RH38_ARATH
ID RH38_ARATH Reviewed; 496 AA.
AC Q93ZG7; Q9SCQ0;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2006, sequence version 2.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=DEAD-box ATP-dependent RNA helicase 38;
DE EC=3.6.4.13;
DE AltName: Full=Low expression of osmotically-responsive genes 4 protein;
DE AltName: Full=Protein CRYOPHYTE;
GN Name=RH38; Synonyms=LOS4; OrderedLocusNames=At3g53110; ORFNames=T4D2.40;
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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;
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 FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=12165572; DOI=10.1073/pnas.172399299;
RA Gong Z., Lee H., Xiong L., Jagendorf A., Stevenson B., Zhu J.-K.;
RT "RNA helicase-like protein as an early regulator of transcription factors
RT for plant chilling and freezing tolerance.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:11507-11512(2002).
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 FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=15598798; DOI=10.1105/tpc.104.027557;
RA Gong Z., Dong C.-H., Lee H., Zhu J., Xiong L., Gong D., Stevenson B.,
RA Zhu J.-K.;
RT "A DEAD box RNA helicase is essential for mRNA export and important for
RT development and stress responses in Arabidopsis.";
RL Plant Cell 17:256-267(2005).
RN [7]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [8]
RP INTERACTION WITH NUP214.
RX PubMed=22898497; DOI=10.1104/pp.112.202192;
RA Braud C., Zheng W., Xiao W.;
RT "LONO1 encoding a nucleoporin is required for embryogenesis and seed
RT viability in Arabidopsis.";
RL Plant Physiol. 160:823-836(2012).
RN [9]
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 essential for mRNA export from the
CC nucleus. Plays an important role in the positive regulation of CBF/DREB
CC transcription factors. {ECO:0000269|PubMed:12165572,
CC ECO:0000269|PubMed:15598798}.
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 -!- SUBUNIT: Interacts with NUP214 (via N-terminus).
CC {ECO:0000269|PubMed:22898497}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:12165572}. Nucleus
CC {ECO:0000269|PubMed:12165572}.
CC -!- TISSUE SPECIFICITY: Constitutively expressed.
CC {ECO:0000269|PubMed:15598798}.
CC -!- INDUCTION: By abscisic acid (ABA).
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. DDX19/DBP5
CC subfamily. {ECO:0000305}.
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DR EMBL; AL132958; CAB64214.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79038.1; -; Genomic_DNA.
DR EMBL; AY057548; AAL09787.1; -; mRNA.
DR EMBL; BT002444; AAO00804.1; -; mRNA.
DR EMBL; BT008867; AAP68306.1; -; mRNA.
DR PIR; T46157; T46157.
DR RefSeq; NP_190879.1; NM_115171.3.
DR AlphaFoldDB; Q93ZG7; -.
DR SMR; Q93ZG7; -.
DR BioGRID; 9794; 5.
DR STRING; 3702.AT3G53110.1; -.
DR iPTMnet; Q93ZG7; -.
DR MetOSite; Q93ZG7; -.
DR PaxDb; Q93ZG7; -.
DR PRIDE; Q93ZG7; -.
DR ProteomicsDB; 236244; -.
DR EnsemblPlants; AT3G53110.1; AT3G53110.1; AT3G53110.
DR GeneID; 824477; -.
DR Gramene; AT3G53110.1; AT3G53110.1; AT3G53110.
DR KEGG; ath:AT3G53110; -.
DR Araport; AT3G53110; -.
DR TAIR; locus:2101993; AT3G53110.
DR eggNOG; KOG0332; Eukaryota.
DR HOGENOM; CLU_003041_1_0_1; -.
DR InParanoid; Q93ZG7; -.
DR OMA; DFKNLCM; -.
DR OrthoDB; 608788at2759; -.
DR PhylomeDB; Q93ZG7; -.
DR PRO; PR:Q93ZG7; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q93ZG7; baseline and differential.
DR Genevisible; Q93ZG7; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0010494; C:cytoplasmic stress granule; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005635; C:nuclear envelope; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0008186; F:ATP-dependent activity, acting on RNA; IDA:TAIR.
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; ISS:TAIR.
DR GO; GO:0016973; P:poly(A)+ mRNA export from nucleus; IDA:TAIR.
DR GO; GO:0009737; P:response to abscisic acid; IMP:TAIR.
DR GO; GO:0009409; P:response to cold; IMP:TAIR.
DR GO; GO:0009408; P:response to heat; 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 1: Evidence at protein level;
KW Acetylation; ATP-binding; Cytoplasm; Helicase; Hydrolase; mRNA transport;
KW Nucleotide-binding; Nucleus; Reference proteome; RNA-binding; Transport.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 2..496
FT /note="DEAD-box ATP-dependent RNA helicase 38"
FT /id="PRO_0000239178"
FT DOMAIN 125..301
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 329..483
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..91
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 91..120
FT /note="Q motif"
FT MOTIF 245..248
FT /note="DEAD box"
FT COMPBIAS 9..27
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 53..73
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 138..145
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CONFLICT 437
FT /note="R -> I (in Ref. 3; AAL09787)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 496 AA; 55384 MW; 3B6956F3573F611B CRC64;
MADTVEKVPT VVESSSSSTV EASNSAEKTE PTTEKKKWGD VEDDDDEEEA VSELNSLSIK
EEEKPDSILE EPEDSNIKAV TSGDTPYTSA SRFEDLNLSP ELMKGLYVEM KFEKPSKIQA
ISLPMIMTPP HKHLIAQAHN GSGKTTCFVL GMLSRVDPTL REPQALCICP TRELANQNME
VLQKMGKFTG ITAELAVPDS TRGAPAATRG APVSAHVVIG TPGTLKKWMA FKRLGLNHLK
ILVFDEADHM LATDGFRDDS LKIMKDIGRV NPNFQVLLFS ATFNETVKDF VARTVKDPNQ
LFVKREDLAL DSVKQYKVVC PKEQNKIEVI KDQIMELGDI GQTIIFVKTK ASAQKVHKAL
AEMGYDVTSV HGNLTESDRD KIVKEFKECL TQVLIATDVI ARGFDQQRVN LVVNYNLPTK
YETGEPDYEV YLHRVGRAGR FGRKGAVFNL LLDDGWDKEV MEKIEKYFEA NVKEIKSWNS
EEEYKSALKE AGLLDE
