P25644 (PAT1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA topoisomerase 2-associated protein PAT1

Alternative name(s):
Decapping activator and translational repressor PAT1
Topoisomerase II-associated protein PAT1
mRNA turnover protein 1

Gene names

Name:	PAT1
Synonyms:	MRT1
Ordered Locus Names:	YCR077C
ORF Names:	YCR77C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	796 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Activator of decapping that functions as a general and active mechanism of translational repression and required for P-body formation. First decay factor recruited to mRNA, at a time when the mRNA is still associated with translation factors. Subsequently, PAT1 recruits the hepta-heterodimer LSM1-LSM7 complex to P-bodies. In association with the LSM1-LSM7 complex, stabilizes the 3' terminus of mRNAs. This association is also required for mosaic virus genomic RNA translation. Modulates the rates of mRNA-decapping that occur following deadenylation. Might be required for promoting the formation or the stabilization of the preinitiation translation complexes. Required for 40S ribosomal subunit joining to capped and/or polyadenylated mRNA. With other P-body components, enhances the formation of retrotransposition-competent Ty1 virus-like particles. Necessary for accurate chromosome transmission during cell division. Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14 Ref.19 Ref.22 Ref.26 Ref.27 Ref.30 Ref.32 Ref.34 Ref.35
Subunit structure	Associates with the 40S ribosomal subunit. Associates with the heptameric LSM1-LSM7 complex. Interacts with DHH1, LSM1, LSM5, RPB4, RPB7 and with topoisomerase TOP2. Interacts with CDC33, PAB1, TIF4631 and TIF4632 in a RNA-dependent manner. Binds mRNAs. Ref.10 Ref.11 Ref.13 Ref.15 Ref.16 Ref.17 Ref.23 Ref.26
Subcellular location	Cytoplasm. Nucleus. Cytoplasm › P-body Ref.10 Ref.13 Ref.21 Ref.24 Ref.25 Ref.27 Ref.32.
Domain	The region at residues 254 to 422 is required for stimulation of decapping. The region at residues 422 to 763 is required for PAT1 and LSM1 to accumulate in P-bodies and responsible for translation repression and P-body assembly. Ref.32
Miscellaneous	Present with 656 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the PAT1 family.

Ontologies

Keywords
Biological process	Cell cycle Cell division Translation regulation mRNA processing
Cellular component	Cytoplasm Nucleus
Ligand	RNA-binding
Molecular function	Repressor
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW cytoplasmic mRNA processing body assembly Inferred from mutant phenotype PubMed 18981231. Source: SGD deadenylation-dependent decapping of nuclear-transcribed mRNA Inferred from mutant phenotype Ref.11. Source: SGD formation of translation preinitiation complex Inferred from mutant phenotype Ref.35. Source: SGD mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW negative regulation of translational initiation Inferred from direct assay Ref.35. Source: SGD
Cellular_component	cytoplasmic mRNA processing body Inferred from direct assay Ref.21. Source: SGD cytosolic small ribosomal subunit Inferred from direct assay Ref.10. Source: SGD nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
DHH1	P39517	5	EBI-204,EBI-158
LSM1	P47017	5	EBI-204,EBI-174
LSM2	P38203	4	EBI-204,EBI-180
LSM4	P40070	6	EBI-204,EBI-188

