ID SKI2_ARATH Reviewed; 1347 AA.
AC F4JAA5; Q9SD77; Q9STG8;
DT 29-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 24-JAN-2024, entry version 82.
DE RecName: Full=DExH-box ATP-dependent RNA helicase DExH11 {ECO:0000305};
DE EC=3.6.4.13;
DE AltName: Full=AtHELPS {ECO:0000303|PubMed:21535471};
DE AltName: Full=Protein SKI2 homolog {ECO:0000303|PubMed:22511887};
DE Short=AtSKI2 {ECO:0000303|PubMed:22511887};
GN Name=SKI2 {ECO:0000303|PubMed:22511887};
GN Synonyms=HELPS {ECO:0000303|PubMed:21535471};
GN OrderedLocusNames=At3g46960 {ECO:0000312|Araport:AT3G46960};
GN ORFNames=F13I12.10 {ECO:0000312|EMBL:CAB61942.1},
GN T6H20.10 {ECO:0000312|EMBL:CAB51169.1};
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 FUNCTION, TISSUE SPECIFICITY, AND INDUCTION.
RX PubMed=21535471; DOI=10.1111/j.1742-4658.2011.08147.x;
RA Xu R.R., Qi S.D., Lu L.T., Chen C.T., Wu C.A., Zheng C.C.;
RT "A DExD/H box RNA helicase is important for K+ deprivation responses and
RT tolerance in Arabidopsis thaliana.";
RL FEBS J. 278:2296-2306(2011).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, SUBCELLULAR LOCATION, AND
RP DISRUPTION PHENOTYPE.
RX PubMed=22511887; DOI=10.1371/journal.pgen.1002652;
RA Dorcey E., Rodriguez-Villalon A., Salinas P., Santuari L., Pradervand S.,
RA Harshman K., Hardtke C.S.;
RT "Context-dependent dual role of SKI8 homologs in mRNA synthesis and
RT turnover.";
RL PLoS Genet. 8:E1002652-E1002652(2012).
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: Component of the SKI complex which is thought to be involved
CC in exosome-mediated RNA decay and associates with transcriptionally
CC active genes in a manner dependent on PAF1 complex (PAF1C)
CC (PubMed:22511887). Involved in the regulation of potassium deprivation
CC stress response (PubMed:21535471). {ECO:0000269|PubMed:21535471,
CC ECO:0000269|PubMed:22511887}.
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 Evidence={ECO:0000305};
CC -!- SUBUNIT: Component of the cytoplasmic SKI complex, which consists of
CC SKI2, SKI3 and VIP3/SKI8. {ECO:0000269|PubMed:22511887}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:22511887}.
CC -!- TISSUE SPECIFICITY: Expressed in vascular tissues of leaves and roots
CC of young plants. {ECO:0000269|PubMed:21535471}.
CC -!- INDUCTION: Induced by low potassium, zeatin and cold stress. Down-
CC regulated by high potassium treatment. {ECO:0000269|PubMed:21535471}.
CC -!- DISRUPTION PHENOTYPE: Dwarf phenotype. {ECO:0000269|PubMed:22511887}.
CC -!- SIMILARITY: Belongs to the DExH box helicase family. SKI2 subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB51169.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB61942.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL096859; CAB51169.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL133292; CAB61942.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE78224.1; -; Genomic_DNA.
DR PIR; T45632; T45632.
DR RefSeq; NP_190280.5; NM_114563.7.
DR AlphaFoldDB; F4JAA5; -.
DR SMR; F4JAA5; -.
DR STRING; 3702.F4JAA5; -.
DR iPTMnet; F4JAA5; -.
DR PaxDb; 3702-AT3G46960-1; -.
DR ProteomicsDB; 232656; -.
DR EnsemblPlants; AT3G46960.1; AT3G46960.1; AT3G46960.
DR GeneID; 823849; -.
DR Gramene; AT3G46960.1; AT3G46960.1; AT3G46960.
DR KEGG; ath:AT3G46960; -.
DR Araport; AT3G46960; -.
DR TAIR; AT3G46960; SKI2.
DR eggNOG; KOG0947; Eukaryota.
DR HOGENOM; CLU_002902_1_2_1; -.
DR InParanoid; F4JAA5; -.
DR OrthoDB; 1352at2759; -.
DR PRO; PR:F4JAA5; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; F4JAA5; baseline and differential.
DR Genevisible; F4JAA5; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0000325; C:plant-type vacuole; HDA:TAIR.
DR GO; GO:0055087; C:Ski complex; IDA:UniProtKB.
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; IEA:UniProtKB-KW.
DR GO; GO:0003724; F:RNA helicase activity; IMP:TAIR.
DR GO; GO:0070478; P:nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay; IMP:UniProtKB.
DR GO; GO:1904278; P:positive regulation of wax biosynthetic process; IGI:TAIR.
DR GO; GO:0016441; P:post-transcriptional gene silencing; IMP:TAIR.
DR GO; GO:0006813; P:potassium ion transport; IMP:TAIR.
