GenomeNet

Database: UniProt
Entry: B9DFG3
LinkDB: B9DFG3
Original site: B9DFG3 
ID   ISE2_ARATH              Reviewed;        1171 AA.
AC   B9DFG3; O04538; Q94EZ6;
DT   15-JUN-2010, integrated into UniProtKB/Swiss-Prot.
DT   15-JUN-2010, sequence version 2.
DT   16-OCT-2019, entry version 79.
DE   RecName: Full=DExH-box ATP-dependent RNA helicase DExH15 chloroplastic {ECO:0000305};
DE            EC=3.6.4.13;
DE   AltName: Full=ATP-dependent RNA helicase ISE2;
DE   AltName: Full=Protein EMBRYO DEFECTIVE 25;
DE   AltName: Full=Protein INCREASED SIZE EXCLUSION LIMIT 2;
DE   AltName: Full=Protein PIGMENT DEFECTIVE 317;
DE   Flags: Precursor;
GN   Name=ISE2; Synonyms=EMB25, PDE317; OrderedLocusNames=At1g70070;
GN   ORFNames=F20P5.20;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;
OC   Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
OC   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.,
RA   White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y.,
RA   Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W.,
RA   Chung M.K., Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K.,
RA   Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y.,
RA   Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L.,
RA   Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E.,
RA   Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B.,
RA   Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P.,
RA   Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A.,
RA   Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I.,
RA   Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D.,
RA   Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M.,
RA   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.,
RA   Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT   "Sequence and analysis of chromosome 1 of the plant Arabidopsis
RT   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
RT   reference genome.";
RL   Plant J. 89:789-804(2017).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA   Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M.,
RA   Seki M., Shinozaki K.;
RT   "Analysis of multiple occurrences of alternative splicing events in
RT   Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL   DNA Res. 16:155-164(2009).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-916.
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.,
RA   Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
RA   Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
RA   Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
RA   Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
RA   Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
RA   Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
RA   Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
RA   Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
RA   Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
RA   Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
RA   Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
RT   "Empirical analysis of transcriptional activity in the Arabidopsis
RT   genome.";
RL   Science 302:842-846(2003).
RN   [5]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=11779812;
RA   McElver J., Tzafrir I., Aux G., Rogers R., Ashby C., Smith K.,
RA   Thomas C., Schetter A., Zhou Q., Cushman M.A., Tossberg J., Nickle T.,
RA   Levin J.Z., Law M., Meinke D., Patton D.;
RT   "Insertional mutagenesis of genes required for seed development in
RT   Arabidopsis thaliana.";
RL   Genetics 159:1751-1763(2001).
RN   [6]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=11874921;
RA   Kim I., Hempel F.D., Sha K., Pfluger J., Zambryski P.C.;
RT   "Identification of a developmental transition in plasmodesmatal
RT   function during embryogenesis in Arabidopsis thaliana.";
RL   Development 129:1261-1272(2002).
RN   [7]
RP   FUNCTION, SUBCELLULAR LOCATION, AND MUTAGENESIS OF ASP-275.
RX   PubMed=17601829; DOI=10.1105/tpc.106.045666;
RA   Kobayashi K., Otegui M.S., Krishnakumar S., Mindrinos M.,
RA   Zambryski P.;
RT   "INCREASED SIZE EXCLUSION LIMIT 2 encodes a putative DEVH box RNA
RT   helicase involved in plasmodesmata function during Arabidopsis
RT   embryogenesis.";
RL   Plant Cell 19:1885-1897(2007).
RN   [8]
RP   IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE
RP   SCALE ANALYSIS].
RX   PubMed=18431481; DOI=10.1371/journal.pone.0001994;
RA   Zybailov B., Rutschow H., Friso G., Rudella A., Emanuelsson O.,
RA   Sun Q., van Wijk K.J.;
RT   "Sorting signals, N-terminal modifications and abundance of the
RT   chloroplast proteome.";
RL   PLoS ONE 3:E1994-E1994(2008).
RN   [9]
RP   REVIEW.
RX   PubMed=20541498; DOI=10.1016/j.cub.2010.03.047;
RA   Lee D.K., Sieburth L.E.;
RT   "Plasmodesmata formation: poking holes in walls with ise.";
RL   Curr. Biol. 20:R488-R490(2010).
RN   [10]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=20434343; DOI=10.1016/j.cub.2010.03.064;
RA   Burch-Smith T.-M., Zambryski P.C.;
RT   "Loss of INCREASED SIZE EXCLUSION LIMIT (ISE)1 or ISE2 increases the
RT   formation of secondary plasmodesmata.";
RL   Curr. Biol. 20:989-993(2010).
RN   [11]
RP   SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX   PubMed=22106293; DOI=10.1073/pnas.1117226108;
RA   Burch-Smith T.M., Brunkard J.O., Choi Y.G., Zambryski P.C.;
RT   "Organelle-nucleus cross-talk regulates plant intercellular
RT   communication via plasmodesmata.";
RL   Proc. Natl. Acad. Sci. U.S.A. 108:E1451-E1460(2011).
