RH56_ARATH
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 03-AUG-2022, entry version 150.
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; ORFNames=F2I11.90;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; 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., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., 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., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis 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 reference
RT 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., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA 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., Lecharny A.;
RT "DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link
RT between quantitative expression, gene structure and evolution of a family
RT 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 family
RT in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza
RT 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., Grasser M.,
RA Grasser K.D.;
RT "Arabidopsis DEAD-box RNA helicase UAP56 interacts with both RNA and DNA as
RT well as with mRNA export factors.";
RL PLoS ONE 8:E60644-E60644(2013).
CC -!- FUNCTION: ATP-dependent RNA helicase involved in pre-mRNA splicing.
CC Required for the export of mRNA out of the nucleus. In addition to
CC 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. {ECO:0000269|PubMed:23555998}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:23555998}.
CC Note=Localizes predominantly to euchromatic regions of the 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 box
CC family of RNA helicases and controls ATP binding and hydrolysis.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DECD subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB96655.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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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 AlphaFoldDB; Q9LFN6; -.
DR SMR; Q9LFN6; -.
DR BioGRID; 16264; 12.
DR BioGRID; 16268; 12.
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 HOGENOM; CLU_003041_1_0_1; -.
DR InParanoid; Q9LFN6; -.
DR OMA; IKPICRK; -.
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:0005634; C:nucleus; 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; IBA:GO_Central.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
DR GO; GO:0008380; P:RNA splicing; 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; 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; Helicase; Hydrolase; mRNA processing;
KW mRNA splicing; mRNA transport; Nucleotide-binding; Nucleus;
KW Reference proteome; RNA-binding; Transport.
FT CHAIN 1..427
FT /note="DEAD-box ATP-dependent RNA helicase 56"
FT /id="PRO_0000239195"
FT DOMAIN 77..250
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 278..423
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..30
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 46..74
FT /note="Q motif"
FT MOTIF 197..200
FT /note="DECD box"
FT BINDING 90..97
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
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
