MTR4_ARATH
ID MTR4_ARATH Reviewed; 988 AA.
AC Q9XIF2;
DT 20-JAN-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 162.
DE RecName: Full=DExH-box ATP-dependent RNA helicase DExH9 {ECO:0000305};
DE EC=3.6.4.13 {ECO:0000305};
DE AltName: Full=Protein MTR4 homolog {ECO:0000305};
DE Short=AtMTR4 {ECO:0000303|PubMed:21682783};
GN Name=MTR4 {ECO:0000303|PubMed:21682783};
GN OrderedLocusNames=At1g59760 {ECO:0000312|Araport:AT1G59760};
GN ORFNames=F23H11.8 {ECO:0000312|EMBL:AAD39319.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=21682783; DOI=10.1111/j.1365-313x.2011.04675.x;
RA Lange H., Sement F.M., Gagliardi D.;
RT "MTR4, a putative RNA helicase and exosome co-factor, is required for
RT proper rRNA biogenesis and development in Arabidopsis thaliana.";
RL Plant J. 68:51-63(2011).
RN [5]
RP GENE FAMILY.
RX PubMed=24265739; DOI=10.1371/journal.pone.0078982;
RA Xu R., Zhang S., Huang J., Zheng C.;
RT "Genome-wide comparative in silico analysis of the RNA helicase gene family
RT in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza
RT sativa.";
RL PLoS ONE 8:E78982-E78982(2013).
RN [6]
RP FUNCTION, SUBCELLULAR LOCATION, AND ASSOCIATION WITH THE RNA EXOSOME
RP COMPLEX.
RX PubMed=25144737; DOI=10.1371/journal.pgen.1004564;
RA Lange H., Zuber H., Sement F.M., Chicher J., Kuhn L., Hammann P.,
RA Brunaud V., Berard C., Bouteiller N., Balzergue S., Aubourg S.,
RA Martin-Magniette M.L., Vaucheret H., Gagliardi D.;
RT "The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear
RT transcripts for degradation by the nuclear exosome in Arabidopsis
RT thaliana.";
RL PLoS Genet. 10:E1004564-E1004564(2014).
CC -!- FUNCTION: ATP-dependent RNA helicase that associates with the RNA
CC exosome complex (PubMed:21682783, PubMed:25144737). Required for proper
CC rRNA biogenesis and development. Involved in the 3'-processing of the
CC 7S pre-RNA to the mature 5.8S rRNA and also in the removal of rRNA
CC maturation by-products (PubMed:21682783). {ECO:0000269|PubMed:21682783,
CC ECO:0000269|PubMed:25144737}.
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:0000305};
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:21682783,
CC ECO:0000269|PubMed:25144737}.
CC -!- TISSUE SPECIFICITY: Ubiquitous but preferentially expressed in active
CC tissues. {ECO:0000269|PubMed:21682783}.
CC -!- DISRUPTION PHENOTYPE: Slower embryogenesis and several developmental
CC defects including aberrant vein patterning, pointed first and second
CC leaves, smaller rosettes and shorter roots.
CC {ECO:0000269|PubMed:21682783}.
CC -!- SIMILARITY: Belongs to the DExH box helicase family. SKI2 subfamily.
CC {ECO:0000305}.
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DR EMBL; AC007258; AAD39319.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE33616.1; -; Genomic_DNA.
DR EMBL; AK176836; BAD44599.1; -; mRNA.
DR PIR; E96621; E96621.
DR RefSeq; NP_176185.1; NM_104669.4.
DR AlphaFoldDB; Q9XIF2; -.
DR SMR; Q9XIF2; -.
DR STRING; 3702.AT1G59760.1; -.
DR iPTMnet; Q9XIF2; -.
DR PaxDb; Q9XIF2; -.
DR PRIDE; Q9XIF2; -.
DR ProteomicsDB; 251362; -.
DR EnsemblPlants; AT1G59760.1; AT1G59760.1; AT1G59760.
DR GeneID; 842269; -.
DR Gramene; AT1G59760.1; AT1G59760.1; AT1G59760.
