GenomeNet

Database: UniProt
Entry: Q9LFN6
LinkDB: Q9LFN6
Original site: Q9LFN6 
ID   RH56_ARATH              Reviewed;         427 AA.
AC   Q9LFN6; Q93VJ8;
DT   30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT   30-MAY-2006, sequence version 2.
DT   13-NOV-2019, entry version 139.
DE   RecName: Full=DEAD-box ATP-dependent RNA helicase 56;
DE            EC=3.6.4.13;
DE   AltName: Full=UAP56 homolog B;
GN   Name=RH56; Synonyms=UAP56B; OrderedLocusNames=At5g11200;
GN   ORFNames=F2I11.90;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;
OC   Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
OC   Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11130714; DOI=10.1038/35048507;
RA   Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA   Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K.,
RA   Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S.,
RA   Nakazaki N., Naruo K., Okumura S., Shinpo S., Takeuchi C., Wada T.,
RA   Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M.,
RA   Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R.,
RA   Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J.,
RA   Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M.,
RA   Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M.,
RA   Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P.,
RA   Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C.,
RA   Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N.,
RA   Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J.,
RA   Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA   Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA   Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA   Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S.,
RA   Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W.,
RA   Ramsperger U., Wedler H., Balke K., Wedler E., Peters S.,
RA   van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R.,
RA   Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S.,
RA   Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W.,
RA   Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H.,
RA   Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.;
RT   "Sequence and analysis of chromosome 5 of the plant Arabidopsis
RT   thaliana.";
RL   Nature 408:823-826(2000).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana
RT   reference genome.";
RL   Plant J. 89:789-804(2017).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=14593172; DOI=10.1126/science.1088305;
RA   Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
RA   Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
RA   Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
RA   Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
RA   Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
RA   Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
RA   Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
RA   Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
RA   Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
RA   Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
RA   Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
RA   Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
RT   "Empirical analysis of transcriptional activity in the Arabidopsis
RT   genome.";
RL   Science 302:842-846(2003).
RN   [4]
RP   GENE FAMILY, AND NOMENCLATURE.
RX   PubMed=17168887; DOI=10.1111/j.1467-7652.2004.00084.x;
RA   Mingam A., Toffano-Nioche C., Brunaud V., Boudet N., Kreis M.,
RA   Lecharny A.;
RT   "DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link
RT   between quantitative expression, gene structure and evolution of a
RT   family of genes.";
RL   Plant Biotechnol. J. 2:401-415(2004).
RN   [5]
RP   GENE FAMILY.
RX   PubMed=24265739; DOI=10.1371/journal.pone.0078982;
RA   Xu R., Zhang S., Huang J., Zheng C.;
RT   "Genome-wide comparative in silico analysis of the RNA helicase gene
RT   family in Zea mays and Glycine max: a comparison with Arabidopsis and
RT   Oryza sativa.";
RL   PLoS ONE 8:E78982-E78982(2013).
RN   [6]
RP   FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH ALY2 AND MOS11.
RX   PubMed=23555998; DOI=10.1371/journal.pone.0060644;
RA   Kammel C., Thomaier M., Sorensen B.B., Schubert T., Langst G.,
RA   Grasser M., Grasser K.D.;
RT   "Arabidopsis DEAD-box RNA helicase UAP56 interacts with both RNA and
RT   DNA as well as with mRNA export factors.";
RL   PLoS ONE 8:E60644-E60644(2013).
CC   -!- FUNCTION: ATP-dependent RNA helicase involved in pre-mRNA
CC       splicing. Required for the export of mRNA out of the nucleus. In
CC       addition to ssRNA and dsRNA, binds dsDNA, but not ssDNA.
CC       {ECO:0000269|PubMed:23555998}.
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   -!- SUBUNIT: Interacts with ALY2 and MOS11.
CC       {ECO:0000269|PubMed:23555998}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:23555998}.
CC       Note=Localizes predominantly to euchromatic regions of the
CC       nucleoplasm.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=1;
CC         Comment=A number of isoforms are produced. According to EST
CC         sequences.;
CC       Name=1;
CC         IsoId=Q9LFN6-1; Sequence=Displayed;
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. DECD
CC       subfamily. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=CAB96655.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
DR   EMBL; AL360314; CAB96655.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002688; AED91645.1; -; Genomic_DNA.
