RH12_ORYSJ
ID RH12_ORYSJ Reviewed; 521 AA.
AC Q109G2; A0A0P0XWK1; B7ELN4; Q109G3; Q337E8; Q53RP3; Q9FVY5;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 03-APR-2007, sequence version 2.
DT 03-AUG-2022, entry version 94.
DE RecName: Full=DEAD-box ATP-dependent RNA helicase 12;
DE EC=3.6.4.13;
GN OrderedLocusNames=Os10g0503700, LOC_Os10g35990;
GN ORFNames=OsJ_32082, OSJNBb0073N24.12;
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=12791992; DOI=10.1126/science.1083523;
RA Yu Y., Rambo T., Currie J., Saski C., Kim H.-R., Collura K., Thompson S.,
RA Simmons J., Yang T.-J., Nah G., Patel A.J., Thurmond S., Henry D.,
RA Oates R., Palmer M., Pries G., Gibson J., Anderson H., Paradkar M.,
RA Crane L., Dale J., Carver M.B., Wood T., Frisch D., Engler F.,
RA Soderlund C., Palmer L.E., Teytelman L., Nascimento L., De la Bastide M.,
RA Spiegel L., Ware D., O'Shaughnessy A., Dike S., Dedhia N., Preston R.,
RA Huang E., Ferraro K., Kuit K., Miller B., Zutavern T., Katzenberger F.,
RA Muller S., Balija V., Martienssen R.A., Stein L., Minx P., Johnson D.,
RA Cordum H., Mardis E., Cheng Z., Jiang J., Wilson R., McCombie W.R.,
RA Wing R.A., Yuan Q., Ouyang S., Liu J., Jones K.M., Gansberger K.,
RA Moffat K., Hill J., Tsitrin T., Overton L., Bera J., Kim M., Jin S.,
RA Tallon L., Ciecko A., Pai G., Van Aken S., Utterback T., Reidmuller S.,
RA Bormann J., Feldblyum T., Hsiao J., Zismann V., Blunt S., de Vazeille A.R.,
RA Shaffer T., Koo H., Suh B., Yang Q., Haas B., Peterson J., Pertea M.,
RA Volfovsky N., Wortman J., White O., Salzberg S.L., Fraser C.M., Buell C.R.,
RA Messing J., Song R., Fuks G., Llaca V., Kovchak S., Young S., Bowers J.E.,
RA Paterson A.H., Johns M.A., Mao L., Pan H., Dean R.A.;
RT "In-depth view of structure, activity, and evolution of rice chromosome
RT 10.";
RL Science 300:1566-1569(2003).
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 turnover, and
CC more specifically in mRNA decapping. {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, P-body {ECO:0000250}. Note=Is
CC concentrated in several cytoplasmic foci called P bodies (or
CC cytoplasmic processing bodies) which represent sites of mRNA decapping
CC and 5' to 3' exonucleotidic decay. {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. DDX6/DHH1
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAX95709.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=ABG66172.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=ABG66173.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC078840; AAG13612.1; -; Genomic_DNA.
DR EMBL; AC084023; AAX95709.1; ALT_SEQ; Genomic_DNA.
DR EMBL; DP000086; ABB47852.2; -; Genomic_DNA.
DR EMBL; DP000086; ABG66172.1; ALT_SEQ; Genomic_DNA.
DR EMBL; DP000086; ABG66173.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008216; BAF26914.2; -; Genomic_DNA.
DR EMBL; AP014966; BAT11553.1; -; Genomic_DNA.
DR EMBL; CM000147; EEE51233.1; -; Genomic_DNA.
DR EMBL; AK073085; BAG93281.1; -; mRNA.
DR RefSeq; XP_015614831.1; XM_015759345.1.
DR AlphaFoldDB; Q109G2; -.
DR SMR; Q109G2; -.
DR STRING; 4530.OS10T0503700-01; -.
DR PaxDb; Q109G2; -.
DR PRIDE; Q109G2; -.
DR EnsemblPlants; Os10t0503700-01; Os10t0503700-01; Os10g0503700.
DR GeneID; 4349053; -.
DR Gramene; Os10t0503700-01; Os10t0503700-01; Os10g0503700.
DR KEGG; osa:4349053; -.
DR eggNOG; KOG0326; Eukaryota.
DR HOGENOM; CLU_003041_30_0_1; -.
DR InParanoid; Q109G2; -.
DR OMA; YGRGPQP; -.
DR OrthoDB; 583315at2759; -.
DR Proteomes; UP000000763; Chromosome 10.
DR Proteomes; UP000007752; Chromosome 10.
DR Proteomes; UP000059680; Chromosome 10.
DR ExpressionAtlas; Q109G2; baseline and differential.
DR Genevisible; Q109G2; OS.
DR GO; GO:0010494; C:cytoplasmic stress granule; IBA:GO_Central.
DR GO; GO:0000932; C:P-body; 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:0003729; F:mRNA binding; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
DR GO; GO:0017148; P:negative regulation of translation; IBA:GO_Central.
DR GO; GO:0033962; P:P-body assembly; IBA:GO_Central.
DR GO; GO:0034063; P:stress granule assembly; IBA:GO_Central.
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; IPR000629; RNA-helicase_DEAD-box_CS.
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; 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; Cytoplasm; Helicase; Hydrolase; mRNA processing;
KW mRNA transport; Nucleotide-binding; Reference proteome; RNA-binding;
KW Translation regulation; Transport.
FT CHAIN 1..521
FT /note="DEAD-box ATP-dependent RNA helicase 12"
FT /id="PRO_0000282460"
FT DOMAIN 178..348
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 358..518
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..97
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 147..175
FT /note="Q motif"
FT MOTIF 296..299
FT /note="DEAD box"
FT COMPBIAS 52..95
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 191..198
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT CONFLICT 380
FT /note="S -> L (in Ref. 1; AAX95709 and 2; BAF26914)"
FT /evidence="ECO:0000305"
FT CONFLICT 449
FT /note="D -> G (in Ref. 1; AAX95709 and 2; BAF26914)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 521 AA; 57950 MW; 26221BEF5781ECF6 CRC64;
MHHPRARYPP GYTSGGGGGG GGGGGGGRGN GGGGFGGGGG GGGGNHGYYG RGPQPQPQQQ
HYHHQAQQLH QHQQQQQHAQ RNSSSQQQQW LRRDQATAAA ASGEVAARTA AQLEAVDSSS
EDWKAQLNLP APDTRYRTED VTATKGNEFE DYFLKRELLM GIYEKGFERP SPIQEESIPI
ALTGSDILAR AKNGTGKTAA FCIPALEKID PEKNAIQVVI LVPTRELALQ TSQVCKELGK
YLNIQVMVST GGTSLKDDIM RLYQPVHLLV GTPGRILDLT RKGICVLKDC SMLVMDEADK
LLAPEFQPSI EQLIHFLPAN RQLLMFSATF PVTVKDFKEK YLPRPYVINL MDELTLKGIT
QYYAFVEERQ KVHCLNTLFS KLQINQSIIF CNSVNRVELL AKKITELGYS CFYIHAKMLQ
DHRNRVFHDF RNGACRNLVC TDLFTRGIDI QAVNVVINFD FPKTSETYLH RVGRSGRFGH
LGLAVNLITY EDRFNLYRIE QELGTEIKTI PPQIDLAVYC Q
