 (31) 12853617
The roles of endonucleolytic cleavage and exonucleolytic digestion in the 5'-end processing of S. cerevisiae box C/D snoRNAs. Lee CY, Lee A, Chanfreau G RNA 2003-11-01 (9) 14561886
Deletion of OSH3 gene confers resistance against ISP-1 in Saccharomyces cerevisiae. Yano T, Inukai M, Isono F Biochem Biophys Res Commun 2004-01-27 (315) 15013450
Posttranscriptional regulation of the karyogamy gene by Kem1p/Xrn1p exoribonuclease and Rok1p RNA helicase of Saccharomyces cerevisiae. Kim J, Jeon S, Yang YS, Kim J Biochem Biophys Res Commun 2004-09-03 (321) 15358132
A role for KEM1 at the START of the cell cycle in Saccharomyces cerevisiae. Pathak R, Bogomolnaya LM, Guo J, Polymenis M Curr Genet 2005-11-01 (48) 16240118
Regulation and surveillance of normal and 3'-extended forms of the yeast aci-reductone dioxygenase mRNA by RNase III cleavage and exonucleolytic degradation. Zer C, Chanfreau G J Biol Chem 2005-08-12 (280) 15967792
Multiple RNA surveillance pathways limit aberrant expression of iron uptake mRNAs and prevent iron toxicity in S. cerevisiae. Lee A, Henras AK, Chanfreau G Mol Cell 2005-07-01 (19) 15989963
Sodium-induced GCN4 expression controls the accumulation of the 5' to 3' RNA degradation inhibitor, 3'-phosphoadenosine 5'-phosphate. Todeschini AL, Condon C, Benard L J Biol Chem 2006-01-10 (281) 16352596
Determinants of Rbp1p localization in specific cytoplasmic mRNA-processing foci, P-bodies. Jang LT, Buu LM, Lee FJ J Biol Chem 2006-09-01 (281) 16885161
Suppression of viral RNA recombination by a host exoribonuclease. Cheng CP, Serviene E, Nagy PD J Virol 2006-03-01 (80) 16501073
Virus-like particles of the Ty3 retrotransposon assemble in association with P-body components. Beliakova-Bethell N, Beckham C, Giddings TH Jr, Winey M, Parker R, Sandmeyer S RNA 2006-02-01 (12) 16373495
Yeast transcripts cleaved by an internal ribozyme provide new insight into the role of the cap and poly(A) tail in translation and mRNA decay. Meaux S, Van Hoof A RNA 2006-07-01 (12) 16714281
The sensitivity of yeast mutants to oleic acid implicates the peroxisome and other processes in membrane function. Lockshon D, Surface LE, Kerr EO, Kaeberlein M, Kennedy BK Genetics 2007-02-01 (175) 17151231
Respiratory deficiency mediates the regulation of CHO1-encoded phosphatidylserine synthase by mRNA stability in Saccharomyces cerevisiae. Choi HS, Carman GM J Biol Chem 2007-10-26 (282) 17761681
Analysis of P-body assembly in Saccharomyces cerevisiae. Teixeira D, Parker R Mol Biol Cell 2007-06-01 (18) 17429074
Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1. Chernyakov I, Whipple JM, Kotelawala L, Grayhack EJ, Phizicky EM Genes Dev 2008-05-15 (22) 18443146
Transcription in the nucleus and mRNA decay in the cytoplasm are coupled processes. Goler-Baron V, Selitrennik M, Barkai O, Haimovich G, Lotan R, Choder M Genes Dev 2008-08-01 (22) 18676807
Synthetic genetic array analysis in Saccharomyces cerevisiae provides evidence for an interaction between RAT8/DBP5 and genes encoding P-body components. Scarcelli JJ, Viggiano S, Hodge CA, Heath CV, Amberg DC, Cole CN Genetics 2008-08-01 (179) 18689878
20S RNA narnavirus defies the antiviral activity of SKI1/XRN1 in Saccharomyces cerevisiae. Esteban R, Vega L, Fujimura T J Biol Chem 2008-09-19 (283) 18640978
The Cth2 ARE-binding protein recruits the Dhh1 helicase to promote the decay of succinate dehydrogenase SDH4 mRNA in response to iron deficiency. Pedro-Segura E, Vergara SV, Rodriguez-Navarro S, Parker R, Thiele DJ, Puig S J Biol Chem 2008-10-17 (283) 18715869
The DEAD-box RNA helicase Ded1p affects and accumulates in Saccharomyces cerevisiae P-bodies. Beckham C, Hilliker A, Cziko AM, Noueiry A, Ramaswami M, Parker R Mol Biol Cell 2008-03-01 (19) 18162578
S. cerevisiae Vts1p induces deadenylation-dependent transcript degradation and interacts with the Ccr4p-Pop2p-Not deadenylase complex. Rendl LM, Bieman MA, Smibert CA RNA 2008-07-01 (14) 18469165
Cordycepin interferes with 3' end formation in yeast independently of its potential to terminate RNA chain elongation. Holbein S, Wengi A, Decourty L, Freimoser FM, Jacquier A, Dichtl B RNA 2009-05-01 (15) 19324962



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Entry added on: 2010-04-12 22:11:48, by a user: kaja

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