ID   RH39_ORYSJ              Reviewed;         625 AA.
AC   Q5VRY0; B9ETI6;
DT   03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT   07-DEC-2004, sequence version 1.
DT   03-AUG-2022, entry version 122.
DE   RecName: Full=DEAD-box ATP-dependent RNA helicase 39;
DE            EC=3.6.4.13;
GN   OrderedLocusNames=Os01g0184500, LOC_Os01g08930;
GN   ORFNames=OsJ_00660 {ECO:0000312|EMBL:EEE54007.1}, P0510F03.6;
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12447438; DOI=10.1038/nature01184;
RA   Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA   Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA   Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA   Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA   Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA   Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA   Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA   Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA   Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA   Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA   Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA   Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA   Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT   "The genome sequence and structure of rice chromosome 1.";
RL   Nature 420:312-316(2002).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [4]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12869764; DOI=10.1126/science.1081288;
RG   The rice full-length cDNA consortium;
RT   "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT   japonica rice.";
RL   Science 301:376-379(2003).
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}.
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DR   EMBL; AP002486; BAD67795.1; -; Genomic_DNA.
DR   EMBL; AP008207; BAF04148.1; -; Genomic_DNA.
DR   EMBL; AP014957; BAS70765.1; -; Genomic_DNA.
DR   EMBL; CM000138; EEE54007.1; -; Genomic_DNA.
DR   EMBL; AK060699; -; NOT_ANNOTATED_CDS; mRNA.
DR   RefSeq; XP_015613578.1; XM_015758092.1.
DR   RefSeq; XP_015613586.1; XM_015758100.1.
DR   AlphaFoldDB; Q5VRY0; -.
DR   SMR; Q5VRY0; -.
DR   STRING; 4530.OS01T0184500-01; -.
DR   PaxDb; Q5VRY0; -.
DR   PRIDE; Q5VRY0; -.
DR   EnsemblPlants; Os01t0184500-01; Os01t0184500-01; Os01g0184500.
DR   GeneID; 4325344; -.
DR   Gramene; Os01t0184500-01; Os01t0184500-01; Os01g0184500.
DR   KEGG; osa:4325344; -.
DR   eggNOG; KOG0331; Eukaryota.
DR   HOGENOM; CLU_003041_1_3_1; -.
DR   InParanoid; Q5VRY0; -.
DR   OMA; VAKKNLM; -.
DR   OrthoDB; 1223767at2759; -.
DR   Proteomes; UP000000763; Chromosome 1.
DR   Proteomes; UP000007752; Chromosome 1.
DR   Proteomes; UP000059680; Chromosome 1.
DR   Genevisible; Q5VRY0; OS.
DR   GO; GO:0009507; C:chloroplast; IEA:GOC.
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; IEA:EnsemblPlants.
DR   GO; GO:0070180; F:large ribosomal subunit rRNA binding; IEA:EnsemblPlants.
DR   GO; GO:0003729; F:mRNA binding; IEA:EnsemblPlants.
DR   GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR   GO; GO:1901259; P:chloroplast rRNA processing; IEA:EnsemblPlants.
DR   GO; GO:1902775; P:mitochondrial large ribosomal subunit assembly; IBA:GO_Central.
DR   GO; GO:0110102; P:ribulose bisphosphate carboxylase complex assembly; IEA:EnsemblPlants.
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..625
FT                   /note="DEAD-box ATP-dependent RNA helicase 39"
FT                   /id="PRO_0000282515"
FT   DOMAIN          141..328
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT   DOMAIN          353..503
FT                   /note="Helicase C-terminal"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT   REGION          36..59
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          72..103
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          505..625
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           110..138
FT                   /note="Q motif"
FT   MOTIF           268..271
FT                   /note="DEAD box"
FT   COMPBIAS        505..520
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        551..586
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         154..161
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT   CONFLICT        319
FT                   /note="D -> G (in Ref. 6; AK060699)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   625 AA;  67860 MW;  AE71A3E2CBAAD320 CRC64;
     MAMAGAAGRC LMLTRPSPLL RLRLLRAALA TTTTTTTAAG ASAVTAPTEP ETTAREAPSR
     HELLLERLRQ RHLKGVPAAT PRPAQREKGR GGGGGGAQEL QQKRRVEVVD SFEELGLGEE
     VMAALGEMGI SKPTEIQCVG VPAVLAGTSV VLGSHTGSGK TLAYLLPLVQ LLRRDEAMLG
     MSMKPRRPRA VVLCPTRELT EQVFRVAKSI SHHARFRSTM VSGGSRIRPQ EDSLNMPVDM
     VVGTPGRILD HIKDGNMVYG DIKYLVLDEA DTMFDQGFGP DIRKFLAPLK NRAAKPGDQG
     FQTVLVTATM TKAVQKLIDE EFEGIVHLRT TTFQKRVATA RHDFIKLSGS ENKLEALLQV
     LEPSLAKGNK VMVFCNTLNS SRAVDHFLTE NQISTVNYHG EVPAEERVEN LNKFRNEEGD
     CPTLVCTDLA ARGLDLDVDH VIMFDFPSNS IDYLHRTGRT ARMGAKGKVT SLVAKKDVTL
     ATRIEEAMKK NESLEALTTN NVRRAAVNPQ YTSTKGRPSA LKVVNQKGRR GVALQTKSSR
     IVKDTTSSRR RSPIRSQPRS KSTSSGKAKP VRSAKPSKSS SPSPKVAKSR PRPEGRKGDA
     LNKLGSKLSV VGFRGRSSGK SAQAS