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Database: UniProt
Entry: Q0DM51
LinkDB: Q0DM51
Original site: Q0DM51 
ID   RH3_ORYSJ               Reviewed;         758 AA.
AC   Q0DM51; A0A0N7KIB7; B7EBF8; Q10B75; Q10B76; Q8SAX7;
DT   03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT   03-APR-2007, sequence version 2.
DT   16-OCT-2019, entry version 92.
DE   RecName: Full=DEAD-box ATP-dependent RNA helicase 3, chloroplastic {ECO:0000305};
DE            EC=3.6.4.13 {ECO:0000305};
DE   Flags: Precursor;
GN   OrderedLocusNames=Os03g0827700 {ECO:0000312|EMBL:BAS87169.1},
GN   LOC_Os03g61220 {ECO:0000312|EMBL:ABF99667.1};
GN   ORFNames=OSJNBa0010E04.4 {ECO:0000312|EMBL:AAL79753.1};
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=16109971; DOI=10.1101/gr.3869505;
RG   The rice chromosome 3 sequencing consortium;
RA   Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R.,
RA   Haas B., Wortman J., Pertea M., Jones K.M., Kim M., Overton L.,
RA   Tsitrin T., Fadrosh D., Bera J., Weaver B., Jin S., Johri S.,
RA   Reardon M., Webb K., Hill J., Moffat K., Tallon L., Van Aken S.,
RA   Lewis M., Utterback T., Feldblyum T., Zismann V., Iobst S., Hsiao J.,
RA   de Vazeille A.R., Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H.,
RA   Rambo T., Currie J., Collura K., Kernodle-Thompson S., Wei F.,
RA   Kudrna K., Ammiraju J.S.S., Luo M., Goicoechea J.L., Wing R.A.,
RA   Henry D., Oates R., Palmer M., Pries G., Saski C., Simmons J.,
RA   Soderlund C., Nelson W., de la Bastide M., Spiegel L., Nascimento L.,
RA   Huang E., Preston R., Zutavern T., Palmer L., O'Shaughnessy A.,
RA   Dike S., McCombie W.R., Minx P., Cordum H., Wilson R., Jin W.,
RA   Lee H.R., Jiang J., Jackson S.;
RT   "Sequence, annotation, and analysis of synteny between rice chromosome
RT   3 and diverged grass species.";
RL   Genome Res. 15:1284-1291(2005).
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.,
RA   McCombie W.R., Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S.,
RA   Childs K.L., Davidson R.M., Lin H., Quesada-Ocampo L.,
RA   Vaillancourt B., Sakai H., Lee S.S., Kim J., Numa H., Itoh T.,
RA   Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using
RT   next generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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   -!- FUNCTION: Nuclear genome-encoded factor involved in ribosome
CC       biogenesis in chloroplasts. Binds specific group II introns in
CC       chloroplasts and facilitates their splicing. Required for normal
CC       development of chloroplasts. {ECO:0000250|UniProtKB:A0A1D6LAB7}.
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         Evidence={ECO:0000305};
CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=3;
CC       Name=1;
CC         IsoId=Q0DM51-1; Sequence=Displayed;
CC         Note=No experimental confirmation available.;
CC       Name=2;
CC         IsoId=Q0DM51-2; Sequence=VSP_024162;
CC         Note=No experimental confirmation available.;
CC       Name=3;
CC         IsoId=Q0DM51-3; Sequence=VSP_024163;
CC         Note=Derived from EST data. May be due to a competing acceptor
CC         splice site. No experimental confirmation available.;
CC   -!- DOMAIN: The Q motif is unique to and characteristic of the DEAD
CC       box family of RNA helicases and controls ATP binding and
CC       hydrolysis.
CC   -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX21/DDX50
CC       subfamily. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAF13687.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAS87169.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
DR   EMBL; AC096687; AAL79753.1; -; Genomic_DNA.
DR   EMBL; DP000009; ABF99667.1; -; Genomic_DNA.
DR   EMBL; DP000009; ABF99668.1; -; Genomic_DNA.
DR   EMBL; AP008209; BAF13687.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP014959; BAS87169.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AK065849; BAG89705.1; -; mRNA.
DR   RefSeq; XP_015630408.1; XM_015774922.1. [Q0DM51-1]
DR   RefSeq; XP_015630409.1; XM_015774923.1. [Q0DM51-3]
DR   SMR; Q0DM51; -.
DR   STRING; 4530.OS03T0827700-01; -.
DR   PaxDb; Q0DM51; -.
