Reviewed, UniProtKB/Swiss-Prot P48561 (TRF5_YEAST)

Names and origin

Protein names

Recommended name:
    Poly(A) RNA polymerase protein 1
    EC=2.7.7.-
Alternative name(s):
    Topoisomerase 1-related protein TRF5

Gene names

Name:	TRF5
Ordered Locus Names:	YNL299W
ORF Names:	N0440

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	642 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Catalytic subunit of the TRAMP5 complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates like cryptic transcripts generated by RNA polymerase II and III, or hypomethylated pre-tRNAi-Met. Polyadenylates RNA processing and degradation intermediates of snRNAs, snoRNAs and mRNAs that accumulate in strains lacking a functional exosome. TRF5 is also required for proper nuclear division in mitosis, DNA damage repair and sister chromatid cohesion. Involved in the regulation of histone mRNA levels. May mediate mitotic chromosome condensation. Ref.1 Ref.4 Ref.6 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14
Subunit structure	Component of the TRAMP5 complex composed of at least AIR1, MTR4 and TFR5. Interacts with POL2, DPB2 and DPB11. Ref.6
Subcellular location	Nucleus › nucleolus Ref.8.
Miscellaneous	Present with 2240 molecules/cell in log phase SD medium. Ref.9
Sequence similarities	Belongs to the DNA polymerase type-B-like family.
Caution	Was originally thought to have DNA polymerase activity.
Sequence caution	The sequence AAC49099.1 differs from that shown. Reason: Frameshift at position 612. The sequence AAC49397.1 differs from that shown. Reason: Frameshift at position 614. The sequence CAA96217.1 differs from that shown. Reason: Frameshift at position 612.

Ontologies

Keywords
Biological process	Cell cycle Cell division DNA damage DNA repair Mitosis
Cellular component	Nucleus
Molecular function	Nucleotidyltransferase Transferase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW U4 snRNA 3'-end processing Ref.12 Inferred from genetic interaction. Source: SGD cell division Inferred from electronic annotation. Source: UniProtKB-KW histone mRNA catabolic process Ref.14 Inferred from genetic interaction. Source: SGD mitosis Inferred from electronic annotation. Source: UniProtKB-KW nuclear polyadenylation-dependent CUT catabolic process Inferred from genetic interaction. Source: SGD nuclear polyadenylation-dependent mRNA catabolic process Ref.12 Inferred from genetic interaction. Source: SGD nuclear polyadenylation-dependent rRNA catabolic process Inferred from mutant phenotype. Source: SGD nuclear polyadenylation-dependent snRNA catabolic process Inferred from genetic interaction. Source: SGD nuclear polyadenylation-dependent snoRNA catabolic process Ref.12 Inferred from genetic interaction. Source: SGD nuclear polyadenylation-dependent tRNA catabolic process Ref.13 Inferred from genetic interaction. Source: SGD polyadenylation-dependent snoRNA 3'-end processing Ref.12 Inferred from genetic interaction. Source: SGD snoRNA polyadenylation Inferred from genetic interaction. Source: SGD
Cellular component	TRAMP complex Ref.11 Inferred from direct assay. Source: SGD nucleolus Ref.8 Inferred from direct assay. Source: SGD
Molecular function	polynucleotide adenylyltransferase activity Ref.10 Ref.11 Inferred from direct assay. Source: SGD protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
MTR4	P47047	3	EBI-19525,EBI-11592

