PRP16_ARATH
ID PRP16_ARATH Reviewed; 1255 AA.
AC F4K2E9; Q9LXT8;
DT 09-DEC-2015, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 73.
DE RecName: Full=Pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH7 {ECO:0000305};
DE EC=3.6.4.13;
DE AltName: Full=DEAH RNA helicase homolog PRP16 {ECO:0000303|PubMed:17008405, ECO:0000303|PubMed:26237376};
DE AltName: Full=Protein CLUMSY VEIN {ECO:0000303|PubMed:25384462};
DE AltName: Full=Protein EMBRYO DEFECTIVE 3011 {ECO:0000305};
DE AltName: Full=Protein PSR1-INTERACTING PROTEIN 1 {ECO:0000303|PubMed:25902521};
GN Name=CUV {ECO:0000303|PubMed:25384462};
GN Synonyms=EMB3011 {ECO:0000305}, PINP1 {ECO:0000303|PubMed:25902521};
GN OrderedLocusNames=At5g13010 {ECO:0000312|Araport:AT5G13010};
GN ORFNames=T24H18_180 {ECO:0000312|EMBL:CAB88265.1};
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=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 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 [4]
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 [5]
RP FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF GLY-974, MOTIFS, SUBCELLULAR
RP LOCATION, AND DEVELOPMENTAL STAGE.
RX PubMed=25384462; DOI=10.1111/tpj.12721;
RA Tsugeki R., Tanaka-Sato N., Maruyama N., Terada S., Kojima M.,
RA Sakakibara H., Okada K.;
RT "CLUMSY VEIN, the Arabidopsis DEAH-box Prp16 ortholog, is required for
RT auxin-mediated development.";
RL Plant J. 81:183-197(2015).
RN [6]
RP FUNCTION.
RX PubMed=26237376; DOI=10.1080/15592324.2015.1074369;
RA Tsugeki R., Terada S.;
RT "The Arabidopsis ortholog of the DEAH-box ATPase Prp16 influences auxin-
RT mediated development.";
RL Plant Signal. Behav. 0:0-0(2015).
RN [7]
RP INTERACTION WITH PSR1, FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=25902521; DOI=10.1073/pnas.1421475112;
RA Qiao Y., Shi J., Zhai Y., Hou Y., Ma W.;
RT "Phytophthora effector targets a novel component of small RNA pathway in
RT plants to promote infection.";
RL Proc. Natl. Acad. Sci. U.S.A. 112:5850-5855(2015).
CC -!- FUNCTION: Involved in pre-mRNA splicing by mediating structural
CC transitions of the spliceosome during the catalytic step. Facilitates
CC expression of genes involved in auxin-mediated development including
CC male-gametophyte transmission, apical-basal patterning of embryonic and
CC gynoecium development, stamen development, phyllotactic flower
CC positioning, and vascular development (PubMed:25384462). Also involved
CC in root-meristem maintenance and planar polarity of root-hair
CC positioning (PubMed:26237376). Acts as a component of RNA silencing
CC that regulates distinct classes of endogenous small RNAs. Functions as
CC a positive regulator of plant immunity (PubMed:25902521).
CC {ECO:0000269|PubMed:25384462, ECO:0000269|PubMed:25902521,
CC ECO:0000269|PubMed:26237376}.
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 the Phytophthora PSR1 protein.
CC {ECO:0000269|PubMed:25902521}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:25384462,
CC ECO:0000269|PubMed:25902521}. Note=Binds to the spliceosome.
CC {ECO:0000250|UniProtKB:P15938}.
CC -!- DEVELOPMENTAL STAGE: Preferentially expressed in developing organs.
CC {ECO:0000269|PubMed:25384462}.
CC -!- DISRUPTION PHENOTYPE: Narrow rosette leaves with altered venation
CC pattern. {ECO:0000269|PubMed:25384462}.
CC -!- MISCELLANEOUS: Silencing of PINP1 renders defects in small RNA
CC accumulation, developmental defects and hypersensitivity to
CC Phytophthora infection. {ECO:0000269|PubMed:25902521}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DEAH subfamily.
CC PRP16 sub-subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB88265.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC -!- WEB RESOURCE: Name=Seed defective Arabidopsis mutants;
CC URL="http://seedgenes.org/MutantList";
CC -!- WEB RESOURCE: Name=Splicing Related Gene Database;
CC URL="http://www.plantgdb.org/SRGD/index.php";
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DR EMBL; AL353013; CAB88265.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED91841.1; -; Genomic_DNA.
DR PIR; T49915; T49915.
DR RefSeq; NP_196805.2; NM_121304.6.
DR AlphaFoldDB; F4K2E9; -.
DR SMR; F4K2E9; -.
DR STRING; 3702.AT5G13010.1; -.
DR iPTMnet; F4K2E9; -.
DR PaxDb; F4K2E9; -.
DR PRIDE; F4K2E9; -.
DR ProMEX; F4K2E9; -.
DR ProteomicsDB; 226377; -.
DR EnsemblPlants; AT5G13010.1; AT5G13010.1; AT5G13010.
DR GeneID; 831141; -.
DR Gramene; AT5G13010.1; AT5G13010.1; AT5G13010.
DR KEGG; ath:AT5G13010; -.
DR Araport; AT5G13010; -.
DR TAIR; locus:2182340; AT5G13010.
DR eggNOG; KOG0924; Eukaryota.
DR HOGENOM; CLU_001832_6_5_1; -.
