MTREX_MOUSE
ID MTREX_MOUSE Reviewed; 1040 AA.
AC Q9CZU3;
DT 19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 172.
DE RecName: Full=Exosome RNA helicase MTR4 {ECO:0000305};
DE EC=3.6.4.13 {ECO:0000250|UniProtKB:P42285};
DE AltName: Full=ATP-dependent helicase SKIV2L2;
DE AltName: Full=Superkiller viralicidic activity 2-like 2;
DE AltName: Full=TRAMP-like complex helicase;
GN Name=Mtrex {ECO:0000312|MGI:MGI:1919448}; Synonyms=Skiv2l2;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=FVB/N; TISSUE=Mammary tumor;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, Heart, Kidney, Liver, Lung, Pancreas, Spleen, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
RN [4]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-76, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Embryonic fibroblast;
RX PubMed=23806337; DOI=10.1016/j.molcel.2013.06.001;
RA Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y.,
RA Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.;
RT "SIRT5-mediated lysine desuccinylation impacts diverse metabolic
RT pathways.";
RL Mol. Cell 50:919-930(2013).
CC -!- FUNCTION: Catalyzes the ATP-dependent unwinding of RNA duplexes with a
CC single-stranded 3' RNA extension. Central subunit of many protein
CC complexes, namely TRAMP-like, nuclear exosome targeting (NEXT) and
CC poly(A) tail exosome targeting (PAXT). NEXT functions as an RNA exosome
CC cofactor that directs a subset of non-coding short-lived RNAs for
CC exosomal degradation. NEXT is involved in surveillance and turnover of
CC aberrant transcripts and non-coding RNAs. PAXT directs a subset of long
CC and polyadenylated poly(A) RNAs for exosomal degradation. The RNA
CC exosome is fundamental for the degradation of RNA in eukaryotic nuclei.
CC Substrate targeting is facilitated by its cofactor ZCCHC8, which links
CC to RNA-binding protein adapters. Associated with the RNA exosome
CC complex and involved in the 3'-processing of the 7S pre-RNA to the
CC mature 5.8S rRNA. May be involved in pre-mRNA splicing. In the context
CC of NEXT complex can also in vitro unwind DNA:RNA heteroduplexes with a
CC 3' poly (A) RNA tracking strand. Can promote unwinding and degradation
CC of structured RNA substrates when associated with the nuclear exosome
CC and its cofactors. Can displace a DNA strand while translocating on RNA
CC to ultimately degrade the RNA within a DNA/RNA heteroduplex (By
CC similarity). Plays a role in DNA damage response (By similarity).
CC {ECO:0000250|UniProtKB:P42285}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC Evidence={ECO:0000250|UniProtKB:P42285};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:13066;
CC Evidence={ECO:0000250|UniProtKB:P42285};
CC -!- ACTIVITY REGULATION: Activated when MTREX is incorporated into NEXT
CC complex an the nuclear RNA exosome complex.
CC {ECO:0000250|UniProtKB:P42285}.
CC -!- SUBUNIT: Component of a TRAMP-like complex, an ATP-dependent exosome
CC regulatory complex consisting of a helicase (MTREX), an oligadenylate
CC polymerase (TENT4B or TENT4A), and a substrate specific RNA-binding
CC factor (ZCCHC7 or ZCCHC8). Several TRAMP-like complexes exist with
CC specific compositions and are associated with nuclear, or nucleolar RNA
CC exosomes. Identified in the spliceosome C complex. Component of the
CC poly(A) tail exosome targeting (PAXT) complex made of PABPN1, ZFC3H1
CC and MTREX that directs a subset of long and polyadenylated poly(A) RNAs
CC for exosomal degradation. Component of the nuclear exosome targeting
CC (NEXT) complex composed of MTREX, ZCCHC8, and RBM7 that directs a
CC subset of non-coding short-lived RNAs for exosomal degradation.
CC Interacts with ZCCHC8; this interaction bridges the interaction between
CC RBM7 and MTREX. Binds to ZFC3H1 and RBM7 in a RNase-insensitive manner.
