RH40_ORYSJ
ID RH40_ORYSJ Reviewed; 792 AA.
AC Q5JKF2; A0A0P0V3W2; Q5JKF3;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 03-APR-2007, sequence version 2.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=DEAD-box ATP-dependent RNA helicase 40;
DE EC=3.6.4.13;
GN OrderedLocusNames=Os01g0549400, LOC_Os01g36860;
GN ORFNames=B1156H12.12-1, B1156H12.12-2, OsJ_02174;
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] (ISOFORMS 1 AND 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: ATP-dependent RNA helicase involved nonsense-mediated mRNA
CC decay and ribosome biogenesis through rRNA processing. {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: Nucleus {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q5JKF2-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q5JKF2-2; Sequence=VSP_024159, VSP_024160;
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. DDX5/DBP2
CC subfamily. {ECO:0000305}.
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DR EMBL; AP004225; BAD88050.1; -; Genomic_DNA.
DR EMBL; AP004225; BAD88051.1; -; Genomic_DNA.
DR EMBL; AP008207; BAF05209.1; -; Genomic_DNA.
DR EMBL; AP014957; BAS72626.1; -; Genomic_DNA.
DR EMBL; AP014957; BAS72627.1; -; Genomic_DNA.
DR EMBL; CM000138; EAZ12284.1; -; Genomic_DNA.
DR EMBL; AK102720; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; AK122104; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015620980.1; XM_015765494.1. [Q5JKF2-1]
DR RefSeq; XP_015620981.1; XM_015765495.1. [Q5JKF2-2]
DR AlphaFoldDB; Q5JKF2; -.
DR SMR; Q5JKF2; -.
DR STRING; 4530.OS01T0549400-01; -.
DR PaxDb; Q5JKF2; -.
DR PRIDE; Q5JKF2; -.
DR EnsemblPlants; Os01t0549400-01; Os01t0549400-01; Os01g0549400. [Q5JKF2-1]
DR EnsemblPlants; Os01t0549400-02; Os01t0549400-02; Os01g0549400. [Q5JKF2-2]
DR GeneID; 4326190; -.
DR Gramene; Os01t0549400-01; Os01t0549400-01; Os01g0549400. [Q5JKF2-1]
DR Gramene; Os01t0549400-02; Os01t0549400-02; Os01g0549400. [Q5JKF2-2]
DR KEGG; osa:4326190; -.
DR eggNOG; KOG0331; Eukaryota.
DR InParanoid; Q5JKF2; -.
DR OMA; DMICVAK; -.
DR OrthoDB; 638613at2759; -.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000007752; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR ExpressionAtlas; Q5JKF2; baseline and differential.
DR Genevisible; Q5JKF2; OS.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:1990904; C:ribonucleoprotein complex; 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; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IBA:GO_Central.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IEA:UniProtKB-KW.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
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 InterPro; IPR001202; WW_dom.
DR InterPro; IPR036020; WW_dom_sf.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF00397; WW; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00456; WW; 1.
DR SUPFAM; SSF51045; SSF51045; 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.
DR PROSITE; PS01159; WW_DOMAIN_1; 1.
DR PROSITE; PS50020; WW_DOMAIN_2; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; ATP-binding; Helicase; Hydrolase;
KW Nonsense-mediated mRNA decay; Nucleotide-binding; Nucleus;
KW Reference proteome; Ribosome biogenesis; RNA-binding; rRNA processing.
FT CHAIN 1..792
FT /note="DEAD-box ATP-dependent RNA helicase 40"
FT /id="PRO_0000282457"
FT DOMAIN 17..51
FT /note="WW"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00224"
FT DOMAIN 181..355
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 384..528
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..25
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 44..118
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 523..792
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 150..178
FT /note="Q motif"
FT MOTIF 303..306
FT /note="DEAD box"
FT COMPBIAS 51..68
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 69..112
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 529..558
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 573..610
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 611..646
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 667..710
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 713..748
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 194..201
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT VAR_SEQ 1..141
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764"
FT /id="VSP_024159"
FT VAR_SEQ 142..164
FT /note="GDNVPAPITSFETGGFPPEILKE -> MLLEPFLLHLAHASQHILDALSF
FT (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764"
FT /id="VSP_024160"
FT CONFLICT 344
FT /note="I -> V (in Ref. 6; AK122104)"
FT /evidence="ECO:0000305"
FT CONFLICT 512
FT /note="I -> T (in Ref. 6; AK102720)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 792 AA; 87980 MW; B0A866D5D26EBBFC CRC64;
MSAGTAPAAP RYAPDDPSLP KPWRGLVDGT TGYLYYWNPE TNITQYEKPL PPEDQLPPPP
PLPPPPPRSG RGDRDRDRRD RSRSRTPPRR DHRDRDRDRD RRHDDHRSAP SHHHPLPAAA
AIAADDPSTE AYRHRHEITV VGDNVPAPIT SFETGGFPPE ILKEIQRAGF SSPTPIQAQS
WPIALQCQDV VAIAKTGSGK TLGYLLPGFM HIKRLQNNPR SGPTVLVLAP TRELATQILE
EAVKFGRSSR ISSTCLYGGA PKGPQLRDLD RGVDVVVATP GRLNDILEMR RISLKQVSYL
VLDEADRMLD MGFEPQIRKI VKEIPPRRQT LMYTATWPKE VRRIAEDLLV HPVQVTIGSV
DELVANSAIT QNVELITPSE KLRRLEQILR SQDSGSKVLI FCTTKRMCDQ LARTLTRQFG
ASAIHGDKSQ SEREKVLSHF RSGRSPILVA TDVAARGLDI KDIRVVINYD FPTGIEDYVH
RIGRTGRAGA TGVAYTFFCD QDSKYAADLI KILEGANQRV PRDLADMASR GGRGGRKRNR
WATRSDRGGS HSELDSRYGG RDGLSGSSGR LDSSRSSRRH DYGDDGRSRR SGRGRSRSRS
RSDSDRYSRS PKRSRRHSRS RTRSRSRSRS RSYTRNRRAS RSRSRSPGAS RRHERSATGS
GSALPDSGHG ERKRTPEADP SRNHTNHSDP KDDRHPEDGK VGKVDLDRSP TPQDKSGPYS
PAYNGKTSRS VSPGNQVEGN NKAAEVSKNP DPSSPPHHGK TREDEEEGMI DEDGEIADDP
RANATVQNGG DN