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 796	796	DNA topoisomerase 2-associated protein PAT1		PRO_0000058235
Regions
	Compositional bias	114 – 235	122	Pro-rich
	Compositional bias	133 – 192	60	Gln-rich
Amino acid modifications
	Modified residue	60	1	Phosphoserine Ref.33
	Modified residue	63	1	Phosphoserine Ref.33
	Modified residue	79	1	Phosphotyrosine Ref.33
	Modified residue	232	1	Phosphoserine Ref.33
	Modified residue	456	1	Phosphoserine Ref.18 Ref.28 Ref.29 Ref.33
	Modified residue	457	1	Phosphoserine Ref.28 Ref.29 Ref.33
	Modified residue	458	1	Phosphotyrosine Ref.18 Ref.33
Experimental info
	Sequence conflict	688	1	D → V in CAC42990. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P25644 [UniParc]. Last modified July 27, 2011. Version 4. Checksum: 2DBE1210C173E468	FASTA	796	88,511
	10 20 30 40 50 60 MSFFGLENSG NARDGPLDFE ESYKGYGEHE LEENDYLNDE TFGDNVQVGT DFDFGNPHSS 70 80 90 100 110 120 GSSGNAIGGN GVGATARSYV AATAEGISGP RTDGTAAAGP LDLKPMESLW STAPPPAMAP 130 140 150 160 170 180 SPQSTMAPAP APQQMAPLQP ILSMQDLERQ QRQMQQQFMN FHAMGHPQGL PQGPPQQQFP 190 200 210 220 230 240 MQPASGQPGP SQFAPPPPPP GVNVNMNQMP MGPVQVPVQA SPSPIGMSNT PSPGPVVGAT 250 260 270 280 290 300 KMPLQSGRRS KRDLSPEEQR RLQIRHAKVE KILKYSGLMT PRDKDFITRY QLSQIVTEDP 310 320 330 340 350 360 YNEDFYFQVY KIIQRGGITS ESNKGLIARA YLEHSGHRLG GRYKRTDIAL QRMQSQVEKA 370 380 390 400 410 420 VTVAKERPSK LKDQQAAAGN SSQDNKQANT VLGKISSTLN SKNPRRQLQI PRQQPSDPDA 430 440 450 460 470 480 LKDVTDSLTN VDLASSGSSS TGSSAAAVAS KQRRRSSYAF NNGNGATNLN KSGGKKFILE 490 500 510 520 530 540 LIETVYEEIL DLEANLRNGQ QTDSTAMWEA LHIDDSSYDV NPFISMLSFD KGIKIMPRIF 550 560 570 580 590 600 NFLDKQQKLK ILQKIFNELS HLQIIILSSY KTTPKPTLTQ LKKVDLFQMI ILKIIVSFLS 610 620 630 640 650 660 NNSNFIEIMG LLLQLIRNNN VSFLTTSKIG LNLITILISR AALIKQDSSR SNILSSPEIS 670 680 690 700 710 720 TWNEIYDKLF TSLESKIQLI FPPREYNDHI MRLQNDKFMD EAYIWQFLAS LALSGKLNHQ 730 740 750 760 770 780 RIIIDEVRDE IFATINEAET LQKKEKELSV LPQRSQELDT ELKSIIYNKE KLYQDLNLFL 790 NVMGLVYRDG EISELK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The complete DNA sequence of yeast chromosome III." Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A., Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M. , Carcano C., Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M., Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C., Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C., Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E., Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P., Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P., Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M., Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P., Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G., Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E., Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F., Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L., Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J., Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M., Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A., Richterich P., Roberts A.B., Rodriguez F., Sanz E., Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J., Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I., Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M., Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M., Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D., Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K., Sgouros J.G. Nature 357:38-46(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[2]	Valles G., Volckaerts G. Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION.
[3]	Saccharomyces Genome Database Submitted (MAR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 688. Strain: ATCC 204508 / S288c.
[4]	"Identification and initial characterization of the cytosolic protein Ycr77p." Rodriguez-Cousino N., Lill R., Neupert W., Court D.A. Yeast 11:581-585(1995) [PubMed] [Europe PMC] [Abstract] Cited for: SEQUENCE REVISION, CHARACTERIZATION.
[5]	"Mutations in trans-acting factors affecting mRNA decapping in Saccharomyces cerevisiae." Hatfield L., Beelman C.A., Stevens A., Parker R. Mol. Cell. Biol. 16:5830-5838(1996) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[6]	"Pat1: a topoisomerase II-associated protein required for faithful chromosome transmission in Saccharomyces cerevisiae." Wang X., Watt P.M., Louis E.J., Borts R.H., Hickson I.D. Nucleic Acids Res. 24:4791-4797(1996) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"Mutations in VPS16 and MRT1 stabilize mRNAs by activating an inhibitor of the decapping enzyme." Zhang S., Williams C.J., Hagan K., Peltz S.W. Mol. Cell. Biol. 19:7568-7576(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[8]	"The topoisomerase II-associated protein, Pat1p, is required for maintenance of rDNA locus stability in Saccharomyces cerevisiae." Wang X., Watt P.M., Borts R.H., Louis E.J., Hickson I.D. Mol. Gen. Genet. 261:831-840(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"A Sm-like protein complex that participates in mRNA degradation." Bouveret E., Rigaut G., Shevchenko A., Wilm M., Seraphin B. EMBO J. 19:1661-1671(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, ASSOCIATION WITH THE LSM1-LSM7 COMPLEX.
[10]	"Deletion of the PAT1 gene affects translation initiation and suppresses a PAB1 gene deletion in yeast." Wyers F., Minet M., Dufour M.E., Vo L.T., Lacroute F. Mol. Cell. Biol. 20:3538-3549(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, ASSOCIATION WITH THE 40S RIBOSOMAL SUBUNIT.
[11]	"The two proteins Pat1p (Mrt1p) and Spb8p interact in vivo, are required for mRNA decay, and are functionally linked to Pab1p." Bonnerot C., Boeck R., Lapeyre B. Mol. Cell. Biol. 20:5939-5946(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH LSM1.
