RH39_ARATH
ID RH39_ARATH Reviewed; 621 AA.
AC Q56X76; Q682L4; Q6NQ85; Q9SZ89;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2006, sequence version 2.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=DEAD-box ATP-dependent RNA helicase 39;
DE EC=3.6.4.13;
GN Name=RH39; OrderedLocusNames=At4g09730; ORFNames=F17A8.80;
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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;
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].
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 (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
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 [6]
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 -!- 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 -!- 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 -!- SIMILARITY: Belongs to the DEAD box helicase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB39640.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB78096.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL049482; CAB39640.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161515; CAB78096.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE82787.1; -; Genomic_DNA.
DR EMBL; BT010574; AAQ65197.1; -; mRNA.
DR EMBL; AK175347; BAD43110.1; -; mRNA.
DR EMBL; AK175353; BAD43116.1; -; mRNA.
DR EMBL; AK175435; BAD43198.1; -; mRNA.
DR EMBL; AK175766; BAD43529.1; -; mRNA.
DR EMBL; AK221801; BAD93963.1; -; mRNA.
DR PIR; T04020; T04020.
DR RefSeq; NP_849348.1; NM_179017.3.
DR AlphaFoldDB; Q56X76; -.
DR SMR; Q56X76; -.
DR STRING; 3702.AT4G09730.1; -.
DR PaxDb; Q56X76; -.
DR PRIDE; Q56X76; -.
DR ProteomicsDB; 236263; -.
DR EnsemblPlants; AT4G09730.1; AT4G09730.1; AT4G09730.
DR GeneID; 826559; -.
DR Gramene; AT4G09730.1; AT4G09730.1; AT4G09730.
DR KEGG; ath:AT4G09730; -.
DR Araport; AT4G09730; -.
DR TAIR; locus:2118509; AT4G09730.
DR eggNOG; KOG0331; Eukaryota.
DR HOGENOM; CLU_003041_1_3_1; -.
DR InParanoid; Q56X76; -.
DR OMA; NARHDFI; -.
DR OrthoDB; 1223767at2759; -.
DR PhylomeDB; Q56X76; -.
DR PRO; PR:Q56X76; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q56X76; baseline and differential.
DR Genevisible; Q56X76; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IDA:TAIR.
DR GO; GO:0070180; F:large ribosomal subunit rRNA binding; IDA:TAIR.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR GO; GO:1901259; P:chloroplast rRNA processing; IMP:TAIR.
DR GO; GO:1902775; P:mitochondrial large ribosomal subunit assembly; IBA:GO_Central.
DR GO; GO:0110102; P:ribulose bisphosphate carboxylase complex assembly; 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; 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; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
PE 2: Evidence at transcript level;
KW ATP-binding; Helicase; Hydrolase; Nucleotide-binding; Reference proteome;
KW RNA-binding.
FT CHAIN 1..621
FT /note="DEAD-box ATP-dependent RNA helicase 39"
FT /id="PRO_0000239179"
FT DOMAIN 143..330
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 355..505
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 497..621
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 112..140
FT /note="Q motif"
FT MOTIF 270..273
FT /note="DEAD box"
FT COMPBIAS 500..533
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 534..568
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 156..163
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT CONFLICT 244
FT /note="V -> A (in Ref. 4; BAD43116)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 621 AA; 68924 MW; 77C57EF665FA49FB CRC64;
MVGASRTILS LSLSSSLFTF SKIPHVFPFL RLHKPRFHHA FRPLYSAAAT TSSPTTETNV
TDPDQLKHTI LLERLRLRHL KESAKPPQQR PSSVVGVEEE SSIRKKSKKL VENFQELGLS
EEVMGALQEL NIEVPTEIQC IGIPAVMERK SVVLGSHTGS GKTLAYLLPI VQLMREDEAN
LGKKTKPRRP RTVVLCPTRE LSEQVYRVAK SISHHARFRS ILVSGGSRIR PQEDSLNNAI
DMVVGTPGRI LQHIEEGNMV YGDIAYLVLD EADTMFDRGF GPEIRKFLAP LNQRALKTND
QGFQTVLVTA TMTMAVQKLV DEEFQGIEHL RTSTLHKKIA NARHDFIKLS GGEDKLEALL
QVLEPSLAKG SKVMVFCNTL NSSRAVDHYL SENQISTVNY HGEVPAEQRV ENLKKFKDEE
GDCPTLVCTD LAARGLDLDV DHVVMFDFPK NSIDYLHRTG RTARMGAKGK VTSLVSRKDQ
MLAARIEEAM RNNESLESLT TDNVRRDAAR THITQEKGRS VKQIREVSKQ RNSRDKPSSS
SPPARSTGGK TPVRKSSSSS FSKPRKASSP PEKSSKPKRK ILKTVGSRSI AARGKTGSDR
RPGKKLSVVG FRGKSSSARA S