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 642	642	Poly(A) RNA polymerase protein 1		PRO_0000120316
Sites
	Active site	235	1	By similarity
Experimental info
	Sequence conflict	354 – 355	2	MH → ID in AAC49397. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P48561-1 [UniParc]. Last modified May 29, 2007. Version 2. Checksum: 67D4CD75AEBAE1A4	FASTA	642	74,179
	10 20 30 40 50 60 MTRLKAKYSP TKGKRKEDKH TKRMRKSSFT RTQKMLEVFN DNRSHFNKYE SLAIDVEDDD 70 80 90 100 110 120 TFGNLVLMEN DKSDVDIPVI EEVTSSEDEQ RAESSKRNNS LEDNQDFIAF SDSSEDETEQ 130 140 150 160 170 180 IKEDDDERSS FLLTDEHEVS KLTSQQSLNT ESACNVEYPW IRNHCHSKQR RIADWLTSEI 190 200 210 220 230 240 KDFVHYISPS KNEIKCRNRT IDKLRRAVKE LWSDADLHVF GSFATDLYLP GSDIDCVVNS 250 260 270 280 290 300 RNRDKEDRNY IYELARHLKN KGLAIRMEVI VKTRVPIIKF IEPQSQLHID VSFERTNGLE 310 320 330 340 350 360 AAKLIREWLR DSPGLRELVL IIKQFLHSRR LNNVHTGGLG GFTVICLVYS FLNMHPRIKS 370 380 390 400 410 420 NDIDVLDNLG VLLIDFFELY GKNFGYDDVA ISISDGYASY IPKSCWRTLE PSRSKFSLAI 430 440 450 460 470 480 QDPGDPNNNI SRGSFNMKDI KKAFAGAFEL LVNKCWELNS ATFKDRVGKS ILGNVIKYRG 490 500 510 520 530 540 QKRDFNDERD LVQNKAIIEN ERYHKRRTRI VQEDLFINDT EDLPVEEIYK LDEPAKKKQK 550 560 570 580 590 600 AKKDKREGEI KKSAIPSPPP DFGVSRSKLK RKVKKTDQGS LLHQNNLSID DLMGLSENDQ 610 620 630 640 ESDQDQKGRD TPSGQDEKSP LETKTVDAQT RRDYWLSKGQ AL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A novel family of TRF (DNA topoisomerase I-related function) genes required for proper nuclear segregation." Castano I.B., Heath-Pagliuso S., Sadoff B.U., Fitzhugh D.J., Christman M.F. Nucleic Acids Res. 24:2404-2410(1996) [PubMed: 8710513] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
[2]	"Sequence analysis of a 30 kb DNA segment from yeast chromosome XIV carrying a ribosomal protein gene cluster, the genes encoding a plasma membrane protein and a subunit of replication factor C, and a novel putative serine/threonine protein kinase gene." Maurer K.C.T., Urbanus J.H.M., Planta R.J. Yeast 11:1303-1310(1995) [PubMed: 8553702] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications." Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J. , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J. Nature 387:93-98(1997) [PubMed: 9169873] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	"Pol kappa: a DNA polymerase required for sister chromatid cohesion." Wang Z., Castano I.B., De Las Penas A., Adams C., Christman M.F. Science 289:774-779(2000) [PubMed: 10926539] [Abstract] Cited for: FUNCTION.
[5]	"Eukaryotic DNA polymerases: proposal for a revised nomenclature." Burgers P.M.J., Koonin E.V., Bruford E., Blanco L., Burtis K.C., Christman M.F., Copeland W.C., Friedberg E.C., Hanaoka F., Hinkle D.C., Lawrence C.W., Nakanishi M., Ohmori H., Prakash L., Prakash S., Reynaud C.-A., Sugino A., Todo T. , Wang Z., Weill J.-C., Woodgate R. J. Biol. Chem. 276:43487-43490(2001) [PubMed: 11579108] [Abstract] Cited for: NOMENCLATURE.
[6]	"Saccharomyces cerevisiae DNA polymerase epsilon and polymerase sigma interact physically and functionally, suggesting a role for polymerase epsilon in sister chromatid cohesion." Edwards S., Li C.M., Levy D.L., Brown J., Snow P.M., Campbell J.L. Mol. Cell. Biol. 23:2733-2748(2003) [PubMed: 12665575] [Abstract] Cited for: FUNCTION, INTERACTION WITH POL2; DPB2 AND DPB11.
[7]	"Sequencing and comparison of yeast species to identify genes and regulatory elements." Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S. Nature 423:241-254(2003) [PubMed: 12748633] [Abstract] Cited for: IDENTIFICATION OF FRAMESHIFT.
[8]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[9]	"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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[10]	"Trf4 and Trf5 proteins of Saccharomyces cerevisiae exhibit poly(A) RNA polymerase activity but no DNA polymerase activity." Haracska L., Johnson R.E., Prakash L., Prakash S. Mol. Cell. Biol. 25:10183-10189(2005) [PubMed: 16260630] [Abstract] Cited for: FUNCTION.
[11]	"Yeast Trf5p is a nuclear poly(A) polymerase." Houseley J., Tollervey D. EMBO Rep. 7:205-211(2006) [PubMed: 16374505] [Abstract] Cited for: IDENTIFICATION IN THE TRAMP5 COMPLEX, FUNCTION OF THE TRAMP5 COMPLEX.
[12]	"Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome." Egecioglu D.E., Henras A.K., Chanfreau G.F. RNA 12:26-32(2006) [PubMed: 16373491] [Abstract] Cited for: FUNCTION.
[13]	"Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA." Kadaba S., Wang X., Anderson J.T. RNA 12:508-521(2006) [PubMed: 16431988] [Abstract] Cited for: FUNCTION.
[14]	"Contribution of Trf4/5 and the nuclear exosome to genome stability through regulation of histone mRNA levels in Saccharomyces cerevisiae." Reis C.C., Campbell J.L. Genetics 175:993-1010(2007) [PubMed: 17179095] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	U47282 Genomic DNA. Translation: AAC49397.1. Frameshift. U23084 Genomic DNA. Translation: AAC49099.1. Frameshift. Z71575 Genomic DNA. Translation: CAA96217.1. Frameshift.
PIR	S60401.
RefSeq	NP_014100.2.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	P48561. 4 interactions.
STRING	P48561.
Genome annotation databases
Ensembl	YNL299W; YNL299W; YNL299W; Saccharomyces cerevisiae. [Genome view]
GeneID	855417.
KEGG	sce:YNL299W.
Organism-specific databases
CYGD	YNL299w.
SGD	S000005243. TRF5.
Phylogenomic databases
HOGENOM	HBG395964.
OrthoDB	EOG9JDJQ0.
Gene expression databases
ArrayExpress	P48561.
Genevestigator	P48561.
GermOnline	YNL299W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR002934. Nucleotidyltransferase. IPR002058. PAP_assoc. [Graphical view]
Pfam	PF01909. NTP_transf_2. 1 hit. PF03828. PAP_assoc. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	979271.

Entry information

Entry name

TRF5_YEAST

Accession

Primary (citable) accession number: P48561

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1996
Last sequence update:	May 29, 2007
Last modified:	December 15, 2009
This is version 72 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)