RH3_ORYSJ
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 03-AUG-2022, entry version 101.
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., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT 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., 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 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 biogenesis
CC in chloroplasts. Binds specific group II introns in chloroplasts and
CC facilitates their splicing. Required for normal development of
CC 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 Name=2;
CC IsoId=Q0DM51-2; Sequence=VSP_024162;
CC Name=3;
CC IsoId=Q0DM51-3; Sequence=VSP_024163;
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 -!- MISCELLANEOUS: [Isoform 3]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
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};
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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 AlphaFoldDB; Q0DM51; -.
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 HOGENOM; CLU_003041_20_1_1; -.
DR InParanoid; Q0DM51; -.
DR OrthoDB; 1139373at2759; -.
DR Proteomes; UP000000763; Chromosome 3.
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; 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: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 GO; GO:0006364; P:rRNA processing; IBA:GO_Central.
DR Gene3D; 3.40.50.300; -; 2.
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; Helicase; Hydrolase;
KW Metal-binding; Nucleotide-binding; Plastid; Reference proteome;
KW Ribosome biogenesis; RNA-binding; Transit peptide; Zinc; Zinc-finger.
FT TRANSIT 1..62
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 63..758
FT /note="DEAD-box ATP-dependent RNA helicase 3,
FT chloroplastic"
FT /id="PRO_0000282473"
FT DOMAIN 135..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 740..757
FT /note="CCHC-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT REGION 71..97
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 625..737
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 104..132
FT /note="Q motif"
FT MOTIF 259..262
FT /note="DEAD box"
FT COMPBIAS 74..97
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 667..699
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 700..737
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 148..155
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT VAR_SEQ 1..161
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764"
FT /id="VSP_024162"
FT VAR_SEQ 735
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000305"
FT /id="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