DR InParanoid; F4K2E9; -.
DR OMA; VMFHRSP; -.
DR OrthoDB; 354219at2759; -.
DR PRO; PR:F4K2E9; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; F4K2E9; baseline and differential.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0005681; C:spliceosomal 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; IEA:UniProtKB-EC.
DR GO; GO:0050832; P:defense response to fungus; IMP:TAIR.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
DR GO; GO:0010467; P:gene expression; IMP:UniProtKB.
DR GO; GO:0045087; P:innate immune response; IEA:UniProtKB-KW.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IMP:UniProtKB.
DR GO; GO:0031334; P:positive regulation of protein-containing complex assembly; IGI:TAIR.
DR GO; GO:0033120; P:positive regulation of RNA splicing; IMP:UniProtKB.
DR GO; GO:0035194; P:post-transcriptional gene silencing by RNA; IMP:UniProtKB.
DR GO; GO:0031053; P:primary miRNA processing; IMP:TAIR.
DR GO; GO:0008380; P:RNA splicing; IMP:TAIR.
DR GO; GO:0048364; P:root development; IMP:UniProtKB.
DR GO; GO:0048767; P:root hair elongation; IGI:TAIR.
DR GO; GO:0010051; P:xylem and phloem pattern formation; IMP:TAIR.
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; 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 1: Evidence at protein level;
KW ATP-binding; Helicase; Hydrolase; Immunity; Innate immunity;
KW mRNA processing; mRNA splicing; Nucleotide-binding; Nucleus;
KW Reference proteome; RNA-mediated gene silencing; Spliceosome;
KW Transcription; Transcription regulation.
FT CHAIN 1..1255
FT /note="Pre-mRNA-splicing factor ATP-dependent RNA helicase
FT DEAH7"
FT /id="PRO_0000434941"
FT DOMAIN 568..731
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 753..933
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..316
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1190..1255
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 144..153
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000303|PubMed:25384462"
FT MOTIF 172..191
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000303|PubMed:25384462"
FT MOTIF 678..681
FT /note="DEAH box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT COMPBIAS 9..60
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 91..105
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 106..139
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 140..220
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 274..298
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 301..316
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1190..1232
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 581..588
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MUTAGEN 974
FT /note="G->R: In cuv-1; altered venation pattern."
FT /evidence="ECO:0000269|PubMed:25384462"
SQ SEQUENCE 1255 AA; 141860 MW; A81F7AD829AB3EF0 CRC64;
MGVDPFKTTE TLEADKETNG GVPVKDKLTF KAPERKSRLG LDARAIEKKD NAKTEGEFKV
PKKSAISVTS SLDEEDKSDV SGLDFGTENT RPVHSSRRYR EKSSRSQSAQ ESTVTTENAG
TSDISITPRT LSCTSSYERG GSNRHREEHR RDRSETPRSR QRNTYDEMDH YRRRESYRQS
DRDYHGEKRR RYNSDWRTPG RSDWDDGQDE WERSPHGDRG SSYSRRPQPS PSPMLAAASP
DARLASPWLD TPRSTMSSAS PWDMGAPSPI PIRASGSSIR SSSSRYGGRS NQLAYSREGD
LTNEGHSDED RSQGAEEFKH EITETMRVEM EYQSDRAWYD TDEGNSLFDA DSASFFLGDD
ASLQKKETEL AKRLVRRDGS KMSLAQSKKY SQLNADNAQW EDRQLLRSGA VRGTEVQTEF
DSEEERKAIL LVHDTKPPFL DGRVVYTKQA EPVMPVKDPT SDMAIISRKG SGLVKEIREK
QSANKSRQRF WELAGSNLGN ILGIEKSAEQ IDADTAVVGD DGEVDFKGEA KFAQHMKKGE
AVSEFAMSKT MAEQRQYLPI FSVRDELLQV IRENQVIVVV GETGSGKTTQ LTQYLHEDGY
TINGIVGCTQ PRRVAAMSVA KRVSEEMETE LGDKIGYAIR FEDVTGPNTV IKYMTDGVLL
RETLKDSDLD KYRVVVMDEA HERSLNTDVL FGILKKVVAR RRDFKLIVTS ATLNAQKFSN
FFGSVPIFNI PGRTFPVNIL YSKTPCEDYV EAAVKQAMTI HITSPPGDIL IFMTGQDEIE
AACFSLKERM EQLVSSSSRE ITNLLILPIY SQLPADLQAK IFQKPEDGAR KCIVATNIAE
TSLTVDGIYY VIDTGYGKMK VFNPRMGMDA LQVFPISRAA SDQRAGRAGR TGPGTCYRLY
TESAYLNEML PSPVPEIQRT NLGNVVLLLK SLKIDNLLDF DFMDPPPQEN ILNSMYQLWV
LGALNNVGGL TDLGWKMVEF PLDPPLAKML LMGERLDCID EVLTIVSMLS VPSVFFRPKE
RAEESDAARE KFFVPESDHL TLLNVYQQWK EHDYRGDWCN DHYLQVKGLR KAREVRSQLL
DILKQLKIEL RSCGPDWDIV RKAICSAYFH NSARLKGVGE YVNCRTGMPC HLHPSSALYG
LGYTPDYVVY HELILTTKEY MQCATSVEPH WLAELGPMFF SVKDSDTSML EHKKKQKEEK
SGMEEEMEKL RRDQVESELR SKERERKKRA KQQQQISGPG LKKGTTFLRP KKLGL
