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Type I inositol polyphosphate 5-phosphatase 13 (At5PTase13) (EC 3.1.3.56)

 IP5PD_ARATH             Reviewed;        1136 AA.
Q9SYK4; F4IAA0; Q712D7;
20-JAN-2009, integrated into UniProtKB/Swiss-Prot.
01-MAY-2000, sequence version 1.
18-JUL-2018, entry version 140.
RecName: Full=Type I inositol polyphosphate 5-phosphatase 13 {ECO:0000303|PubMed:15574849};
Short=At5PTase13 {ECO:0000303|PubMed:15574849};
EC=3.1.3.56 {ECO:0000269|PubMed:15574849};
Name=IP5P13 {ECO:0000305};
Synonyms=5PTASE13 {ECO:0000303|PubMed:22573619}, IPP6;
OrderedLocusNames=At1g05630 {ECO:0000312|Araport:AT1G05630};
ORFNames=F3F20.8 {ECO:0000312|EMBL:AAD30615.1};
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1), FUNCTION, TISSUE
SPECIFICITY, INDUCTION, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND
CATALYTIC ACTIVITY.
STRAIN=cv. Columbia;
PubMed=15574849; DOI=10.1093/pcp/pch187;
Zhong R., Ye Z.-H.;
"Molecular and biochemical characterization of three WD-repeat-domain-
containing inositol polyphosphate 5-phosphatases in Arabidopsis
thaliana.";
Plant Cell Physiol. 45:1720-1728(2004).
[2]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION, TISSUE SPECIFICITY,
DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
STRAIN=cv. Columbia; TISSUE=Hypocotyl;
PubMed=16299182; DOI=10.1104/pp.105.067140;
Lin W.-H., Wang Y., Mueller-Roeber B., Brearley C.A., Xu Z.-H.,
Xue H.-W.;
"At5PTase13 modulates cotyledon vein development through regulating
auxin homeostasis.";
Plant Physiol. 139:1677-1691(2005).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130712; DOI=10.1038/35048500;
Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S.,
White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y.,
Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W.,
Chung M.K., Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K.,
Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y.,
Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L.,
Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E.,
Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B.,
Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P.,
Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A.,
Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I.,
Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D.,
Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M.,
Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M.,
Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.;
"Sequence and analysis of chromosome 1 of the plant Arabidopsis
thaliana.";
Nature 408:816-820(2000).
[4]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[5]
GENE FAMILY.
PubMed=11402208; DOI=10.1104/pp.126.2.801;
Berdy S.E., Kudla J., Gruissem W., Gillaspy G.E.;
"Molecular characterization of At5PTase1, an inositol phosphatase
capable of terminating inositol trisphosphate signaling.";
Plant Physiol. 126:801-810(2001).
[6]
FUNCTION, INDUCTION, DISRUPTION PHENOTYPE, AND LACK OF INTERACTION
WITH PHOT1.
STRAIN=cv. Columbia;
PubMed=18252844; DOI=10.1105/tpc.107.052670;
Chen X., Lin W.-H., Wang Y., Luan S., Xue H.-W.;
"An inositol polyphosphate 5-phosphatase functions in PHOTOTROPIN1
signaling in Arabidopis by altering cytosolic Ca2+.";
Plant Cell 20:353-366(2008).
[7]
INTERACTION WITH KIN10, FUNCTION, DISRUPTION PHENOTYPE, AND
SUBCELLULAR LOCATION.
STRAIN=cv. Columbia;
PubMed=18931139; DOI=10.1104/pp.108.130575;
Ananieva E.A., Gillaspy G.E., Ely A., Burnette R.N., Erickson F.L.;
"Interaction of the WD40 domain of a myoinositol polyphosphate 5-
phosphatase with SnRK1 links inositol, sugar, and stress signaling.";
Plant Physiol. 148:1868-1882(2008).
[8]
DISRUPTION PHENOTYPE, AND FUNCTION.
PubMed=19736566; DOI=10.1038/cr.2009.105;
Wang Y., Lin W.H., Chen X., Xue H.W.;
"The role of Arabidopsis 5PTase13 in root gravitropism through
modulation of vesicle trafficking.";
Cell Res. 19:1191-1204(2009).
[9]
DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, AND FUNCTION.
PubMed=22573619; DOI=10.1242/dev.081224;
Wang Y., Chu Y.J., Xue H.W.;
"Inositol polyphosphate 5-phosphatase-controlled Ins(1,4,5)P3/Ca2+ is
crucial for maintaining pollen dormancy and regulating early
germination of pollen.";
Development 139:2221-2233(2012).