CC Interacts with EXOSC10; the interaction mediates the association of
CC MTREX with nuclear RNA exosomes. Interacts with isoform 1 of NVL in an
CC ATP-dependent manner; the interaction is required to associate NVL with
CC nuclear RNA exosome. Interacts with WDR74; the interaction dissociation
CC in a late stage of rRNA synthesis is required for appropriate
CC maturation of pre-60S particles and depends on the ATPase activity of
CC NVL. Interacts with MPHOSPH6. Interacts with the RNA cap-binding
CC complex proteins NCBP1 and SRRT. Interacts with NRDE2; the interaction
CC is direct and negatively regulates MTREX function in exosomal
CC degradation by changing its conformation precluding interaction with
CC ZFC3H1, the RNA cap-binding complex proteins NCBP1 and SRRT, and
CC association with the exosome. Interacts with the nuclear RNA exosome
CC complex. {ECO:0000250|UniProtKB:P42285}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm {ECO:0000250}. Nucleus,
CC nucleolus {ECO:0000250}. Nucleus {ECO:0000250|UniProtKB:P42285}.
CC Nucleus speckle {ECO:0000250|UniProtKB:P42285}.
CC -!- SIMILARITY: Belongs to the helicase family. SKI2 subfamily.
CC {ECO:0000305}.
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DR EMBL; AK012158; BAB28066.1; -; mRNA.
DR EMBL; BC029230; AAH29230.1; -; mRNA.
DR CCDS; CCDS26778.1; -.
DR RefSeq; NP_082427.1; NM_028151.2.
DR AlphaFoldDB; Q9CZU3; -.
DR SMR; Q9CZU3; -.
DR BioGRID; 215213; 43.
DR ELM; Q9CZU3; -.
DR IntAct; Q9CZU3; 2.
DR STRING; 10090.ENSMUSP00000022281; -.
DR iPTMnet; Q9CZU3; -.
DR PhosphoSitePlus; Q9CZU3; -.
DR SwissPalm; Q9CZU3; -.
DR EPD; Q9CZU3; -.
DR MaxQB; Q9CZU3; -.
DR PaxDb; Q9CZU3; -.
DR PeptideAtlas; Q9CZU3; -.
DR PRIDE; Q9CZU3; -.
DR ProteomicsDB; 290114; -.
DR Antibodypedia; 23424; 222 antibodies from 29 providers.
DR DNASU; 72198; -.
DR Ensembl; ENSMUST00000022281; ENSMUSP00000022281; ENSMUSG00000016018.
DR GeneID; 72198; -.
DR KEGG; mmu:72198; -.
DR UCSC; uc007rws.1; mouse.
DR CTD; 23517; -.
DR MGI; MGI:1919448; Mtrex.
DR VEuPathDB; HostDB:ENSMUSG00000016018; -.
DR eggNOG; KOG0948; Eukaryota.
DR GeneTree; ENSGT00940000156183; -.
DR HOGENOM; CLU_002902_0_1_1; -.
DR InParanoid; Q9CZU3; -.
DR OMA; IMLKNYN; -.
DR OrthoDB; 176060at2759; -.
DR PhylomeDB; Q9CZU3; -.
DR TreeFam; TF300597; -.
DR Reactome; R-MMU-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR Reactome; R-MMU-72163; mRNA Splicing - Major Pathway.
DR BioGRID-ORCS; 72198; 26 hits in 75 CRISPR screens.
DR ChiTaRS; Skiv2l2; mouse.
DR PRO; PR:Q9CZU3; -.
DR Proteomes; UP000000589; Chromosome 13.
DR RNAct; Q9CZU3; protein.
DR Bgee; ENSMUSG00000016018; Expressed in indifferent gonad and 256 other tissues.
DR Genevisible; Q9CZU3; MM.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; ISO:MGI.
DR GO; GO:0000178; C:exosome (RNase complex); ISO:MGI.
DR GO; GO:0000176; C:nuclear exosome (RNase complex); ISO:MGI.
DR GO; GO:0016607; C:nuclear speck; IEA:UniProtKB-SubCell.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0031499; C:TRAMP complex; ISO:MGI.
DR GO; GO:0005524; F:ATP binding; ISS:UniProtKB.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0003724; F:RNA helicase activity; ISS:UniProtKB.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; ISS:UniProtKB.
DR GO; GO:0000460; P:maturation of 5.8S rRNA; ISO:MGI.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0006401; P:RNA catabolic process; ISS:UniProtKB.
