TRF41_DROME
ID TRF41_DROME Reviewed; 1001 AA.
AC Q7KVS9; A8JV36;
DT 30-NOV-2016, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=Non-canonical poly(A) RNA polymerase protein Trf4-1 {ECO:0000305};
DE EC=2.7.7.19 {ECO:0000269|PubMed:18765642};
DE AltName: Full=Topoisomerase 1-related protein 4-1 {ECO:0000303|PubMed:18765642};
GN Name=Trf4-1 {ECO:0000303|PubMed:18765642, ECO:0000312|FlyBase:FBgn0030049};
GN ORFNames=CG11265 {ECO:0000312|FlyBase:FBgn0030049};
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227 {ECO:0000312|Proteomes:UP000000803};
RN [1] {ECO:0000312|Proteomes:UP000000803}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley {ECO:0000312|Proteomes:UP000000803};
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [2] {ECO:0000312|Proteomes:UP000000803}
RP GENOME REANNOTATION.
RC STRAIN=Berkeley {ECO:0000312|Proteomes:UP000000803};
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN [3] {ECO:0000312|EMBL:AAQ23600.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Berkeley {ECO:0000312|EMBL:AAQ23600.1};
RC TISSUE=Embryo {ECO:0000312|EMBL:AAQ23600.1};
RA Stapleton M., Brokstein P., Hong L., Agbayani A., Carlson J., Champe M.,
RA Chavez C., Dorsett V., Dresnek D., Farfan D., Frise E., George R.,
RA Gonzalez M., Guarin H., Kronmiller B., Li P., Liao G., Miranda A.,
RA Mungall C.J., Nunoo J., Pacleb J., Paragas V., Park S., Patel S.,
RA Phouanenavong S., Wan K., Yu C., Lewis S.E., Rubin G.M., Celniker S.;
RL Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases.
RN [4] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, DEVELOPMENTAL STAGE, DISRUPTION
RP PHENOTYPE, AND MUTAGENESIS OF 328-ASP--ASP-330.
RX PubMed=18765642; DOI=10.1128/mcb.00448-08;
RA Nakamura R., Takeuchi R., Takata K., Shimanouchi K., Abe Y., Kanai Y.,
RA Ruike T., Ihara A., Sakaguchi K.;
RT "TRF4 is involved in polyadenylation of snRNAs in Drosophila
RT melanogaster.";
RL Mol. Cell. Biol. 28:6620-6631(2008).
RN [5] {ECO:0000305}
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=26786835; DOI=10.1261/rna.053942.115;
RA Harnisch C., Cuzic-Feltens S., Dohm J.C., Goetze M., Himmelbauer H.,
RA Wahle E.;
RT "Oligoadenylation of 3' decay intermediates promotes cytoplasmic mRNA
RT degradation in Drosophila cells.";
RL RNA 22:428-442(2016).
CC -!- FUNCTION: Involved in a post-transcriptional quality control mechanism
CC limiting inappropriate expression of genetic information
CC (PubMed:18765642, PubMed:26786835). Polyadenylation is required for the
CC degradative activity of the exosome on several of its nuclear RNA
CC substrates (PubMed:26786835). Polyadenylates RNA processing and
CC degradation intermediates of snRNAs and mRNAs (PubMed:18765642,
CC PubMed:26786835). {ECO:0000269|PubMed:18765642,
CC ECO:0000269|PubMed:26786835}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + RNA(n) = diphosphate + RNA(n)-3'-adenine ribonucleotide;
CC Xref=Rhea:RHEA:11332, Rhea:RHEA-COMP:14527, Rhea:RHEA-COMP:17347,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:140395,
CC ChEBI:CHEBI:173115; EC=2.7.7.19;
CC Evidence={ECO:0000269|PubMed:18765642};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:18765642};
CC Note=Low activity with Mg(2+). {ECO:0000269|PubMed:18765642};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:26786835}.
CC Note=Enriched in 3 to 6 cytoplasmic foci.