DR KEGG; ath:AT1G59760; -.
DR Araport; AT1G59760; -.
DR TAIR; locus:2026001; AT1G59760.
DR eggNOG; KOG0948; Eukaryota.
DR HOGENOM; CLU_002902_0_1_1; -.
DR InParanoid; Q9XIF2; -.
DR OMA; IMLKNYN; -.
DR OrthoDB; 176060at2759; -.
DR PhylomeDB; Q9XIF2; -.
DR PRO; PR:Q9XIF2; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9XIF2; baseline and differential.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0005654; C:nucleoplasm; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003724; F:RNA helicase activity; IBA:GO_Central.
DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000460; P:maturation of 5.8S rRNA; IBA:GO_Central.
DR GO; GO:0006401; P:RNA catabolic process; IBA:GO_Central.
DR GO; GO:0031125; P:rRNA 3'-end processing; IMP:TAIR.
DR GO; GO:0006364; P:rRNA processing; IMP:TAIR.
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 2: Evidence at transcript level;
KW ATP-binding; Helicase; Hydrolase; Nucleotide-binding; Nucleus;
KW Reference proteome; RNA-binding; rRNA processing; rRNA-binding.
FT CHAIN 1..988
FT /note="DExH-box ATP-dependent RNA helicase DExH9"
FT /id="PRO_0000435298"
FT DOMAIN 76..232
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 307..509
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..27
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 180..183
FT /note="DEVH box"
FT /evidence="ECO:0000305"
FT BINDING 89..96
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
SQ SEQUENCE 988 AA; 111887 MW; 0C1A456657B14FE8 CRC64;
MGSVKRKSVE ESSDSAPPQK VQREDDSTQI INEELVGCVH DVSFPENYVP LAPSVHNKPP
AKDFPFTLDS FQSEAIKCLD NGESVMVSAH TSAGKTVVAS YAIAMSLKEN QRVIYTSPIK
ALSNQKYRDF KEEFSDVGLM TGDVTIDPNA SCLVMTTEIL RSMQYKGSEI MREVAWIIFD
EVHYMRDSER GVVWEESIVM APKNSRFVFL SATVPNAKEF ADWVAKVHQQ PCHIVYTDYR
PTPLQHYVFP AGGNGLYLVV DEKSKFHEDS FQKSLNALVP TNESDKKRDN GKFQKGLVIG
KLGEESDIFK LVKMIIQRQY DPVILFSFSK KECEALAMQM SKMVLNSDDE KDAVETIFAS
AIDMLSDDDK KLPQVSNILP ILKRGIGVHH SGLLPILKEV IEILFQEGLI KCLFATETFS
IGLNMPAKTV VFTNVRKFDG DKFRWLSSGE YIQMSGRAGR RGIDKRGICI LMVDEKMEPA
VAKSMLKGSA DSLNSAFHLS YNMLLNQLRC EEGDPENLLR NSFFQFQADR AIPDLEKQIK
SLEEERDSLV IEEEESLKNY YNLILQYKSL KKDIREIVFT PKYCLPFLLP NRAVCLDCTN
DDEEPQSFSI EDQDTWGVIM KFNKVKSLSE DDDSRRPEDA NYTVDVLTRC MVSKDGVGKK
KVKAVPIKER GEPVVVTVPL SQIKSLSSAI MNIPKDLVPL EARENALKKV SELLSRHPDG
IPLDPEVDMK IKSSSYKKTV RRLEALENLF EKHKIAKSPL ITEKLKVLQM KEELIAKIKS
LKKTVRSSTA LAFKDELKAR KRVLRRLGYI TSDNVVELKG KVACEISSAE ELTLTELMFS
GIFKDAKVEE LVSLLSCFVW RERLPDAAKP REELDLLFIQ LQDTARRVAE VQLDCKVEID
VESFVQSFRP DIMEAVYAWA KGSKFYEVME IARVFEGSLI RAIRRMEEVL QQLIVAAKSI
GETQLEAKLE EAVSKIKRDI VFAASLYL
