RH42_ARATH
ID RH42_ARATH Reviewed; 1166 AA.
AC Q8H0U8; A8MQH2; Q9SYP6;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2006, sequence version 2.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=DEAD-box ATP-dependent RNA helicase 42;
DE EC=3.6.4.13;
DE AltName: Full=DEAD-box RNA helicase RCF1;
DE AltName: Full=REGULATOR OF CBF GENE EXPRESSION 1;
GN Name=RH42; Synonyms=RCF1; OrderedLocusNames=At1g20920; ORFNames=F9H16.10;
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] OF 605-1166.
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 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 [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-210 AND SER-324, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
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).
RN [7]
RP FUNCTION, MUTAGENESIS OF GLU-687 AND GLY-808, SUBCELLULAR LOCATION, AND
RP INDUCTION BY COLD.
RX PubMed=23371945; DOI=10.1105/tpc.112.108340;
RA Guan Q., Wu J., Zhang Y., Jiang C., Liu R., Chai C., Zhu J.;
RT "A DEAD box RNA helicase is critical for pre-mRNA splicing, cold-responsive
RT gene regulation, and cold tolerance in Arabidopsis.";
RL Plant Cell 25:342-356(2013).
CC -!- FUNCTION: Helicase required for pre-mRNA splicing, cold-responsive gene
CC regulation and cold tolerance. {ECO:0000269|PubMed:23371945}.
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:0000269|PubMed:23371945}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8H0U8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8H0U8-2; Sequence=VSP_053521;
CC -!- INDUCTION: Up-regulated by cold. {ECO:0000269|PubMed:23371945}.
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. DDX46/PRP5
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAN72041.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AC007369; AAD30599.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE30040.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE30041.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59668.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59669.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59670.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59671.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59672.1; -; Genomic_DNA.
DR EMBL; BT002030; AAN72041.1; ALT_INIT; mRNA.
DR PIR; H86341; H86341.
DR RefSeq; NP_001077571.1; NM_001084102.1. [Q8H0U8-2]
DR RefSeq; NP_001322011.1; NM_001332479.1. [Q8H0U8-1]
DR RefSeq; NP_001322012.1; NM_001332478.1. [Q8H0U8-1]
DR RefSeq; NP_001322013.1; NM_001332481.1. [Q8H0U8-1]
DR RefSeq; NP_001322014.1; NM_001332480.1. [Q8H0U8-1]
DR RefSeq; NP_001322015.1; NM_001332477.1. [Q8H0U8-1]
DR RefSeq; NP_173516.1; NM_101945.4. [Q8H0U8-1]
DR AlphaFoldDB; Q8H0U8; -.
DR SMR; Q8H0U8; -.
DR BioGRID; 23924; 2.
DR STRING; 3702.AT1G20920.1; -.
DR iPTMnet; Q8H0U8; -.
DR PaxDb; Q8H0U8; -.
DR PRIDE; Q8H0U8; -.
DR ProteomicsDB; 236246; -. [Q8H0U8-1]
DR EnsemblPlants; AT1G20920.1; AT1G20920.1; AT1G20920. [Q8H0U8-1]
DR EnsemblPlants; AT1G20920.2; AT1G20920.2; AT1G20920. [Q8H0U8-2]
DR EnsemblPlants; AT1G20920.3; AT1G20920.3; AT1G20920. [Q8H0U8-1]
DR EnsemblPlants; AT1G20920.4; AT1G20920.4; AT1G20920. [Q8H0U8-1]
DR EnsemblPlants; AT1G20920.5; AT1G20920.5; AT1G20920. [Q8H0U8-1]
DR EnsemblPlants; AT1G20920.6; AT1G20920.6; AT1G20920. [Q8H0U8-1]
DR EnsemblPlants; AT1G20920.7; AT1G20920.7; AT1G20920. [Q8H0U8-1]
DR GeneID; 838685; -.
DR Gramene; AT1G20920.1; AT1G20920.1; AT1G20920. [Q8H0U8-1]
DR Gramene; AT1G20920.2; AT1G20920.2; AT1G20920. [Q8H0U8-2]
DR Gramene; AT1G20920.3; AT1G20920.3; AT1G20920. [Q8H0U8-1]
DR Gramene; AT1G20920.4; AT1G20920.4; AT1G20920. [Q8H0U8-1]
DR Gramene; AT1G20920.5; AT1G20920.5; AT1G20920. [Q8H0U8-1]
DR Gramene; AT1G20920.6; AT1G20920.6; AT1G20920. [Q8H0U8-1]
DR Gramene; AT1G20920.7; AT1G20920.7; AT1G20920. [Q8H0U8-1]
DR KEGG; ath:AT1G20920; -.