DR   PRIDE; Q0DM51; -.
DR   GeneID; 4334649; -.
DR   KEGG; osa:4334649; -.
DR   eggNOG; KOG0331; Eukaryota.
DR   eggNOG; COG0513; LUCA.
DR   HOGENOM; HOG000268805; -.
DR   InParanoid; Q0DM51; -.
DR   OrthoDB; 1139373at2759; -.
DR   Proteomes; UP000059680; Chromosome 3.
DR   Genevisible; Q0DM51; OS.
DR   GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR   GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR   GO; GO:0005634; C:nucleus; IEA:InterPro.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; IBA:GO_Central.
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; ISS:UniProtKB.
DR   GO; GO:0000373; P:Group II intron splicing; ISS:UniProtKB.
DR   GO; GO:0042254; P:ribosome biogenesis; ISS:UniProtKB.
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; IPR014014; RNA_helicase_DEAD_Q_motif.
DR   InterPro; IPR001878; Znf_CCHC.
DR   InterPro; IPR036875; Znf_CCHC_sf.
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; SSF52540; 1.
DR   SUPFAM; SSF57756; SSF57756; 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   2: Evidence at transcript level;
KW   Alternative splicing; ATP-binding; Chloroplast; Complete proteome;
KW   Helicase; Hydrolase; Metal-binding; Nucleotide-binding; Plastid;
KW   Reference proteome; Ribosome biogenesis; RNA-binding; Transit peptide;
KW   Zinc; Zinc-finger.
FT   TRANSIT       1     62       Chloroplast. {ECO:0000255}.
FT   CHAIN        63    758       DEAD-box ATP-dependent RNA helicase 3,
FT                                chloroplastic.
FT                                /FTId=PRO_0000282473.
FT   DOMAIN      135    311       Helicase ATP-binding.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00541}.
FT   DOMAIN      340    485       Helicase C-terminal.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00542}.
FT   NP_BIND     148    155       ATP. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00541}.
FT   ZN_FING     740    757       CCHC-type. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00047}.
FT   MOTIF       104    132       Q motif.
FT   MOTIF       259    262       DEAD box.
FT   COMPBIAS     75     81       Poly-Glu.
FT   COMPBIAS    682    739       Ser-rich.
FT   VAR_SEQ       1    161       Missing (in isoform 2).
FT                                {ECO:0000303|PubMed:12869764}.
FT                                /FTId=VSP_024162.
FT   VAR_SEQ     735    735       Missing (in isoform 3). {ECO:0000305}.
FT                                /FTId=VSP_024163.
SQ   SEQUENCE   758 AA;  81615 MW;  E2E6486829E73467 CRC64;
     MASLLTLPSL SLSNPSASAA AAGAGAAPSL RLRAAFRCWA LRRAGGGRWA AAGAIASPNS
     VLSEHAFKRL QLSDEEEEEE EGAYGSDEEG VEAVGGGEGD EDELAIARLG LPEQLVSTLE
     KRGITHLFPI QRAVLIPALD GRDLIARAKT GTGKTLAFGI PMIKQLMEED DGRSVRRGRI
     PRVLVLAPTR ELAKQVEKEI KESAPKLSTV CVYGGVSYNV QQNALSRGVD VVVGTPGRII
     DLINGGSLQL GEVKYLVLDE ADQMLAVGFE EDVETILQQL PAERQSMLFS ATMPGWVKKL
     SRRYLNNPLT IDLVGDQDEK LAEGIKLYAI PLTSTSKRTV LSDLITVYAK GGKTIVFTKT
     KRDADEVSLA LTNSIASEAL HGDISQHQRE RTLNGFRQGK FTVLVATDVA ARGLDIPNVD
     LIIHYELPND PETFVHRSGR TGRAGKAGTA ILMFTNSQRR TVRSLERDVG CRFDFISPPA
     IEDVLESSAE HVIATLRGVH TESIQYFIPA AERLQEELGP NALASALAHL SGFSQPPSSR
     SLISHEQGWV TLQLTRDPGY GRGFFSPRSV TGFLSDVSSA AADEVGKIFL TADEKVQGAV
     FDLPEEIARD LLSMELPPGN TITKVTKLPA LQDDGPATDS YGRFSNSDRG FRNRRSRGGG
     SRGGRGGWDS DGEDRFRRGG RSFRSDNDSW SDDDFGGGRR SNRSSSFGGR GSSYGSRSSS
     SFGGRSSSFG SRDSSRSFSG ACFNCGESGH RASDCPNK
//
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