RN   [12]
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
RT   family in Zea mays and Glycine max: a comparison with Arabidopsis and
RT   Oryza sativa.";
RL   PLoS ONE 8:E78982-E78982(2013).
RN   [13]
RP   SUBCELLULAR LOCATION, AND FUNCTION.
RX   PubMed=26147377; DOI=10.1111/pce.12603;
RA   Carlotto N., Wirth S., Furman N., Ferreyra Solari N., Ariel F.,
RA   Crespi M., Kobayashi K.;
RT   "The chloroplastic DEVH-box RNA helicase INCREASED SIZE EXCLUSION
RT   LIMIT 2 involved in plasmodesmata regulation is required for group II
RT   intron splicing.";
RL   Plant Cell Environ. 39:165-173(2016).
CC   -!- FUNCTION: RNA helicase involved in group II intron splicing
CC       (PubMed:26147377). Essential protein required during
CC       embryogenesis. Involved in post-transcriptional gene silencing.
CC       Modulates the determination of cell fate. Necessary for normal
CC       plasmodesmata (PD) development and aperture regulation.
CC       {ECO:0000269|PubMed:11779812, ECO:0000269|PubMed:11874921,
CC       ECO:0000269|PubMed:17601829, ECO:0000269|PubMed:20434343,
CC       ECO:0000269|PubMed:26147377}.
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: Plastid, chloroplast
CC       {ECO:0000269|PubMed:18431481, ECO:0000269|PubMed:22106293,
CC       ECO:0000269|PubMed:26147377}. Cytoplasmic granule
CC       {ECO:0000269|PubMed:17601829}. Note=Localizes to granule-like
CC       structures, probably stress granules (SGs), which number increases
CC       upon stress. {ECO:0000269|PubMed:17601829}.
CC   -!- DISRUPTION PHENOTYPE: Embryogenesis arrested at cotyledon stage.
CC       Altered size exclusion limit of PD; abnormally maintained dilated
CC       PD at the torpedo stage, and increased formation of secondary
CC       branched PD. Chlorosis. Altered plastid development.
CC       {ECO:0000269|PubMed:11779812, ECO:0000269|PubMed:11874921,
CC       ECO:0000269|PubMed:20434343, ECO:0000269|PubMed:22106293}.
CC   -!- SIMILARITY: Belongs to the DExH box helicase family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAB61106.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
DR   EMBL; AC002062; AAB61106.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002684; AEE35013.1; -; Genomic_DNA.
DR   EMBL; AK316759; BAH19480.1; -; mRNA.
DR   EMBL; AF387007; AAK62452.1; -; mRNA.
DR   PIR; D96723; D96723.
DR   RefSeq; NP_177164.1; NM_105675.2.
DR   SMR; B9DFG3; -.
DR   BioGrid; 28564; 4.
DR   STRING; 3702.AT1G70070.1; -.
DR   iPTMnet; B9DFG3; -.
DR   PaxDb; B9DFG3; -.
DR   PRIDE; B9DFG3; -.
DR   EnsemblPlants; AT1G70070.1; AT1G70070.1; AT1G70070.
DR   GeneID; 843343; -.
DR   Gramene; AT1G70070.1; AT1G70070.1; AT1G70070.
DR   KEGG; ath:AT1G70070; -.
DR   Araport; AT1G70070; -.
DR   TAIR; locus:2020573; AT1G70070.
DR   eggNOG; KOG0947; Eukaryota.
DR   eggNOG; COG4581; LUCA.
DR   HOGENOM; HOG000245391; -.
DR   InParanoid; B9DFG3; -.
DR   OMA; CAMDDGD; -.
DR   OrthoDB; 176060at2759; -.
DR   PhylomeDB; B9DFG3; -.
DR   PRO; PR:B9DFG3; -.
DR   Proteomes; UP000006548; Chromosome 1.
DR   ExpressionAtlas; B9DFG3; baseline and differential.
DR   Genevisible; B9DFG3; AT.
DR   GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
DR   GO; GO:0009570; C:chloroplast stroma; IDA:TAIR.
DR   GO; GO:0010494; C:cytoplasmic stress granule; IDA:TAIR.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; IDA:UniProtKB.
DR   GO; GO:0003724; F:RNA helicase activity; ISS:TAIR.
DR   GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
DR   GO; GO:0031047; P:gene silencing by RNA; IEA:UniProtKB-KW.
DR   GO; GO:0000373; P:Group II intron splicing; IMP:UniProtKB.
DR   GO; GO:0006397; P:mRNA processing; IMP:UniProtKB.
DR   GO; GO:0010497; P:plasmodesmata-mediated intercellular transport; IMP:TAIR.