DR Araport; AT1G20920; -.
DR TAIR; locus:2037416; AT1G20920.
DR eggNOG; KOG0334; Eukaryota.
DR InParanoid; Q8H0U8; -.
DR OMA; CGLGVQT; -.
DR OrthoDB; 245118at2759; -.
DR PhylomeDB; Q8H0U8; -.
DR PRO; PR:Q8H0U8; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q8H0U8; baseline and differential.
DR Genevisible; Q8H0U8; AT.
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:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IBA:GO_Central.
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; Coiled coil; Helicase; Hydrolase;
KW Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome;
KW RNA-binding.
FT CHAIN 1..1166
FT /note="DEAD-box ATP-dependent RNA helicase 42"
FT /id="PRO_0000239182"
FT DOMAIN 560..738
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 749..910
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..460
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 14..95
FT /evidence="ECO:0000255"
FT COILED 130..302
FT /evidence="ECO:0000255"
FT MOTIF 529..557
FT /note="Q motif"
FT MOTIF 686..689
FT /note="DEAD box"
FT COMPBIAS 1..45
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 68..83
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 92..311
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 325..346
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 416..430
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 573..580
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOD_RES 210
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT MOD_RES 324
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT VAR_SEQ 1..338
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_053521"
FT MUTAGEN 687
FT /note="E->A: Loss of ATPase activity."
FT /evidence="ECO:0000269|PubMed:23371945"
FT MUTAGEN 808
FT /note="G->R: In rcf1-1; loss of function and reduced cold
FT tolerance."
FT /evidence="ECO:0000269|PubMed:23371945"
FT CONFLICT 894
FT /note="A -> D (in Ref. 3; AAN72041)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1166 AA; 133033 MW; 597BD171F02666B5 CRC64;
MEVEKSKYRS EDLDVVEEEA DLKKSRRDRD RSNERKKDKG SEKRREKDRR KKRVKSSDSE
DDYDRDDDEE REKRKEKERE RRRRDKDRVK RRSERRKSSD SEDDVEEEDE RDKRRVNEKE
RGHREHERDR GKDRKRDRER EERKDKERER EKDRERRERE REEREKERVK ERERREREDG
ERDRREREKE RGSRRNRERE RSREVGNEES DDDVKRDLKR RRKEGGERKE KEREKSVGRS
SRHEDSPKRK SVEDNGEKKE KKTREEELED EQKKLDEEVE KRRRRVQEWQ ELKRKKEEAE
SESKGDADGN EPKAGKAWTL EGESDDEEGH PEEKSETEMD VDEETKPEND GDAKMVDLEN
ETAATVSESG GDGAVDEEEI DPLDAFMNTM VLPEVEKFCN GAPPPAVNDG TLDSKMNGKE
SGDRPKKGFN KALGRIIQGE DSDSDYSEPK NDDDPSLDED DEEFMKRVKK TKAEKLSLVD
HSKIEYEPFR KNFYIEVKDI SRMTQEEVNT YRKELELKVH GKDVPRPIKF WHQTGLTSKI
LDTMKKLNYE KPMPIQTQAL PIIMSGRDCI GVAKTGSGKT LGFVLPMLRH IKDQPPVEAG
DGPIGLVMAP TRELVQQIHS DIRKFSKPLG IRCVPVYGGS GVAQQISELK RGTEIVVCTP
GRMIDILCTS SGKITNLRRV TFLVMDEADR MFDMGFEPQI TRIIQNIRPE RQTVLFSATF
PRQVETLARK VLNKPVEIQV GGRSVVNKDI TQLVEVRPES DRFLRLLELL GEWSEKGKIL
VFVQSQEKCD ALYRDMIKSS YPCLSLHGGK DQTDRESTIS DFKNDVCNLL IATSVAARGL
DVKELELVVN FDAPNHYEDY VHRVGRTGRA GRKGCAVTFI SEDDAKYAPD LVKALELSEQ
PVPDDLKALA DGFMVKVKQG IEQAHGTGYG GSGFKFNEEE EEVRKAAKKA QAKEYGFEED
KSDSEDENDV VRKAGGGEIS QQQATFAQIA AIAAAAKAAA AAPVSAPVTA NQLLANGGGL
AAMPGVLPVT VPTLPSEGAG RAAAMVAAMN LQHNLAKIQA DAMPEHYEAE LEINDFPQNA
RWKVTHKETL GPISEWTGAA ITTRGQFYPT GRIPGPGERK LYLFIEGPSE KSVKHAKAEL
KRVLEDITNQ AMSSLPGGAS GRYSVL