CC {ECO:0000269|PubMed:26786835}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative initiation; Named isoforms=2;
CC Name=E {ECO:0000312|FlyBase:FBgn0030049}; Synonyms=C
CC {ECO:0000312|FlyBase:FBgn0030049}, H {ECO:0000312|FlyBase:FBgn0030049},
CC I {ECO:0000312|FlyBase:FBgn0030049}, J
CC {ECO:0000312|FlyBase:FBgn0030049};
CC IsoId=Q7KVS9-1; Sequence=Displayed;
CC Name=F {ECO:0000312|FlyBase:FBgn0030049}; Synonyms=G
CC {ECO:0000312|FlyBase:FBgn0030049};
CC IsoId=Q7KVS9-2; Sequence=VSP_058688;
CC -!- DEVELOPMENTAL STAGE: High expression in unfertilized eggs and from 0 to
CC 4 hours in early embryos. Low expression in later developmental stages,
CC with slight increase in 8-16 hour-old embryos and in adults.
CC {ECO:0000269|PubMed:18765642}.
CC -!- DISRUPTION PHENOTYPE: RNAi-mediated knockdown causes lethality at the
CC third-instar larval or early pupal stage.
CC {ECO:0000269|PubMed:18765642}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-B-like family.
CC {ECO:0000305}.
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DR EMBL; AE014298; AAF46390.3; -; Genomic_DNA.
DR EMBL; AE014298; AAS65288.2; -; Genomic_DNA.
DR EMBL; AE014298; AAS65289.2; -; Genomic_DNA.
DR EMBL; AE014298; AAS65290.1; -; Genomic_DNA.
DR EMBL; AE014298; ABW09362.1; -; Genomic_DNA.
DR EMBL; AE014298; ABW09363.1; -; Genomic_DNA.
DR EMBL; AE014298; AGB95183.1; -; Genomic_DNA.
DR EMBL; BT010282; AAQ23600.1; -; mRNA.
DR RefSeq; NP_001096913.1; NM_001103443.2. [Q7KVS9-2]
DR RefSeq; NP_001096914.1; NM_001103444.2. [Q7KVS9-2]
DR RefSeq; NP_001259340.1; NM_001272411.1. [Q7KVS9-1]
DR RefSeq; NP_572490.2; NM_132262.3. [Q7KVS9-1]
DR RefSeq; NP_996381.1; NM_206658.4. [Q7KVS9-1]
DR RefSeq; NP_996382.2; NM_206659.3. [Q7KVS9-1]
DR RefSeq; NP_996383.2; NM_206660.2. [Q7KVS9-1]
DR AlphaFoldDB; Q7KVS9; -.
DR SMR; Q7KVS9; -.
DR STRING; 7227.FBpp0071159; -.
DR PaxDb; Q7KVS9; -.
DR DNASU; 31795; -.
DR EnsemblMetazoa; FBtr0071212; FBpp0071158; FBgn0030049. [Q7KVS9-1]
DR EnsemblMetazoa; FBtr0071213; FBpp0071159; FBgn0030049. [Q7KVS9-1]
DR EnsemblMetazoa; FBtr0112963; FBpp0111876; FBgn0030049. [Q7KVS9-2]
DR EnsemblMetazoa; FBtr0112964; FBpp0111877; FBgn0030049. [Q7KVS9-2]
DR EnsemblMetazoa; FBtr0331723; FBpp0304112; FBgn0030049. [Q7KVS9-1]
DR EnsemblMetazoa; FBtr0331724; FBpp0304113; FBgn0030049. [Q7KVS9-1]
DR EnsemblMetazoa; FBtr0331725; FBpp0304114; FBgn0030049. [Q7KVS9-1]
DR GeneID; 31795; -.
DR KEGG; dme:Dmel_CG11265; -.
DR UCSC; CG11265-RC; d. melanogaster. [Q7KVS9-1]
DR UCSC; CG11265-RF; d. melanogaster.
DR CTD; 31795; -.
DR FlyBase; FBgn0030049; Trf4-1.
DR VEuPathDB; VectorBase:FBgn0030049; -.
DR eggNOG; KOG1906; Eukaryota.
DR GeneTree; ENSGT00940000169468; -.
DR InParanoid; Q7KVS9; -.
DR PhylomeDB; Q7KVS9; -.
DR BioGRID-ORCS; 31795; 1 hit in 3 CRISPR screens.
DR GenomeRNAi; 31795; -.
DR PRO; PR:Q7KVS9; -.
DR Proteomes; UP000000803; Chromosome X.
DR Bgee; FBgn0030049; Expressed in egg cell and 17 other tissues.
DR ExpressionAtlas; Q7KVS9; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005730; C:nucleolus; IBA:GO_Central.
DR GO; GO:0031499; C:TRAMP complex; IBA:GO_Central.