DR GO; GO:0035864; P:response to potassium ion; IMP:TAIR.
DR GO; GO:0000292; P:RNA fragment catabolic process; IMP:TAIR.
DR CDD; cd18795; SF2_C_Ski2; 1.
DR Gene3D; 1.10.3380.30; -; 2.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR048392; MTR4-like_stalk.
DR InterPro; IPR025696; MTR4_beta-barrel.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR016438; SKI2-like.
DR InterPro; IPR012961; Ski2/MTR4_C.
DR InterPro; IPR040801; Ski2_N.
DR PANTHER; PTHR12131; ATP-DEPENDENT RNA AND DNA HELICASE; 1.
DR PANTHER; PTHR12131:SF24; DEXH-BOX ATP-DEPENDENT RNA HELICASE DEXH11; 1.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF08148; DSHCT; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF21408; MTR4-like_stalk; 1.
DR Pfam; PF13234; MTR4_beta-barrel; 1.
DR Pfam; PF17911; Ski2_N; 1.
DR PIRSF; PIRSF005198; Antiviral_helicase_SKI2; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM01142; DSHCT; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cytoplasm; Helicase; Hydrolase; Nucleotide-binding;
KW Reference proteome; RNA-binding; Transcription; Transcription regulation.
FT CHAIN 1..1347
FT /note="DExH-box ATP-dependent RNA helicase DExH11"
FT /id="PRO_0000432767"
FT DOMAIN 369..524
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 673..838
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 263..291
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 566..625
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 472..475
FT /note="DEVH box"
FT /evidence="ECO:0000305"
FT COMPBIAS 263..281
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 570..590
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 591..611
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 382..389
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
SQ SEQUENCE 1347 AA; 151184 MW; A9643FBC3997E0C2 CRC64;
MNKVEAGNEL GFRVGFSGHG GHLRVEPFYT AERDDALNSL PDFVSPPAFA KETKESIKKH
IEEKYLIPRL EPDQFSAEKA ENQWDFDWFS RVKMPLQPSL PRSVVVPTWE LPFRRQKEDT
ENGAWEPKSV EVDLSEQMYG DQDSGFFPRM VGPPKDFLRG SVNNRPFRPG GLEDSQSSER
VLPEGVSSGQ WVQELLNGGP AQTVPPSFKQ SLDLGDLMPY PQTWSVYEDH SSHGNASDEN
SSKLSIQFDD LFKKAWEEDT FSELEGDDHT AGSESPKAEA EPDAKASISN EVSKGLETDV
TVLDEILSSA KTAIMSEEAV TGSSDKQLRK EGWATKGDSQ DIADRFYELV PDMAIEFPFE
LDNFQKEAIC CLEKGESVFV AAHTSAGKTV VAEYAFALAT KHCTRAVYTA PIKTISNQKY
RDFCGKFDVG LLTGDVSIRP EASCLIMTTE ILRSMLYRGA DIIRDIEWVI FDEVHYVNDV
ERGVVWEEVI IMLPRHINFV LLSATVPNTF EFADWIGRTK QKEIRVTGTT KRPVPLEHCL
FYSGELYKVC ENEVFLSKGI KDAKDSQKKK NSNAVSVAPK QQMGSSAHQD GSKSQKHEAH
SRGKQNKHSS VKDVGKSSYS GNSQNNGAFR RSAASNWLLL INKLSKMSLL PVVVFCFSKN
YCDRCADALT GTDLTSSSEK SEIRVFCDKA FSRLKGSDRN LPQVLRLQSL LHRGIGVHHA
GLLPIVKEVV EMLFCRGVIK VLFSTETFAM GVNAPARTVV FDALRKFDGK EFRQLLPGEY
TQMAGRAGRR GLDKTGTVVV MCRDEVPDES DLRRVIVGSA TRLESQFRLT YIMILHLLRV
EELKVEDMLK RSFAEFHAQK KLPEKQQLLM IKRSLPTKHI ECIKGEPAIE DYYDMYMEAN
EYNNKMSEAV MQSPYAQSFL VQGRVVVMKS GMGIDNLLGI VLKGPSNTNR QYVVLVIKSE
IPPPEKNMVS IGKKSSDPSQ GYFIAPKSKR GFEEEFYTKP SSRKGPVVIK IELPYHGVAA
GVGYEVKGFD NKEFLCICDS KIKIDQVRLL EDGNKAAFSQ TVQQLLDLKS DGNKFPPALD
PVKDLKLKDA ELVETYYKWT NLLQKMSMNK CHGCVKLEEH MKLAREIKKH KTDLKDLEFQ
MSDEALLQMP AFQGRIDVLK NIGCIDDDLV VQIKGRVACE MNSGEELICT VCLFENQFEE
LEPEEAVAIM SAFVFQQKNT SAPTLTPKLA KAKQRLYDTA IRLGELQAQY NLQIDPEEYA
QENLKFGLVE VVYEWAKGTP FAEICELTDV PEGLIVRTIV RLDETCREFK NAAAIMGNSA
LHKKMDAASN AIKRDIVFAA SLYVTGV
//
