ID RH3_ARATH Reviewed; 748 AA.
AC Q8L7S8; O65255; Q0WMJ9; Q8LPE9; Q8RUW1; Q9SB96;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2006, sequence version 2.
DT 27-MAR-2024, entry version 143.
DE RecName: Full=DEAD-box ATP-dependent RNA helicase 3, chloroplastic;
DE EC=3.6.4.13;
DE AltName: Full=Protein EMBRYO DEFECTIVE 1138;
DE Flags: Precursor;
GN Name=RH3; Synonyms=EMB1138; OrderedLocusNames=At5g26742;
GN ORFNames=F21E10.1, T7I7.6;
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 [MRNA] (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 [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 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 [5]
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 [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, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RX PubMed=18431481; DOI=10.1371/journal.pone.0001994;
RA Zybailov B., Rutschow H., Friso G., Rudella A., Emanuelsson O., Sun Q.,
RA van Wijk K.J.;
RT "Sorting signals, N-terminal modifications and abundance of the chloroplast
RT proteome.";
RL PLoS ONE 3:E1994-E1994(2008).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-724, AND IDENTIFICATION BY
RP 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 [9]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=22576849; DOI=10.1104/pp.112.197525;
RA Asakura Y., Galarneau E., Watkins K.P., Barkan A., van Wijk K.J.;
RT "Chloroplast RH3 DEAD box RNA helicases in maize and Arabidopsis function
RT in splicing of specific group II introns and affect chloroplast ribosome
RT biogenesis.";
RL Plant Physiol. 159:961-974(2012).
RN [10]
RP FUNCTION, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RX PubMed=23227895; DOI=10.1111/tpj.12055;
RA Lee K.H., Park J., Williams D.S., Xiong Y., Hwang I., Kang B.H.;
RT "Defective chloroplast development inhibits maintenance of normal levels of
RT abscisic acid in a mutant of the Arabidopsis RH3 DEAD-box protein during
RT early post-germination growth.";
RL Plant J. 73:720-732(2013).
RN [11]
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 [12]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=25043599; DOI=10.1016/j.plaphy.2014.07.006;
RA Gu L., Xu T., Lee K., Lee K.H., Kang H.;
RT "A chloroplast-localized DEAD-box RNA helicase AtRH3 is essential for
RT intron splicing and plays an important role in the growth and stress
RT response in Arabidopsis thaliana.";
RL Plant Physiol. Biochem. 82:309-318(2014).
CC -!- FUNCTION: Nuclear genome-encoded factor involved in ribosome biogenesis
CC in chloroplasts (PubMed:22576849, PubMed:23227895, PubMed:25043599).
CC Binds specific group II introns in chloroplasts and facilitates their
CC splicing. Is required for rRNA maturation in plastids and may
CC contribute to the assembly of the large (50S) ribosomal subunit
CC (PubMed:22576849). Required for normal development of chloroplasts
CC (PubMed:22576849, PubMed:23227895, PubMed:25043599). Required for the
CC expression of transcripts encoding plastid-localized enzymes involved
CC in abscisic acid (ABA) biosynthesis. Required for maintenance of ABA
CC levels and response to salt stress (PubMed:23227895). Possesses RNA
CC chaperone activity for proper splicing of introns in chloroplasts.
CC Essential for chloroplast function and abiotic stress responses
CC (PubMed:25043599). {ECO:0000269|PubMed:22576849,
CC ECO:0000269|PubMed:23227895, ECO:0000269|PubMed:25043599}.
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: Plastid, chloroplast
CC {ECO:0000269|PubMed:18431481}. Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:23227895}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8L7S8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8L7S8-2; Sequence=VSP_019097;
CC -!- TISSUE SPECIFICITY: Highly expressed in young seedlings.
CC {ECO:0000269|PubMed:23227895}.
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 -!- DISRUPTION PHENOTYPE: Embryonic lethality when homozygous.
CC {ECO:0000269|PubMed:22576849}.
CC -!- MISCELLANEOUS: Plants with the weak allele rh3-4 exhibits albino
CC cotyledons, pale green leaf phenotype, slow growth, short petioles,
CC small leaves, reduced content of chlorophyll, altered structure of
CC chloroplast ribosomes and reduced levels of chloroplast proteins.
CC {ECO:0000269|PubMed:22576849, ECO:0000269|PubMed:23227895,
CC ECO:0000269|PubMed:25043599}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX21/DDX50
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC13590.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AJ010457; CAA09196.1; -; mRNA.
DR EMBL; AC137518; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AF058914; AAC13590.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED93564.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93565.1; -; Genomic_DNA.
DR EMBL; AY080625; AAL85971.1; -; mRNA.
DR EMBL; AY091068; AAM13888.1; -; mRNA.
DR EMBL; AY094485; AAM19851.1; -; mRNA.
DR EMBL; AY123000; AAM67533.1; -; mRNA.
DR EMBL; AY128278; AAM91087.1; -; mRNA.
DR EMBL; BT000713; AAN31856.1; -; mRNA.
DR EMBL; BT002289; AAN72300.1; -; mRNA.
DR EMBL; BT002456; AAO00816.1; -; mRNA.
DR EMBL; AY102126; AAM26693.1; -; mRNA.
DR EMBL; BT004533; AAO42779.1; -; mRNA.
DR EMBL; AK229821; BAF01652.1; -; mRNA.
DR PIR; T01202; T01202.
DR PIR; T51738; T51738.
DR RefSeq; NP_001031943.1; NM_001036866.4. [Q8L7S8-1]
DR RefSeq; NP_680225.2; NM_147920.4. [Q8L7S8-2]
DR AlphaFoldDB; Q8L7S8; -.
