PRP22_ARATH
ID PRP22_ARATH Reviewed; 717 AA.
AC F4IE66; Q9FZC3;
DT 09-DEC-2015, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 70.
DE RecName: Full=Pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH10;
DE EC=3.6.4.13;
DE AltName: Full=DEAH RNA helicase homolog PRP22 {ECO:0000303|PubMed:23771891};
DE AltName: Full=Protein ROOT INITIATION DEFECTIVE 1 {ECO:0000303|PubMed:23771891};
GN Name=RID1 {ECO:0000303|PubMed:23771891};
GN OrderedLocusNames=At1g26370 {ECO:0000312|Araport:AT1G26370};
GN ORFNames=T1K7.25 {ECO:0000312|EMBL:AAF98584.1};
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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 FUNCTION, MUTAGENESIS OF LEU-295, SUBCELLULAR LOCATION, TISSUE SPECIFICITY,
RP AND DISRUPTION PHENOTYPE.
RX PubMed=23771891; DOI=10.1105/tpc.113.111922;
RA Ohtani M., Demura T., Sugiyama M.;
RT "Arabidopsis root initiation defective1, a DEAH-box RNA helicase involved
RT in pre-mRNA splicing, is essential for plant development.";
RL Plant Cell 25:2056-2069(2013).
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: Involved in pre-mRNA splicing. Plays a role during
CC development in processes such as meristem maintenance, leaf
CC morphogenesis and root morphogenesis. {ECO:0000269|PubMed:23771891}.
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:23771891}. Nucleus,
CC nucleolus {ECO:0000269|PubMed:23771891}.
CC -!- TISSUE SPECIFICITY: Widely expressed but spatially and temporally
CC regulated during development. {ECO:0000269|PubMed:23771891}.
CC -!- DISRUPTION PHENOTYPE: Defects in female gametophyte development.
CC {ECO:0000269|PubMed:23771891}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DEAH subfamily.
CC PRP22 sub-subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF98584.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BT008611; 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; AC013427; AAF98584.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE30683.1; -; Genomic_DNA.
DR EMBL; BT008611; -; NOT_ANNOTATED_CDS; mRNA.
DR PIR; D86390; D86390.
DR RefSeq; NP_173961.3; NM_102401.4.
DR AlphaFoldDB; F4IE66; -.
DR SMR; F4IE66; -.
DR STRING; 3702.AT1G26370.1; -.
DR PaxDb; F4IE66; -.
DR PRIDE; F4IE66; -.
DR ProteomicsDB; 226218; -.
DR EnsemblPlants; AT1G26370.1; AT1G26370.1; AT1G26370.
DR GeneID; 839179; -.
DR Gramene; AT1G26370.1; AT1G26370.1; AT1G26370.
DR KEGG; ath:AT1G26370; -.
DR Araport; AT1G26370; -.
DR TAIR; locus:2197965; AT1G26370.
DR eggNOG; KOG0922; Eukaryota.
DR HOGENOM; CLU_001832_5_11_1; -.
DR InParanoid; F4IE66; -.
DR OMA; NHKYIRN; -.
DR OrthoDB; 354219at2759; -.
DR PRO; PR:F4IE66; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; F4IE66; baseline and differential.
DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
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: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:0045943; P:positive regulation of transcription by RNA polymerase I; IBA:GO_Central.
DR GO; GO:0043484; P:regulation of RNA splicing; IMP:UniProtKB.
DR GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR011709; DEAD-box_helicase_OB_fold.
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; PF04408; HA2; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF07717; OB_NTP_bind; 1.
DR SMART; SM00382; AAA; 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; mRNA processing; mRNA splicing;
KW Nucleotide-binding; Nucleus; Reference proteome; Spliceosome;
KW Transit peptide.
FT CHAIN 1..717
FT /note="Pre-mRNA-splicing factor ATP-dependent RNA helicase
FT DEAH10"
FT /id="PRO_0000434942"
FT DOMAIN 51..256
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 278..453
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..29
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 162..165
FT /note="DEAH box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT COMPBIAS 8..29
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 64..71
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MUTAGEN 295
FT /note="L->P: In rid1-1; Reduced efficiency of pre-mRNA
FT splicing."
SQ SEQUENCE 717 AA; 80515 MW; 57CDA8DD563E7A21 CRC64;
MPSMAQGELK SFVQNSRPNP KSPTVSPFSM RQKIAEHRRS LPIASVEKRL VEEVQKNDIL
IIVGETGSGK TTQLPQFLYN AGFCREGKMI GITQPRRIAA VTVAKRVAEE CEVQLGQKVG
YSIRFDDTTS GSTRLKYMTD GLLLREALLD PHLSRYSVII VDEAHDRSVH TDVLLALLKK
IQRTRSQPVS EKTEFGNVAS QVQTTTRDAN GPQQNGVLKG YQGRKLSPLK LIIMSASLDA
RVFSEYFGGA KAVHVQGRQF PVDILYTVHP ESDYVDATLV TIFQIHFEEK PGDILVFLTG
QDEIESVERL VQERLQNIPE DKRKLLPLAI FSALPSEQQM KVFAPAPTGF RKVILATNIA
ETSITIPGIR YVIDPGFVKA RSYDPSKGME SLDVVPASKA QTLQRSGRAG REGPGKSFRL
YPEREFEKLE DSTKPEIKRC NLSNIILQLK ALGIDDIVGF DFIDKPSRGA IIKALAELHS
LGALADDGKL ENPVGYQMSR LPLEPVYSKA LILANQFNCL EEMLITVAVL SVESIFYDPR
EKREEARTSK NHFASVEGDH LTYLSVYRES DEFLEKRKAA GSGNNIDKIM KKWCKENYVN
SRSLKHARDI YRQIREHVEQ IGFNVSSCGN DMLAFRRCLA ASFFLKAAQR QLDGTYRALE
SGEVVHIHPT SVLFRAKPEC VIFNELMQTS KKYIKNLTII DSLWLSELAP HHFQTAE