[12]	"mRNA decapping in yeast requires dissociation of the cap binding protein, eukaryotic translation initiation factor 4E." Schwartz D.C., Parker R. Mol. Cell. Biol. 20:7933-7942(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[13]	"Yeast Sm-like proteins function in mRNA decapping and decay." Tharun S., He W., Mayes A.E., Lennertz P., Beggs J.D., Parker R. Nature 404:515-518(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH LSM1 AND LSM5.
[14]	"The yeast cytoplasmic LsmI/Pat1p complex protects mRNA 3' termini from partial degradation." He W., Parker R. Genetics 158:1445-1455(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[15]	"Targeting an mRNA for decapping: displacement of translation factors and association of the Lsm1p-7p complex on deadenylated yeast mRNAs." Tharun S., Parker R. Mol. Cell 8:1075-1083(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH CDC33; PAB1; TIF4631 AND TIF4632, MRNA-BINDING.
[16]	"The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes." Coller J.M., Tucker M., Sheth U., Valencia-Sanchez M.A., Parker R. RNA 7:1717-1727(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH DHH1.
[17]	"The DEAD box protein Dhh1 stimulates the decapping enzyme Dcp1." Fischer N., Weis K. EMBO J. 21:2788-2797(2002) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH DHH1.
[18]	"Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae." Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., White F.M. Nat. Biotechnol. 20:301-305(2002) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-456 AND TYR-458, MASS SPECTROMETRY. Strain: 2124.
[19]	"Yeast Lsm1p-7p/Pat1p deadenylation-dependent mRNA-decapping factors are required for brome mosaic virus genomic RNA translation." Noueiry A.O., Diez J., Falk S.P., Chen J., Ahlquist P. Mol. Cell. Biol. 23:4094-4106(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[20]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[21]	"Decapping and decay of messenger RNA occur in cytoplasmic processing bodies." Sheth U., Parker R. Science 300:805-808(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[22]	"General translational repression by activators of mRNA decapping." Coller J., Parker R. Cell 122:875-886(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[23]	"The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs." Lotan R., Bar-On V.G., Harel-Sharvit L., Duek L., Melamed D., Choder M. Genes Dev. 19:3004-3016(2005) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RPB4.
[24]	"Processing bodies require RNA for assembly and contain nontranslating mRNAs." Teixeira D., Sheth U., Valencia-Sanchez M.A., Brengues M., Parker R. RNA 11:371-382(2005) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[25]	"Targeting of aberrant mRNAs to cytoplasmic processing bodies." Sheth U., Parker R. Cell 125:1095-1109(2006) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[26]	"The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms." Lotan R., Goler-Baron V., Duek L., Haimovich G., Choder M. J. Cell Biol. 178:1133-1143(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH RPB7.
[27]	"Analysis of P-body assembly in Saccharomyces cerevisiae." Teixeira D., Parker R. Mol. Biol. Cell 18:2274-2287(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[28]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-456 AND SER-457, MASS SPECTROMETRY.
[29]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-456 AND SER-457, MASS SPECTROMETRY.
[30]	"The decapping activator Lsm1p-7p-Pat1p complex has the intrinsic ability to distinguish between oligoadenylated and polyadenylated RNAs." Chowdhury A., Mukhopadhyay J., Tharun S. RNA 13:998-1016(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[31]	"Purification and analysis of the decapping activator Lsm1p-7p-Pat1p complex from yeast." Tharun S. Methods Enzymol. 448:41-55(2008) [PubMed] [Europe PMC] [Abstract] Cited for: MASS SPECTROMETRY, ASSOCIATION WITH THE LSM1-LSM7 COMPLEX.
[32]	"Pat1 contains distinct functional domains that promote P-body assembly and activation of decapping." Pilkington G.R., Parker R. Mol. Cell. Biol. 28:1298-1312(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, DOMAIN, RNA-BINDING.
[33]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-60; SER-63; TYR-79; SER-232; SER-456; SER-457 AND TYR-458, MASS SPECTROMETRY.
[34]	"P-body components are required for Ty1 retrotransposition during assembly of retrotransposition-competent virus-like particles." Checkley M.A., Nagashima K., Lockett S.J., Nyswaner K.M., Garfinkel D.J. Mol. Cell. Biol. 30:382-398(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[35]	"Decapping activators in Saccharomyces cerevisiae act by multiple mechanisms." Nissan T., Rajyaguru P., She M., Song H., Parker R. Mol. Cell 39:773-783(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X59720 Genomic DNA. Translation: CAC42990.1. BK006937 Genomic DNA. Translation: DAA07549.2.
PIR	S53590.
RefSeq	NP_010002.3. NM_001178786.2.
3D structure databases
ProteinModelPortal	P25644.
SMR	P25644. Positions 472-647.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-883N.
IntAct	P25644. 36 interactions.
MINT	MINT-414364.
STRING	4932.YCR077C.
Proteomic databases
PaxDb	P25644.
PeptideAtlas	P25644.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YCR077C; YCR077C; YCR077C.
GeneID	850440.
KEGG	sce:YCR077C.
Organism-specific databases
CYGD	YCR077c.
SGD	S000000673. PAT1.
Phylogenomic databases
eggNOG	NOG287050.
HOGENOM	HOG000246501.
KO	K12617.
OMA	PYNEDFY.
OrthoDB	EOG4NPBBK.
Gene expression databases
Genevestigator	P25644.
GermOnline	YCR077C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR019167. Topo_II-assoc_PAT1. [Graphical view]
Pfam	PF09770. PAT1. 2 hits. [Graphical view]
ProtoNet	Search...
Other
NextBio	966042.

Entry information

Entry name

PAT1_YEAST

Accession

Primary (citable) accession number: P25644
Secondary accession number(s): D6VR80, Q8NKJ3

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1992
Last sequence update:	July 27, 2011
Last modified:	May 1, 2013
This is version 109 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program