DR SMR; Q8L7S8; -.
DR BioGRID; 17988; 5.
DR STRING; 3702.Q8L7S8; -.
DR iPTMnet; Q8L7S8; -.
DR PaxDb; 3702-AT5G26742-2; -.
DR ProteomicsDB; 236941; -. [Q8L7S8-1]
DR EnsemblPlants; AT5G26742.1; AT5G26742.1; AT5G26742. [Q8L7S8-2]
DR EnsemblPlants; AT5G26742.2; AT5G26742.2; AT5G26742. [Q8L7S8-1]
DR GeneID; 832713; -.
DR Gramene; AT5G26742.1; AT5G26742.1; AT5G26742. [Q8L7S8-2]
DR Gramene; AT5G26742.2; AT5G26742.2; AT5G26742. [Q8L7S8-1]
DR KEGG; ath:AT5G26742; -.
DR Araport; AT5G26742; -.
DR TAIR; AT5G26742; EMB1138.
DR eggNOG; KOG0331; Eukaryota.
DR HOGENOM; CLU_003041_20_2_1; -.
DR InParanoid; Q8L7S8; -.
DR OrthoDB; 1188at2759; -.
DR PhylomeDB; Q8L7S8; -.
DR BRENDA; 3.6.4.13; 399.
DR PRO; PR:Q8L7S8; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8L7S8; baseline and differential.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009941; C:chloroplast envelope; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; IDA:UniProtKB.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
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:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0009658; P:chloroplast organization; IMP:UniProtKB.
DR GO; GO:0000373; P:Group II intron splicing; IMP:UniProtKB.
DR GO; GO:0009651; P:response to salt stress; IMP:UniProtKB.
DR GO; GO:0042254; P:ribosome biogenesis; IMP:UniProtKB.
DR CDD; cd00268; DEADc; 1.
DR CDD; cd12938; GUCT_Hera; 1.
DR CDD; cd18787; SF2_C_DEAD; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 2.
DR Gene3D; 4.10.60.10; Zinc finger, CCHC-type; 1.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR012562; GUCT.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR001878; Znf_CCHC.
DR InterPro; IPR036875; Znf_CCHC_sf.
DR PANTHER; PTHR47959:SF13; ATP-DEPENDENT RNA HELICASE RHLE; 1.
DR PANTHER; PTHR47959; ATP-DEPENDENT RNA HELICASE RHLE-RELATED; 1.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF08152; GUCT; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF00098; zf-CCHC; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00343; ZnF_C2HC; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
DR SUPFAM; SSF57756; Retrovirus zinc finger-like domains; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
DR PROSITE; PS50158; ZF_CCHC; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; ATP-binding; Chloroplast; Helicase; Hydrolase;
KW Metal-binding; Nucleotide-binding; Phosphoprotein; Plastid;
KW Reference proteome; Ribosome biogenesis; RNA-binding; Transit peptide;
KW Zinc; Zinc-finger.
FT TRANSIT 1..60
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 61..748
FT /note="DEAD-box ATP-dependent RNA helicase 3,
FT chloroplastic"
FT /id="PRO_0000239145"
FT DOMAIN 133..311
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 340..485
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT ZN_FING 727..744
FT /note="CCHC-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT REGION 621..748
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 102..130
FT /note="Q motif"
FT MOTIF 259..262
FT /note="DEAD box"
FT COMPBIAS 685..722
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 146..153
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOD_RES 724
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT VAR_SEQ 723
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_019097"
FT CONFLICT 354
FT /note="T -> N (in Ref. 4; AAM91087)"
FT /evidence="ECO:0000305"
FT CONFLICT 686
FT /note="S -> I (in Ref. 1; CAA09196)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 748 AA; 81156 MW; 739A3A2C9FC156FA CRC64;
MASTVGVPSL YQVPHLEISK PNSKKRSNCL SLSLDKPFFT PLSLVRRTRR IHSSSLLVPS
AVATPNSVLS EEAFKSLGLS DHDEYDLDGD NNNVEADDGE ELAISKLSLP QRLEESLEKR
GITHLFPIQR AVLVPALQGR DIIARAKTGT GKTLAFGIPI IKRLTEEAGD YTAFRRSGRL
PKFLVLAPTR ELAKQVEKEI KESAPYLSTV CVYGGVSYTI QQSALTRGVD VVVGTPGRII
DLIEGRSLKL GEVEYLVLDE ADQMLAVGFE EAVESILENL PTKRQSMLFS ATMPTWVKKL
ARKYLDNPLN IDLVGDQDEK LAEGIKLYAI ATTSTSKRTI LSDLITVYAK GGKTIVFTQT
KRDADEVSLA LSNSIATEAL HGDISQHQRE RTLNAFRQGK FTVLVATDVA SRGLDIPNVD
LVIHYELPND PETFVHRSGR TGRAGKEGSA ILMHTSSQKR TVRSLERDVG CHFEFISPPT
VGDLLESSAD QVVATLNGVH PDSIKFFSAT AQKLYEEKGT DALAAALAHL SGFSQPPSSR
SLLSHEKGWV TLQLIRDPTN ARGFLSARSV TGFLSDLYRT AADEVGKIFL IADDRIQGAV
FDLPEEIAKE LLEKDVPEGN SLSMITKLPP LQDDGPSSDN YGRFSSRDRM PRGGGGSRGS
RGGRGGSSRG RDSWGGDDDR GSRRSSGGGS SWSRGGSSSR GSSDDWLIGG RSSSSSRAPS
RERSFGGSCF ICGKSGHRAT DCPDKRGF
//