DR GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR GO; GO:0006364; P:rRNA processing; ISS:UniProtKB.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR025696; rRNA_proc-arch_dom.
DR InterPro; IPR016438; Ski2-like.
DR InterPro; IPR012961; Ski2_C.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF08148; DSHCT; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF13234; rRNA_proc-arch; 1.
DR PIRSF; PIRSF005198; Antiviral_helicase_SKI2; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM01142; DSHCT; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
PE 1: Evidence at protein level;
KW Acetylation; ATP-binding; DNA damage; Helicase; Hydrolase; Isopeptide bond;
KW mRNA processing; mRNA splicing; Nucleotide-binding; Nucleus;
KW Phosphoprotein; Reference proteome; rRNA processing; Spliceosome;
KW Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:P42285"
FT CHAIN 2..1040
FT /note="Exosome RNA helicase MTR4"
FT /id="PRO_0000102095"
FT DOMAIN 146..302
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 403..575
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 16..77
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 250..253
FT /note="DEIH box"
FT COMPBIAS 19..48
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 56..77
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 137
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P42285"
FT BINDING 159..166
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 162
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P42285"
FT BINDING 164
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P42285"
FT BINDING 165
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P42285"
FT BINDING 166
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P42285"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0000250|UniProtKB:P42285"
FT MOD_RES 38
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P42285"
FT MOD_RES 49
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P42285"
FT MOD_RES 76
FT /note="N6-acetyllysine"
FT /evidence="ECO:0007744|PubMed:23806337"
FT CROSSLNK 24
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P42285"
FT CROSSLNK 356
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P42285"
FT CROSSLNK 682
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P42285"
FT CROSSLNK 721
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P42285"
SQ SEQUENCE 1040 AA; 117636 MW; 76C1243DB5C27F65 CRC64;
MADAFGDELF SVFEDDSTSA AGAKKDKEKE KWKGPPGSAD KAGKRLDTKL QSESASGGKN
KRDLDVEGTD EPIFGKKPRI EDSINEDLSL ADLMPRVKVQ SVETVEGCTH EVALPADEDY
IPLKPRVGKA AKEYPFILDA FQREAIQCVD NNQSVLVSAH TSAGKTVCAE YAIALALREK
QRVIFTSPIK ALSNQKYREM YEEFQDVGLM TGDVTINPTA SCLVMTTEIL RSMLYRGSEV
MREVAWVIFD EIHYMRDSER GVVWEETIIL LPDNVHYVFL SATIPNARQF AEWICHLHKQ
PCHVIYTDYR PTPLQHYIFP AGGDGLHLVV DENGDFREDN FNTAMQVLRD AGDLAKGDQK
GRKGGTKGPS NVFKIVKMIM ERNFQPVIIF SFSKKDCEAY ALQMTKLDFN TDEEKKMVEE
VFNNAIDCLS DEDKKLPQVE HVLPLLKRGI GIHHGGLLPI LKETIEILFS EGLIKALFAT
ETFAMGINMP ARTVLFTNAR KYDGKDFRWI SSGEYIQMSG RAGRRGMDDR GIVILMVDEK
MSPTIGKQLL KGSADPLNSA FHLTYNMVLN LLRVEEINPE YMLEKSFYQF QHYRAIPGVV
EKVKNSEEQY NKIVIPNEEN VVIYYKIRQQ LAKLGKEIEE YIHKPKYCLP FLQPGRLVKV
KNEGDDFGWG VVVNFSKKSN VKPNSGELDP LYVVEVLLRC SKESLKNSAT EAAKPAKPDE
KGEMQVVPVL VHLLSAISTV RLYIPKDLRP VDNRQSVLKS IQEVQRRFPD GVPLLDPIDD
MGIQDQGLKK VIQKVEAFEH RMYSHPLHND PNLETVYTLC ERKAQIALDI KSAKRELKKA
RTVLQMDELK CRKRVLRRLG FATSSDVIEM KGRVACEISS ADELLLTEMM FNGLFNDLSS
EQATALLSCF VFQENSSEMP KLTEQLAGPL RQMQECAKRI AKVSAEAKLE IDEETYLSSF
KPHLMDVVYT WATGATFAHI CKMTDVFEGS IIRCMRRLEE LLRQMCQAAK AIGNTELENK
FAEGITKIKR DIVFAASLYL
