IP5PD_ARATH
ID IP5PD_ARATH Reviewed; 1136 AA.
AC Q9SYK4; F4IAA0; Q712D7;
DT 20-JAN-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=Type I inositol polyphosphate 5-phosphatase 13 {ECO:0000303|PubMed:15574849};
DE Short=At5PTase13 {ECO:0000303|PubMed:15574849};
DE EC=3.1.3.56 {ECO:0000269|PubMed:15574849};
GN Name=IP5P13 {ECO:0000305};
GN Synonyms=5PTASE13 {ECO:0000303|PubMed:22573619}, IPP6;
GN OrderedLocusNames=At1g05630 {ECO:0000312|Araport:AT1G05630};
GN ORFNames=F3F20.8 {ECO:0000312|EMBL:AAD30615.1};
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] (ISOFORM 1), FUNCTION, TISSUE
RP SPECIFICITY, INDUCTION, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP CATALYTIC ACTIVITY.
RC STRAIN=cv. Columbia;
RX PubMed=15574849; DOI=10.1093/pcp/pch187;
RA Zhong R., Ye Z.-H.;
RT "Molecular and biochemical characterization of three WD-repeat-domain-
RT containing inositol polyphosphate 5-phosphatases in Arabidopsis thaliana.";
RL Plant Cell Physiol. 45:1720-1728(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION, TISSUE SPECIFICITY,
RP DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia; TISSUE=Hypocotyl;
RX PubMed=16299182; DOI=10.1104/pp.105.067140;
RA Lin W.-H., Wang Y., Mueller-Roeber B., Brearley C.A., Xu Z.-H., Xue H.-W.;
RT "At5PTase13 modulates cotyledon vein development through regulating auxin
RT homeostasis.";
RL Plant Physiol. 139:1677-1691(2005).
RN [3]
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 [4]
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 [5]
RP GENE FAMILY.
RX PubMed=11402208; DOI=10.1104/pp.126.2.801;
RA Berdy S.E., Kudla J., Gruissem W., Gillaspy G.E.;
RT "Molecular characterization of At5PTase1, an inositol phosphatase capable
RT of terminating inositol trisphosphate signaling.";
RL Plant Physiol. 126:801-810(2001).
RN [6]
RP FUNCTION, INDUCTION, DISRUPTION PHENOTYPE, AND LACK OF INTERACTION WITH
RP PHOT1.
RC STRAIN=cv. Columbia;
RX PubMed=18252844; DOI=10.1105/tpc.107.052670;
RA Chen X., Lin W.-H., Wang Y., Luan S., Xue H.-W.;
RT "An inositol polyphosphate 5-phosphatase functions in PHOTOTROPIN1
RT signaling in Arabidopis by altering cytosolic Ca2+.";
RL Plant Cell 20:353-366(2008).
RN [7]
RP INTERACTION WITH KIN10, FUNCTION, DISRUPTION PHENOTYPE, AND SUBCELLULAR
RP LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=18931139; DOI=10.1104/pp.108.130575;
RA Ananieva E.A., Gillaspy G.E., Ely A., Burnette R.N., Erickson F.L.;
RT "Interaction of the WD40 domain of a myoinositol polyphosphate 5-
RT phosphatase with SnRK1 links inositol, sugar, and stress signaling.";
RL Plant Physiol. 148:1868-1882(2008).
RN [8]
RP DISRUPTION PHENOTYPE, AND FUNCTION.
RX PubMed=19736566; DOI=10.1038/cr.2009.105;
RA Wang Y., Lin W.H., Chen X., Xue H.W.;
RT "The role of Arabidopsis 5PTase13 in root gravitropism through modulation
RT of vesicle trafficking.";
RL Cell Res. 19:1191-1204(2009).
RN [9]
RP DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, AND FUNCTION.
