ID RH21_ORYSJ Reviewed; 736 AA.
AC Q53RK8; B7EG14;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 27-MAR-2024, entry version 118.
DE RecName: Full=DEAD-box ATP-dependent RNA helicase 21;
DE EC=3.6.4.13;
GN OrderedLocusNames=Os03g0708600, LOC_Os03g50090; ORFNames=OsJ_12293;
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 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 -!- FUNCTION: ATP-dependent RNA helicase involved in mRNA splicing. May
CC destabilize the U1/5'-splice site duplex to permit an effective
CC competition for the 5'-splice site by the U6 snRNA, resulting in the
CC switch between U1 and U6 at the 5'-splice site. May also act to unwind
CC the U4/U6 base-pairing interaction in the U4/U6/U5 snRNP, facilitating
CC the first covalent step of splicing (By similarity). {ECO:0000250}.
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: Cytoplasm {ECO:0000250}. Nucleus {ECO:0000250}.
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. DDX23/PRP28
CC subfamily. {ECO:0000305}.
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DR EMBL; AC087181; AAX95674.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF98484.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF98485.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF98486.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF12952.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS85997.1; -; Genomic_DNA.
DR EMBL; CM000140; EAZ28319.1; -; Genomic_DNA.
DR EMBL; AK069199; BAG91311.1; -; mRNA.
DR RefSeq; XP_015631547.1; XM_015776061.1.
DR RefSeq; XP_015631548.1; XM_015776062.1.
DR RefSeq; XP_015631549.1; XM_015776063.1.
DR AlphaFoldDB; Q53RK8; -.
DR SMR; Q53RK8; -.
DR STRING; 39947.Q53RK8; -.
DR PaxDb; 39947-Q53RK8; -.
DR EnsemblPlants; Os03t0708600-01; Os03t0708600-01; Os03g0708600.
DR EnsemblPlants; Os03t0708600-02; Os03t0708600-02; Os03g0708600.
DR GeneID; 4333866; -.
DR Gramene; Os03t0708600-01; Os03t0708600-01; Os03g0708600.
DR Gramene; Os03t0708600-02; Os03t0708600-02; Os03g0708600.
DR KEGG; osa:4333866; -.
DR eggNOG; KOG0333; Eukaryota.
DR HOGENOM; CLU_003041_11_2_1; -.
DR InParanoid; Q53RK8; -.
DR OMA; ARDIKHM; -.
DR OrthoDB; 5487240at2759; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR Genevisible; Q53RK8; OS.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; IBA:GO_Central.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
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; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IBA:GO_Central.
DR CDD; cd17945; DEADc_DDX23; 1.
DR CDD; cd18787; SF2_C_DEAD; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 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 PANTHER; PTHR47958; ATP-DEPENDENT RNA HELICASE DBP3; 1.
DR PANTHER; PTHR47958:SF56; RNA HELICASE; 1.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 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 2: Evidence at transcript level;
KW ATP-binding; Coiled coil; Cytoplasm; Helicase; Hydrolase; mRNA processing;
KW mRNA splicing; Nucleotide-binding; Nucleus; Reference proteome;
KW RNA-binding.
FT CHAIN 1..736
FT /note="DEAD-box ATP-dependent RNA helicase 21"
FT /id="PRO_0000282477"
FT DOMAIN 346..541
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 568..712
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 25..178
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 231..263
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 704..736
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 14..38
FT /evidence="ECO:0000255"
FT COILED 137..167
FT /evidence="ECO:0000255"
FT MOTIF 315..343
FT /note="Q motif"
FT MOTIF 472..475
FT /note="DEAD box"
FT COMPBIAS 44..60
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 63..174
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 710..724
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 359..366
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
SQ SEQUENCE 736 AA; 84521 MW; 5D7ED635FC1AD629 CRC64;
MKRAADGMEK PKFLTREERE KLALERRQAA VTDQRRSALD LLQSLPRPPP PPPPPLSNPP
RDSSSSHHRD SSDRDRDRDR DRDRDRDRDR DRERRRDDDS RRDRDRDRDR DRGDSSRRDR
DRERGDRDRD RDRERGDRDR ERGDREKDRL EKMAEREREK ELDAIKEQYL GSKKPKKRVI
KPSEKFRFSF DWENTEDTSR DMNSLYQSPH EARLLYGRGF LAGIDRREQK KVAAAHEKET
RAEQRRKAGL DDRPEDDAVD KKEADAAAKY DAFDMRVDRH WTQKSLDEMT ERDWRIFRED
FNISYKGSKV PRPMRKWSES KLGTELLRAV EKAGYKEPSP IQMASIPLGL QQRDVIGIAE
TGSGKTAAFV LPMLSYITRL PPISEENEAE GPYAVVMAPT RELAQQIEEE TVKFATYLGI
KVVSIVGGQS IEEQGFKIRQ GCEVVIATPG RLLDCLERRY AVLNQCNYVV LDEADRMIDM
GFEPQVVGVL DAMPSSNLKP ENEDEELDAK TIYRTTYMFS ATMPPAVERL ARKYLRNPVV
VTIGTAGKAT DLITQNVIMT KESEKMSRLQ KILTDLGDKP AIVFCNTKKS ADARAKDLDK
AGFRVTTLHG GKSQEQRETS LDGFRNRRFT VLVATDVAGR GIDIPDVAHV INYEMPSSID
TYTHRIGRTG RAGKKGLATS FLTLENTDIF FDLKQMLIQS NSPVPPELAR HEASKFKPGS
VPDRPPRRND TVYATH
//
