DEAH2_ARATH
ID DEAH2_ARATH Reviewed; 726 AA.
AC Q9LZQ9;
DT 09-DEC-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=Probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH2 {ECO:0000305};
DE EC=3.6.4.13;
DE AltName: Full=DEAH RNA helicase homolog PRP43 {ECO:0000303|PubMed:17008405};
GN OrderedLocusNames=At3g62310 {ECO:0000312|Araport:AT3G62310};
GN ORFNames=T12C14_10 {ECO:0000312|EMBL:CAB82945.1};
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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 IDENTIFICATION.
RX PubMed=17008405; DOI=10.1073/pnas.0606536103;
RA Herr A.J., Molnar A., Jones A., Baulcombe D.C.;
RT "Defective RNA processing enhances RNA silencing and influences flowering
RT of Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:14994-15001(2006).
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).
CC -!- FUNCTION: May be involved in pre-mRNA splicing. {ECO:0000305}.
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 -!- SIMILARITY: Belongs to the DEAD box helicase family. DEAH subfamily.
CC PRP43 sub-subfamily. {ECO:0000305}.
CC -!- WEB RESOURCE: Name=Splicing Related Gene Database;
CC URL="http://www.plantgdb.org/SRGD/index.php";
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DR EMBL; AL162507; CAB82945.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE80337.1; -; Genomic_DNA.
DR EMBL; AY120782; AAM53340.1; -; mRNA.
DR EMBL; BT010331; AAQ56774.1; -; mRNA.
DR PIR; T48023; T48023.
DR RefSeq; NP_191790.1; NM_116096.5.
DR AlphaFoldDB; Q9LZQ9; -.
DR SMR; Q9LZQ9; -.
DR IntAct; Q9LZQ9; 3.
DR STRING; 3702.AT3G62310.1; -.
DR iPTMnet; Q9LZQ9; -.
DR PaxDb; Q9LZQ9; -.
DR PRIDE; Q9LZQ9; -.
DR ProteomicsDB; 224617; -.
DR EnsemblPlants; AT3G62310.1; AT3G62310.1; AT3G62310.
DR GeneID; 825404; -.
DR Gramene; AT3G62310.1; AT3G62310.1; AT3G62310.
DR KEGG; ath:AT3G62310; -.
DR Araport; AT3G62310; -.
DR TAIR; locus:2095989; AT3G62310.
DR eggNOG; KOG0925; Eukaryota.
DR HOGENOM; CLU_001832_5_11_1; -.
DR InParanoid; Q9LZQ9; -.
DR OMA; PQVGDMK; -.
DR OrthoDB; 354219at2759; -.
DR PhylomeDB; Q9LZQ9; -.
DR PRO; PR:Q9LZQ9; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LZQ9; baseline and differential.
DR GO; GO:0005730; C:nucleolus; HDA:TAIR.
DR GO; GO:0005681; C:spliceosomal complex; IEA:UniProtKB-KW.
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; IDA:TAIR.
DR GO; GO:0003723; F:RNA 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:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR CDD; cd17973; DEXHc_DHX15; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011709; DEAD-box_helicase_OB_fold.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR044756; DHX15_DEXHc.
DR InterPro; IPR007502; Helicase-assoc_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF04408; HA2; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF07717; OB_NTP_bind; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00847; HA2; 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.
PE 2: Evidence at transcript level;
KW ATP-binding; Helicase; Hydrolase; mRNA processing; mRNA splicing;
KW Nucleotide-binding; Reference proteome; Spliceosome.
FT CHAIN 1..726
FT /note="Probable pre-mRNA-splicing factor ATP-dependent RNA
FT helicase DEAH2"
FT /id="PRO_0000434933"
FT DOMAIN 71..240
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 265..445
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT MOTIF 187..190
FT /note="DEAH box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 84..91
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
SQ SEQUENCE 726 AA; 82694 MW; 31621A1606D04B30 CRC64;
MGTERKRKIS LFDVMDDPSA PAKNAKTSGL PDGGINSLIN KWNGKPYSQR YYDILEKRRT
LPVWLQKEEF LKTLNNNQTL ILVGETGSGK TTQIPQFVID AVDAETSDKR RKWLVGCTQP
RRVAAMSVSR RVAEEMDVTI GEEVGYSIRF EDCSSPRTVL KYLTDGMLLR EAMADPLLER
YKVIILDEAH ERTLATDVLF GLLKEVLKNR PDLKLVVMSA TLEAEKFQDY FSGAPLMKVP
GRLHPVEIFY TQEPERDYLE AAIRTVVQIH MCEPPGDILV FLTGEEEIED ACRKINKEVG
NLGDQVGPIK VVPLYSTLPP AMQQKIFDPA PEPVTEGGPP GRKIVVSTNI AETSLTIDGI
VYVIDPGFAK QKVYNPRIRV ESLLVSPISK ASAHQRSGRA GRTRPGKCFR LYTEKSFNND
LQPQTYPEIL RSNLANTVLT LKKLGIDDLV HFDFMDPPAP ETLMRALEVL NYLGALDDDG
NLTKTGEIMS EFPLDPQMAK MLIVSPEFNC SNEILSVSAM LSVPNCFIRP REAQKAADEA
KARFGHIEGD HLTLLNVYHA FKQNNEDPNW CYENFINNRA MKSADNVRQQ LVRIMSRFNL
KMCSTDFNSR DYYINIRKAM LAGYFMQVAH LERTGHYLTV KDNQVVHLHP SNCLDHKPEW
VIYNEYVLTS RNFIRTVTDI RGEWLVDVAS HYYDLSNFPN CEAKRVIEKL YKKREREKEE
SKKNRK
