DEAH5_ARATH
ID DEAH5_ARATH Reviewed; 1168 AA.
AC Q38953; Q9LRV0;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 10-JAN-2003, sequence version 2.
DT 03-AUG-2022, entry version 167.
DE RecName: Full=Probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH5 {ECO:0000305};
DE EC=3.6.4.13;
DE AltName: Full=DEAH RNA helicase homolog PRP22 {ECO:0000303|PubMed:17008405};
GN OrderedLocusNames=At3g26560 {ECO:0000312|Araport:AT3G26560};
GN ORFNames=MFE16.8 {ECO:0000312|EMBL:BAB01838.1};
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 [GENOMIC DNA / MRNA].
RC STRAIN=cv. Columbia; TISSUE=Shoot;
RX PubMed=8932388; DOI=10.1093/nar/24.21.4313;
RA Quigley F., Dao P., Cottet A., Mache R.;
RT "Sequence analysis of an 81 kb contig from Arabidopsis thaliana chromosome
RT III.";
RL Nucleic Acids Res. 24:4313-4318(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(2000).
RN [3]
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 [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 PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-411, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Root;
RX PubMed=18433157; DOI=10.1021/pr8000173;
RA de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E.,
RA Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J.,
RA Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H.;
RT "Site-specific phosphorylation profiling of Arabidopsis proteins by mass
RT spectrometry and peptide chip analysis.";
RL J. Proteome Res. 7:2458-2470(2008).
RN [6]
RP SUBCELLULAR LOCATION, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-411,
RP AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-411, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [8]
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 -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19245862}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DEAH subfamily.
CC PRP22 sub-subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA66613.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=CAA66825.1; Type=Frameshift; Evidence={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; X98130; CAA66825.1; ALT_FRAME; Genomic_DNA.
DR EMBL; X97970; CAA66613.1; ALT_FRAME; mRNA.
DR EMBL; AB028611; BAB01838.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE77178.1; -; Genomic_DNA.
DR RefSeq; NP_189288.1; NM_113564.4.
DR AlphaFoldDB; Q38953; -.
DR SMR; Q38953; -.
DR BioGRID; 7595; 2.
DR STRING; 3702.AT3G26560.1; -.
DR iPTMnet; Q38953; -.
DR PaxDb; Q38953; -.
DR PRIDE; Q38953; -.
DR ProteomicsDB; 224181; -.
DR EnsemblPlants; AT3G26560.1; AT3G26560.1; AT3G26560.
DR GeneID; 822264; -.
DR Gramene; AT3G26560.1; AT3G26560.1; AT3G26560.
DR KEGG; ath:AT3G26560; -.
DR Araport; AT3G26560; -.
DR TAIR; locus:2088847; AT3G26560.
DR eggNOG; KOG0922; Eukaryota.
DR HOGENOM; CLU_001832_2_0_1; -.
DR InParanoid; Q38953; -.
DR OMA; DPMVAPE; -.
DR OrthoDB; 354219at2759; -.
DR PhylomeDB; Q38953; -.
DR PRO; PR:Q38953; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q38953; baseline and differential.
DR Genevisible; Q38953; AT.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0009506; C:plasmodesma; HDA:TAIR.
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; HDA: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:0000390; P:spliceosomal complex disassembly; IBA:GO_Central.
DR CDD; cd17971; DEXHc_DHX8; 1.
DR Gene3D; 2.40.50.140; -; 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; IPR044762; DHX8/Prp22_DEXHc.
DR InterPro; IPR002464; DNA/RNA_helicase_DEAH_CS.
DR InterPro; IPR007502; Helicase-assoc_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR022967; S1_dom.
DR InterPro; IPR003029; S1_domain.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF04408; HA2; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF07717; OB_NTP_bind; 1.
DR Pfam; PF00575; S1; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00847; HA2; 1.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00316; S1; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS00690; DEAH_ATP_HELICASE; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS50126; S1; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Helicase; Hydrolase; mRNA processing; mRNA splicing;
KW Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome;
KW Spliceosome.
FT CHAIN 1..1168
FT /note="Probable pre-mRNA-splicing factor ATP-dependent RNA
FT helicase DEAH5"
FT /id="PRO_0000055132"
FT DOMAIN 214..283
FT /note="S1 motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00180"
FT DOMAIN 525..688
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 706..886
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 76..206
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 289..326
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 635..638
FT /note="DEAH box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT COMPBIAS 79..206
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 295..310
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 538..545
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOD_RES 411
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157,
FT ECO:0007744|PubMed:19245862, ECO:0007744|PubMed:19376835"
SQ SEQUENCE 1168 AA; 134157 MW; B3632DE4A7A7690C CRC64;
MEKEELNKLN HLSLVSNVCN ELETHLGSAE KVLAEFIIDL GRHSETVDEF DKNLKEAGAE
MPDYFVRSLL TTIHGIYPPK PKSEKKKEEG DDQKFKGLAI KDTKDKVKEL EKEIEREAEE
RRREEDRNRD RDRRESGRDR DRDRNRDRDD RRDRHRDRER NRGDEEGEDR RSDRRHRERG
RGDGGEGEDR RRDRRAKDEY VEEDKGGANE PELYQVYKGR VTRVMDAGCF VQFDKFRGKE
GLVHVSQMAT RRVDKAKEFV KRDMEVYVKV ISISSDKYSL SMRDVDQNTG RDLIPLRKPS
DEDDSSRSNP SYRTKDGQVT KTGISGIRIV EENDVAPSRR PLKKMSSPER WEAKQLIASG
VLRVDEFPMY DEDGDGMLYQ EEGAEEELEI EMNEDEPAFL QGQTRYSVDM SPVKIFKNPE
GSLSRAAALQ SALTKERREM REQQQRTMLD SIPKDLNRPW EDPMPETGER HLAQELRGVG
LSAYDMPEWK KDAFGKTPTF GQRSKLSIQE QRESLPIYKL KKELIQAVHD NQVLVVIGET
GSGKTTQVTQ YLAEAGYTTK GKIGCTQPRR VAAMSVAKRV AEEFGCRLGE EVGYAIRFED
CTGPDTVIKY MTDGMLLREI LIDENLSQYS VIMLDEAHER TIHTDVLFGL LKKLMKRRLD
LRLIVTSATL DAEKFSGYFF NCNIFTIPGR TFPVEILYTK QPETDYLDAA LITVLQIHLT
EPEGDILVFL TGQEEIDSAC QSLYERMKGL GKNVPELIIL PVYSALPSEM QSRIFDPPPP
GKRKVVVATN IAEASLTIDG IYYVVDPGFA KQNVYNPKQG LESLVITPIS QASAKQRAGR
AGRTGPGKCY RLYTESAYRN EMPPTSIPEI QRINLGMTTL TMKAMGINDL LSFDFMDPPQ
PQALISAMEQ LYSLGALDEE GLLTKLGRKM AEFPLEPPLS KMLLASVDLG CSDEILTMIA
MIQTGNIFYR PREKQAQADQ KRAKFFQPEG DHLTLLAVYE AWKAKNFSGP WCFENFIQSR
SLRRAQDVRK QLLSIMDKYK LDVVTAGKNF TKIRKAITAG FFFHGARKDP QEGYRTLVEN
QPVYIHPSSA LFQRQPDWVI YHDLVMTTKE YMREVTVIDP KWLVELAPRF FKVSDPTKMS
KRKRQERIEP LYDRYHEPNS WRLSKRRA