RX PubMed=22573619; DOI=10.1242/dev.081224;
RA Wang Y., Chu Y.J., Xue H.W.;
RT "Inositol polyphosphate 5-phosphatase-controlled Ins(1,4,5)P3/Ca2+ is
RT crucial for maintaining pollen dormancy and regulating early germination of
RT pollen.";
RL Development 139:2221-2233(2012).
CC -!- FUNCTION: Converts inositol 1,4,5-trisphosphate (Ins(1,4,5)P3) to
CC inositol 1,4-bisphosphate. Modulates cotyledon vein development through
CC regulating auxin homeostasis. Involved in blue light responses.
CC Decreases the amount of KIN10 degraded by the proteasome under low
CC nutrient conditions. Participates with IP5P12 in the control of
CC Ins(1,4,5)P3/Ca(2+) levels that is crucial for maintaining pollen
CC dormancy and regulating early germination of pollen. May modulate auxin
CC transport by regulating vesicle trafficking and thereby plays a role in
CC root gravitropism. {ECO:0000269|PubMed:15574849,
CC ECO:0000269|PubMed:16299182, ECO:0000269|PubMed:18252844,
CC ECO:0000269|PubMed:18931139, ECO:0000269|PubMed:19736566,
CC ECO:0000269|PubMed:22573619}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1D-myo-inositol 1,4,5-trisphosphate + H2O = 1D-myo-inositol
CC 1,4-bisphosphate + phosphate; Xref=Rhea:RHEA:19797,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:43474, ChEBI:CHEBI:58282,
CC ChEBI:CHEBI:203600; EC=3.1.3.56;
CC Evidence={ECO:0000269|PubMed:15574849};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:15574849};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=651 uM for Ins(1,4,5)P3 {ECO:0000269|PubMed:15574849};
CC -!- SUBUNIT: Interacts with KIN10, but not with PHOT1.
CC {ECO:0000269|PubMed:18931139}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:18931139}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9SYK4-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9SYK4-2; Sequence=VSP_036161;
CC -!- TISSUE SPECIFICITY: Expressed in young seedlings and flowers. Highly
CC expressed in anther and pollen grains, but not in pistils. Not detected
CC in maturated roots, stems and rosette leaves.
CC {ECO:0000269|PubMed:15574849, ECO:0000269|PubMed:16299182,
CC ECO:0000269|PubMed:22573619}.
CC -!- DEVELOPMENTAL STAGE: Detected in cotyledons prior to seed germination.
CC Restricted to the cotyledon tip until 2 days after seed germination and
CC then detected in the cotyledon or cotyledon veins on days 3 to 7.
CC {ECO:0000269|PubMed:16299182}.
CC -!- INDUCTION: By abscisic acid, wounding and at a lower level, by cold and
CC salt treatment. Down-regulated by blue light irradiation.
CC {ECO:0000269|PubMed:15574849, ECO:0000269|PubMed:18252844}.
CC -!- DOMAIN: The WD40 domain (1-533) is interacting with KIN10.
CC -!- DISRUPTION PHENOTYPE: Defect in development of the cotyledon veins.
CC Altered auxin homeostasis and reduced abscisic acid sensitivity.
CC Shortened hypocotyls and expanded cotyledons in response to blue light
CC irradiation. Precocious pollen germination within anthers. Elevated
CC sensitivity to gravistimulation in root gravitropic responses.
CC {ECO:0000269|PubMed:16299182, ECO:0000269|PubMed:18252844,
CC ECO:0000269|PubMed:18931139, ECO:0000269|PubMed:19736566,
CC ECO:0000269|PubMed:22573619}.
CC -!- SIMILARITY: Belongs to the inositol polyphosphate 5-phosphatase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAC82096.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AY761188; AAV87315.1; -; mRNA.
DR EMBL; AY761192; AAV87319.1; -; Genomic_DNA.
DR EMBL; AC007153; AAD30615.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE27868.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE27869.1; -; Genomic_DNA.
DR EMBL; AJ297426; CAC82096.1; ALT_FRAME; mRNA.
DR PIR; D86190; D86190.