DR GO; GO:0016853; F:isomerase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004652; F:polynucleotide adenylyltransferase activity; IDA:FlyBase.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0043630; P:ncRNA polyadenylation involved in polyadenylation-dependent ncRNA catabolic process; IMP:FlyBase.
DR GO; GO:0031123; P:RNA 3'-end processing; IBA:GO_Central.
DR Gene3D; 3.30.460.10; -; 1.
DR InterPro; IPR043519; NT_sf.
DR InterPro; IPR002058; PAP_assoc.
DR InterPro; IPR002934; Polymerase_NTP_transf_dom.
DR InterPro; IPR045862; Trf4-like.
DR PANTHER; PTHR23092; PTHR23092; 1.
DR Pfam; PF01909; NTP_transf_2; 1.
DR Pfam; PF03828; PAP_assoc; 1.
DR SUPFAM; SSF81301; SSF81301; 1.
PE 1: Evidence at protein level;
KW Alternative initiation; Cytoplasm; Isomerase; Magnesium; Manganese;
KW Metal-binding; mRNA processing; Nucleotidyltransferase; Reference proteome;
KW Transferase.
FT CHAIN 1..1001
FT /note="Non-canonical poly(A) RNA polymerase protein Trf4-1"
FT /id="PRO_0000438592"
FT DOMAIN 458..517
FT /note="PAP-associated"
FT /evidence="ECO:0000255"
FT REGION 44..92
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 115..238
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 631..652
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 687..740
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 767..963
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 977..1001
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 115..226
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 687..713
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 714..730
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 767..791
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 802..818
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 836..881
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 882..911
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 925..963
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 977..993
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 328
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O13833"
FT BINDING 330
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O13833"
FT VAR_SEQ 1..199
FT /note="Missing (in isoform F)"
FT /id="VSP_058688"
FT MUTAGEN 328..330
FT /note="DID->AIA: Loss of activity."
FT /evidence="ECO:0000269|PubMed:18765642"
SQ SEQUENCE 1001 AA; 108718 MW; EB3D2DB3B7B101CA CRC64;
MDPFVGWFQK EQEGPSLCTW LKIWETNAQE MGALLNQQLQ QATTINGSTS SSSSSSNSGN
NNNNNNNNII NNTITNTTNN TGNNSSAKPY LSRPYSSLNR VLNFRADSLE ILQQQQQQQQ
LNGTTQRNST NINTTSGGST SSSADSTTNR DNNSPANSSS TNGPGAGTGT STGAGGTGTN
SPATTASSTA ATTTGPATSM SDTSNNPPQS TTTPASRTNS IYYNPSRKKR PENKAGGAHY
YMNNHMEMIA KYKGEPWRKP DYPYGEGVIG LHEEIEHFYQ YVLPTPCEHA IRNEVVKRIE
AVVHSIWPQA VVEIFGSFRT GLFLPTSDID LVVLGLWEKL PLRTLEFELV SRGIAEACTV
RVLDKASVPI IKLTDRETQV KVDISFNMQS GVQSAELIKK FKRDYPVLEK LVLVLKQFLL
LRDLNEVFTG GISSYSLILM CISFLQMHPR GIYHDTANLG VLLLEFFELY GRRFNYMKIG
ISIKNGGRYM PKDELQRDMV DGHRPSLLCI EDPLTPGNDI GRSSYGVFQV QQAFKCAYRV
LALAVSPLNL LGIDPRVNSI LGRIIHITDD VIDYREWIRE NFEHLVVVDR ISPLPTAAPT
AYATANGAPK YVIMPSGAVV QQLYHHPVQV PTAHGHSHAH SHSHGHAHPG AHLCQPYVTG
TTVSAVTTTT TMAVVTVGVS AGGVQQQQQQ QNATAHTHSQ QQTQNQSQSR HRRGSTSSGD
DSEDSKDGDV VETTSSAQEV VDIALSTPNG LANMSMPMPV HAVGMPASNS WSGNGNGNGN
SSSSTGSSPE IAHIAAQEMD PELEDQQQQQ QHQETSGGNG FIRPGDVGTG SNRGGGDGSG
GRNYNQRNNH NSSGYYHQQY YVPPPMQQQL SKSNSSSNYH QQHHHSHSHG NHSHRQQHHH
QQQHHHQQRP QHLRVGGGNR YQKSLGGSPI ISAGNASNSS SNCSNSSSSS GSNNSRLPPL
RGTLVNSSSA ISIISISSES SIASSSSSSS RSGQDQQRDE R