DR   GO; GO:0016441; P:posttranscriptional gene silencing; IMP:TAIR.
DR   InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR   InterPro; IPR014001; Helicase_ATP-bd.
DR   InterPro; IPR001650; Helicase_C.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR012961; Ski2_C.
DR   Pfam; PF00270; DEAD; 1.
DR   Pfam; PF08148; DSHCT; 1.
DR   SMART; SM00487; DEXDc; 1.
DR   SMART; SM01142; DSHCT; 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; Chloroplast; Complete proteome; Helicase; Hydrolase;
KW   mRNA processing; mRNA splicing; Nucleotide-binding; Plastid;
KW   Reference proteome; RNA-binding; RNA-mediated gene silencing;
KW   Transit peptide.
FT   TRANSIT       1     58       Chloroplast. {ECO:0000255}.
FT   CHAIN        59   1171       DExH-box ATP-dependent RNA helicase
FT                                DExH15 chloroplastic.
FT                                /FTId=PRO_0000395028.
FT   DOMAIN      163    327       Helicase ATP-binding.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00541}.
FT   DOMAIN      424    620       Helicase C-terminal.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00542}.
FT   NP_BIND     176    183       ATP. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00541}.
FT   MOTIF       275    278       DEVH box. {ECO:0000305}.
FT   COMPBIAS     67    102       Asp-rich.
FT   MUTAGEN     275    275       D->N: In emb25, ise2-2; embryo
FT                                development arrested at cotyledon stage,
FT                                abnormal PD regulation end development.
FT                                {ECO:0000269|PubMed:17601829}.
FT   CONFLICT    234    234       A -> D (in Ref. 4; AAK62452).
FT                                {ECO:0000305}.
FT   CONFLICT    395    395       D -> N (in Ref. 3; BAH19480).
FT                                {ECO:0000305}.
SQ   SEQUENCE   1171 AA;  132437 MW;  34668CF0D4A03EFB CRC64;
     MNTLPVVSLT ASSSFKFFHF PSLHRSLSHS PNFSFTKSLI LNPNHLSFKS TLNSLSPSQS
     QLYEEEDDEE EEEEDEDDDD EAADEYDNIS DEIRNSDDDD DDEETEFSVD LPTESARERV
     EFRWQRVEKL RSLVRDFGVE MIDIDELISI YDFRIDKFQR LAIEAFLRGS SVVVSAPTSS
     GKTLIAEAAA VSTVAKGRRL FYTTPLKALS NQKFREFRET FGDDNVGLLT GDSAINKDAQ
     IVIMTTEILR NMLYQSVGMA SSGTGLFHVD AIVLDEVHYL SDISRGTVWE EIVIYCPKEV
     QLICLSATVA NPDELAGWIG EIHGKTELVT STRRPVPLTW YFSTKHSLLP LLDEKGINVN
     RKLSLNYLQL SASEARFRDD DDGYRKRRSK KRGGDTSYNN LVNVTDYPLS KNEINKIRRS
     QVPQISDTLW HLQGKNMLPA IWFIFNRRGC DAAVQYVENF QLLDDCEKSE VELALKKFRV
     LYPDAVRESA EKGLLRGIAA HHAGCLPLWK SFIEELFQRG LVKVVFATET LAAGINMPAR
     TAVISSLSKK AGNERIELGP NELYQMAGRA GRRGIDEKGY TVLVQTAFEG AEECCKLVFA
     GVKPLVSQFT ASYGMVLNLV AGSKVTRKSS GTEAGKVLQA GRSLEEAKKL VEKSFGNYVS
     SNVTVAAKQE LAEIDNKIEI LSSEISDEAI DKKSRKLLSA RDYKEITVLK EELREEKRKR
     AEQRRRMELE RFLALKPLLK GMEEGNLPFI CLEFKDSEGR EQSVPAVYLG HIDSFQGSKL
     QKMMSLDESF ALNLIEDELA ADEPGKPNVK PSYYVALGSD NSWYLFTEKW VRTVYRTGFP
     NIALALGDAL PREIMKNLLD KADMQWDKLA ESELGSLWRL EGSLETWSWS LNVPVLSSLS
     DEDEVLHMSE EYDNAAQKYK EQRSKISRLK KKMSRSEGFR EYKKILENAN LTVEKMKRLK
     ARSRRLINRL EQIEPSGWKD FMRISNVIHE SRALDINTHL IFPLGETAAA IRGENELWLA
     MVLRNKALVD LKPPQLAGVC ASLVSEGIKV RPWRDNNYIY EPSDTVVDMV NFLEDQRSSL
     IKLQEKHEVM IPCCLDVQFS GMVEAWASGL SWKEMMMECA MDEGDLARLL RRTIDLLAQI
     PKLPDIDPVL QRSAAAAADI MDRPPISELA G
//
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