DR RefSeq; NP_001030976.1; NM_001035899.2. [Q9SYK4-1]
DR RefSeq; NP_172054.3; NM_100443.5. [Q9SYK4-2]
DR AlphaFoldDB; Q9SYK4; -.
DR SMR; Q9SYK4; -.
DR BioGRID; 22311; 1.
DR IntAct; Q9SYK4; 1.
DR STRING; 3702.AT1G05630.1; -.
DR iPTMnet; Q9SYK4; -.
DR PaxDb; Q9SYK4; -.
DR PRIDE; Q9SYK4; -.
DR ProteomicsDB; 238945; -. [Q9SYK4-1]
DR EnsemblPlants; AT1G05630.1; AT1G05630.1; AT1G05630. [Q9SYK4-2]
DR EnsemblPlants; AT1G05630.2; AT1G05630.2; AT1G05630. [Q9SYK4-1]
DR GeneID; 837069; -.
DR Gramene; AT1G05630.1; AT1G05630.1; AT1G05630. [Q9SYK4-2]
DR Gramene; AT1G05630.2; AT1G05630.2; AT1G05630. [Q9SYK4-1]
DR KEGG; ath:AT1G05630; -.
DR Araport; AT1G05630; -.
DR TAIR; locus:2031933; AT1G05630.
DR eggNOG; KOG0565; Eukaryota.
DR InParanoid; Q9SYK4; -.
DR OrthoDB; 106112at2759; -.
DR PhylomeDB; Q9SYK4; -.
DR BioCyc; ARA:AT1G05630-MON; -.
DR BioCyc; MetaCyc:AT1G05630-MON; -.
DR BRENDA; 3.1.3.36; 399.
DR BRENDA; 3.1.3.56; 399.
DR SABIO-RK; Q9SYK4; -.
DR PRO; PR:Q9SYK4; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9SYK4; baseline and differential.
DR Genevisible; Q9SYK4; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0052659; F:inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0052658; F:inositol-1,4,5-trisphosphate 5-phosphatase activity; IDA:TAIR.
DR GO; GO:0004445; F:inositol-polyphosphate 5-phosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004439; F:phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity; IBA:GO_Central.
DR GO; GO:0010252; P:auxin homeostasis; IMP:TAIR.
DR GO; GO:0009630; P:gravitropism; IMP:UniProtKB.
DR GO; GO:0046855; P:inositol phosphate dephosphorylation; IDA:TAIR.
DR GO; GO:0010087; P:phloem or xylem histogenesis; IMP:TAIR.
DR GO; GO:0046856; P:phosphatidylinositol dephosphorylation; IBA:GO_Central.
DR GO; GO:0009846; P:pollen germination; IGI:UniProtKB.
DR GO; GO:0009737; P:response to abscisic acid; IMP:TAIR.
DR GO; GO:0009637; P:response to blue light; IMP:TAIR.
DR GO; GO:0009743; P:response to carbohydrate; IMP:TAIR.
DR GO; GO:0007584; P:response to nutrient; IMP:TAIR.
DR GO; GO:0009611; P:response to wounding; IEP:TAIR.
DR GO; GO:0048364; P:root development; IMP:TAIR.
DR GO; GO:0010182; P:sugar mediated signaling pathway; IMP:TAIR.
DR Gene3D; 2.130.10.10; -; 2.
DR Gene3D; 3.60.10.10; -; 1.
DR InterPro; IPR036691; Endo/exonu/phosph_ase_sf.
DR InterPro; IPR005135; Endo/exonuclease/phosphatase.
DR InterPro; IPR000300; IPPc.
DR InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR InterPro; IPR001680; WD40_repeat.
DR Pfam; PF03372; Exo_endo_phos; 1.
DR SMART; SM00128; IPPc; 1.
DR SMART; SM00320; WD40; 4.
DR SUPFAM; SSF56219; SSF56219; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Hydrolase; Isopeptide bond; Magnesium; Metal-binding;
KW Nucleus; Reference proteome; Repeat; Ubl conjugation; WD repeat.