DR   EMBL; AF378868; AAK55671.1; -; mRNA.
DR   EMBL; AY059168; AAL15393.1; -; mRNA.
DR   RefSeq; NP_568244.2; NM_121155.4. [Q9LFN6-1]
DR   RefSeq; NP_568245.1; NM_121158.4. [Q9LFN6-1]
DR   SMR; Q9LFN6; -.
DR   BioGrid; 16264; 3.
DR   BioGrid; 16268; 3.
DR   PRIDE; Q9LFN6; -.
DR   EnsemblPlants; AT5G11170.1; AT5G11170.1; AT5G11170.
DR   EnsemblPlants; AT5G11200.1; AT5G11200.1; AT5G11200.
DR   GeneID; 830986; -.
DR   GeneID; 830990; -.
DR   Gramene; AT5G11170.1; AT5G11170.1; AT5G11170.
DR   Gramene; AT5G11200.1; AT5G11200.1; AT5G11200.
DR   KEGG; ath:AT5G11170; -.
DR   KEGG; ath:AT5G11200; -.
DR   Araport; AT5G11200; -.
DR   eggNOG; KOG0329; Eukaryota.
DR   eggNOG; COG0513; LUCA.
DR   InParanoid; Q9LFN6; -.
DR   KO; K12812; -.
DR   OMA; CGYQKMT; -.
DR   OrthoDB; 779000at2759; -.
DR   PhylomeDB; Q9LFN6; -.
DR   PRO; PR:Q9LFN6; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   ExpressionAtlas; Q9LFN6; baseline and differential.
DR   Genevisible; Q9LFN6; AT.
DR   GO; GO:0000346; C:transcription export complex; IBA:GO_Central.
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:0000398; P:mRNA splicing, via spliceosome; IBA:GO_Central.
DR   GO; GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
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; 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; PS51192; HELICASE_ATP_BIND_1; 1.
DR   PROSITE; PS51194; HELICASE_CTER; 1.
DR   PROSITE; PS51195; Q_MOTIF; 1.
PE   1: Evidence at protein level;
KW   Alternative splicing; ATP-binding; Complete proteome; Helicase;
KW   Hydrolase; mRNA processing; mRNA splicing; mRNA transport;
KW   Nucleotide-binding; Nucleus; Reference proteome; RNA-binding;
KW   Transport.
FT   CHAIN         1    427       DEAD-box ATP-dependent RNA helicase 56.
FT                                /FTId=PRO_0000239195.
FT   DOMAIN       77    250       Helicase ATP-binding.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00541}.
FT   DOMAIN      278    423       Helicase C-terminal.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00542}.
FT   NP_BIND      90     97       ATP. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00541}.
FT   MOTIF        46     74       Q motif.
FT   MOTIF       197    200       DECD box.
SQ   SEQUENCE   427 AA;  48337 MW;  AA17923A9B6D1271 CRC64;
     MGDARDNEAY EEELLDYEEE DEKVPDSGNK VNGEAVKKGY VGIHSSGFRD FLLKPELLRA
     IVDSGFEHPS EVQHECIPQA ILGMDVICQA KSGMGKTAVF VLSTLQQIEP SPGQVSALVL
     CHTRELAYQI CNEFVRFSTY LPDTKVSVFY GGVNIKIHKD LLKNECPHIV VGTPGRVLAL
     AREKDLSLKN VRHFILDECD KMLESLDMRR DVQEIFKMTP HDKQVMMFSA TLSKEIRPVC
     KKFMQDPMEI YVDDEAKLTL HGLVQHYIKL SEMEKNRKLN DLLDALDFNQ VVIFVKSVSR
     AAELNKLLVE CNFPSICIHS GMSQEERLTR YKSFKEGHKR ILVATDLVGR GIDIERVNIV
     INYDMPDSAD TYLHRVGRAG RFGTKGLAIT FVASASDSEV LNQVQERFEV DIKELPEQID
     TSTYMPS
//
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