RH30_ARATH
ID RH30_ARATH Reviewed; 591 AA.
AC Q8W4R3; Q0WVX4; Q9FML1; Q9ZRZ7;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2006, sequence version 2.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=DEAD-box ATP-dependent RNA helicase 30;
DE EC=3.6.4.13;
GN Name=RH30; OrderedLocusNames=At5g63120; ORFNames=MDC12.8;
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=9501997; DOI=10.1093/dnares/4.6.401;
RA Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence
RT features of the regions of 1,191,918 bp covered by seventeen physically
RT assigned P1 clones.";
RL DNA Res. 4:401-414(1997).
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] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 257-519 (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=9862990; DOI=10.1093/nar/27.2.628;
RA Aubourg S., Kreis M., Lecharny A.;
RT "The DEAD box RNA helicase family in Arabidopsis thaliana.";
RL Nucleic Acids Res. 27:628-636(1999).
RN [6]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=17168887; DOI=10.1111/j.1467-7652.2004.00084.x;
RA Mingam A., Toffano-Nioche C., Brunaud V., Boudet N., Kreis M., Lecharny A.;
RT "DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link
RT between quantitative expression, gene structure and evolution of a family
RT of genes.";
RL Plant Biotechnol. J. 2:401-415(2004).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=17272265; DOI=10.1074/mcp.m600408-mcp200;
RA Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
RT "Multidimensional protein identification technology (MudPIT) analysis of
RT ubiquitinated proteins in plants.";
RL Mol. Cell. Proteomics 6:601-610(2007).
RN [8]
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).
CC -!- FUNCTION: ATP-dependent RNA helicase involved nonsense-mediated mRNA
CC decay and ribosome biogenesis through rRNA processing. {ECO:0000250}.
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 -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8W4R3-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8W4R3-2; Sequence=VSP_019104, VSP_019105;
CC -!- DOMAIN: The Q motif is unique to and characteristic of the DEAD box
CC family of RNA helicases and controls ATP binding and hydrolysis.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX5/DBP2
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB10554.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB008265; BAB10554.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED97706.1; -; Genomic_DNA.
DR EMBL; CP002688; AED97707.1; -; Genomic_DNA.
DR EMBL; AY060589; AAL31214.1; -; mRNA.
DR EMBL; BT000610; AAN18177.1; -; mRNA.
DR EMBL; AK226611; BAE98724.1; -; mRNA.
DR EMBL; AJ010476; CAA09215.1; -; mRNA.
DR PIR; T51349; T51349.
DR RefSeq; NP_568964.1; NM_125706.2. [Q8W4R3-2]
DR RefSeq; NP_974985.1; NM_203256.2. [Q8W4R3-1]
DR AlphaFoldDB; Q8W4R3; -.
DR SMR; Q8W4R3; -.
DR STRING; 3702.AT5G63120.2; -.
DR iPTMnet; Q8W4R3; -.
DR PaxDb; Q8W4R3; -.
DR PRIDE; Q8W4R3; -.
DR ProteomicsDB; 236913; -. [Q8W4R3-1]
DR EnsemblPlants; AT5G63120.1; AT5G63120.1; AT5G63120. [Q8W4R3-2]
DR EnsemblPlants; AT5G63120.2; AT5G63120.2; AT5G63120. [Q8W4R3-1]
DR GeneID; 836432; -.
DR Gramene; AT5G63120.1; AT5G63120.1; AT5G63120. [Q8W4R3-2]
DR Gramene; AT5G63120.2; AT5G63120.2; AT5G63120. [Q8W4R3-1]
DR KEGG; ath:AT5G63120; -.
DR Araport; AT5G63120; -.
DR TAIR; locus:2162022; AT5G63120.
DR eggNOG; KOG0331; Eukaryota.
DR InParanoid; Q8W4R3; -.
DR OMA; GTSHPQY; -.
DR PhylomeDB; Q8W4R3; -.
DR PRO; PR:Q8W4R3; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8W4R3; baseline and differential.
DR Genevisible; Q8W4R3; AT.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IBA:GO_Central.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IEA:UniProtKB-KW.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
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; IPR000629; RNA-helicase_DEAD-box_CS.
DR InterPro; IPR014014; RNA_helicase_DEAD_Q_motif.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS00039; DEAD_ATP_HELICASE; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; ATP-binding; Helicase; Hydrolase;
KW Nonsense-mediated mRNA decay; Nucleotide-binding; Nucleus;
KW Reference proteome; Ribosome biogenesis; RNA-binding; rRNA processing.
FT CHAIN 1..591
FT /note="DEAD-box ATP-dependent RNA helicase 30"
FT /id="PRO_0000239170"
FT DOMAIN 196..371
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 399..544
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..109
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 547..591
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 165..193
FT /note="Q motif"
FT MOTIF 319..322
FT /note="DEAD box"
FT COMPBIAS 17..31
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 574..591
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 209..216
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT VAR_SEQ 475..484
FT /note="DVKDIKCVVN -> VSSGIREKST (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_019104"
FT VAR_SEQ 485..591
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_019105"
SQ SEQUENCE 591 AA; 64621 MW; 2F4F6A57CFC3CDCB CRC64;
MSSYDRRFAD PNSYRQRSGA PVGSSQPMDP SAAPYNPRYT GGGGGYGPSP VMAGDNSGYN
RYPSFQPPSG GFSVGRGGGR GGYGQYGDRN GGGNWGGGGG RGGSSKRELD SVSLPKQNFG
NLVHFEKNFY VESPTVQAMT EQDVAMYRTE RDISVEGRDV PKPMKMFQDA NFPDNILEAI
AKLGFTEPTP IQAQGWPMAL KGRDLIGIAE TGSGKTLAYL LPALVHVSAQ PRLGQDDGPI
VLILAPTREL AVQIQEESRK FGLRSGVRST CIYGGAPKGP QIRDLRRGVE IVIATPGRLI
DMLECQHTNL KRVTYLVLDE ADRMLDMGFE PQIRKIVSQI RPDRQTLLWS ATWPREVETL
ARQFLRDPYK AIIGSTDLKA NQSINQVIEI VPTPEKYNRL LTLLKQLMDG SKILIFVETK
RGCDQVTRQL RMDGWPALAI HGDKTQSERD RVLAEFKSGR SPIMTATDVA ARGLDVKDIK
CVVNYDFPNT LEDYIHRIGR TGRAGAKGMA FTFFTHDNAK FARELVKILQ EAGQVVPPTL
SALVRSSGSG YGGSGGGRNF RPRGGGRGGG FGDKRSRSTS NFVPHGGKRT W