FT CHAIN 1..1136
FT /note="Type I inositol polyphosphate 5-phosphatase 13"
FT /id="PRO_0000359743"
FT REPEAT 147..185
FT /note="WD 1"
FT REPEAT 205..244
FT /note="WD 2"
FT REPEAT 259..297
FT /note="WD 3"
FT REPEAT 436..475
FT /note="WD 4"
FT REPEAT 515..552
FT /note="WD 5"
FT REGION 782..798
FT /note="Catalytic 1"
FT /evidence="ECO:0000250|UniProtKB:Q84MA2"
FT REGION 861..876
FT /note="Catalytic 2"
FT /evidence="ECO:0000250|UniProtKB:Q84MA2"
FT REGION 1104..1136
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1104..1120
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1121..1136
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CROSSLNK 940
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000250|UniProtKB:O80560"
FT VAR_SEQ 750
FT /note="A -> AAGMVPYLFLSCSLGFSTYLFWLLYSSGLPWALSL (in isoform
FT 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_036161"
FT CONFLICT 739
FT /note="V -> I (in Ref. 3; CAC82096)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1136 AA; 125698 MW; 4E90EE8E43900687 CRC64;
MDSLIIEEED EEALATLVPV PPRRKTHSYS LQFDHKPHHQ IRKHSLDEVP RSATLASEAV
YFDSSDDEFS TGGNITENAA DETNAGAEEY TIVNPPPNVG LGDDDTEPLP EFIGAGGGSG
IFKVPVRAAV HPGRPPCLEL RPHPLRETQT GRFLRNIACT ETQLWAGQEN GIRFWNLEDA
YEAGCGIGGQ VPRGDEDTAP FHESVTTSPT MCLVADQSNK LLWSGHKDGK IRAWKMDQSS
VSHDDDDSDP FKERVSWLAH RGPVNSIVIS SYGDMWSCSE GGVIKIWPWD TLEKSLLLKP
EEKHMAALLV ERSAIDLRSQ VTVNGTCSIS SSEVKFLLAD SVRAKVWAVQ SLSFSIWDAR
SKDLLKVLNV DGQVENRGDL PPIQDQQVDD EMKLKFFSAS KREKPQGFLQ RSRNAIMGAA
GAVRRVATRS AGAFSEDTRK TEAIVLAVDG TIWTGSISGL IVQWDGNGNR LRDVNHHHRP
VLCFCTFGDR IYVGYASGYI QVLDLDGKLI SSWVSHNEPV IKLAAGGGFI FSLATHGGVR
GWYVTSPGPL DNIIRTELSQ KETLYARQDN VRILIGTWNV GQGRASHDAL MSWLGSVTSD
VGIVAVGLQE VEMGAGFLAM SAAKETVGLE GSAVGQWWID AIGKALDEKN TFERMGSRQL
AGLLISLWAR KDIRTHVGDL DVAAVPCGFG RAIGNKGGVG LRIRVYDRIM CFVNCHLAAH
LEAVNRRNAD FNHIFRLMVF SRGQNLSNAA AAGVSTSAYT TKSNTIPSTG AEEIKSDLAA
ADMVAFFGDF NYRLFGITYD EARDFISQRS FDWLRERDQL RAEMKVGKVF QGMREALITF
PPTYKFERNR SGLGGYDSGE KKRIPAWCDR VIYRDTQSSP FSESNLQCPV VSSVIMYEAC
MDVTESDHKP VRCKFHATIA HVDKSVRRQE LGKIIRSNEK ILSIFEDLRF VPETSVSTNN
IVLQSQDTVI LTITNNSPTS QAIFNILCGG QAVVKDDGED ADYNPRGSFG LPRWLEVSPA
AGIINPEGSV DVKVHHEDFY SMEEYVDGIP QNWWCEDTRD KEAILMVNIR GSCSTTLRSH
SVKVRHCFSA RVCLLENRPT NLTKNLGGSR RYPTDITRNG STRPRTEDSV RRGKSR