-!- FUNCTION: Converts inositol 1,4,5-trisphosphate (Ins(1,4,5)P3) to
inositol 1,4-bisphosphate. Modulates cotyledon vein development
through regulating auxin homeostasis. Involved in blue light
responses. Decreases the amount of KIN10 degraded by the
proteasome under low nutrient conditions. Participates with IP5P12
in the control of Ins(1,4,5)P3/Ca(2+) levels that is crucial for
maintaining pollen dormancy and regulating early germination of
pollen. May modulate auxin transport by regulating vesicle
trafficking and thereby plays a role in root gravitropism.
{ECO:0000269|PubMed:15574849, ECO:0000269|PubMed:16299182,
ECO:0000269|PubMed:18252844, ECO:0000269|PubMed:18931139,
ECO:0000269|PubMed:19736566, ECO:0000269|PubMed:22573619}.
-!- CATALYTIC ACTIVITY: D-myo-inositol 1,4,5-trisphosphate + H(2)O =
myo-inositol 1,4-bisphosphate + phosphate.
{ECO:0000269|PubMed:15574849}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:15574849};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=651 uM for Ins(1,4,5)P3 {ECO:0000269|PubMed:15574849};
-!- SUBUNIT: Interacts with KIN10, but not with PHOT1.
{ECO:0000269|PubMed:18931139}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:18931139}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q9SYK4-1; Sequence=Displayed;
Name=2;
IsoId=Q9SYK4-2; Sequence=VSP_036161;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: Expressed in young seedlings and flowers.
Highly expressed in anther and pollen grains, but not in pistils.
Not detected in maturated roots, stems and rosette leaves.
{ECO:0000269|PubMed:15574849, ECO:0000269|PubMed:16299182,
ECO:0000269|PubMed:22573619}.
-!- DEVELOPMENTAL STAGE: Detected in cotyledons prior to seed
germination. Restricted to the cotyledon tip until 2 days after
seed germination and then detected in the cotyledon or cotyledon
veins on days 3 to 7. {ECO:0000269|PubMed:16299182}.
-!- INDUCTION: By abscisic acid, wounding and at a lower level, by
cold and salt treatment. Down-regulated by blue light irradiation.
{ECO:0000269|PubMed:15574849, ECO:0000269|PubMed:18252844}.
-!- DOMAIN: The WD40 domain (1-533) is interacting with KIN10.
-!- DISRUPTION PHENOTYPE: Defect in development of the cotyledon
veins. Altered auxin homeostasis and reduced abscisic acid
sensitivity. Shortened hypocotyls and expanded cotyledons in
response to blue light irradiation. Precocious pollen germination
within anthers. Elevated sensitivity to gravistimulation in root
gravitropic responses. {ECO:0000269|PubMed:16299182,
ECO:0000269|PubMed:18252844, ECO:0000269|PubMed:18931139,
ECO:0000269|PubMed:19736566, ECO:0000269|PubMed:22573619}.
-!- SIMILARITY: Belongs to the inositol polyphosphate 5-phosphatase
family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=CAC82096.1; Type=Frameshift; Positions=1051; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AY761188; AAV87315.1; -; mRNA.
EMBL; AY761192; AAV87319.1; -; Genomic_DNA.
EMBL; AC007153; AAD30615.1; -; Genomic_DNA.
EMBL; CP002684; AEE27868.1; -; Genomic_DNA.
EMBL; CP002684; AEE27869.1; -; Genomic_DNA.
EMBL; AJ297426; CAC82096.1; ALT_FRAME; mRNA.
PIR; D86190; D86190.
RefSeq; NP_001030976.1; NM_001035899.2. [Q9SYK4-1]
RefSeq; NP_172054.3; NM_100443.5. [Q9SYK4-2]
UniGene; At.42385; -.
ProteinModelPortal; Q9SYK4; -.
BioGrid; 22311; 1.
IntAct; Q9SYK4; 1.
STRING; 3702.AT1G05630.1; -.
iPTMnet; Q9SYK4; -.
PaxDb; Q9SYK4; -.
PRIDE; Q9SYK4; -.
EnsemblPlants; AT1G05630.1; AT1G05630.1; AT1G05630. [Q9SYK4-2]
EnsemblPlants; AT1G05630.2; AT1G05630.2; AT1G05630. [Q9SYK4-1]
GeneID; 837069; -.
Gramene; AT1G05630.1; AT1G05630.1; AT1G05630. [Q9SYK4-2]
Gramene; AT1G05630.2; AT1G05630.2; AT1G05630. [Q9SYK4-1]
KEGG; ath:AT1G05630; -.
Araport; AT1G05630; -.
TAIR; locus:2031933; AT1G05630.
eggNOG; KOG0565; Eukaryota.
eggNOG; COG5411; LUCA.
HOGENOM; HOG000242921; -.
InParanoid; Q9SYK4; -.
OMA; PTNLTKN; -.
OrthoDB; EOG093600RQ; -.
PhylomeDB; Q9SYK4; -.
BioCyc; ARA:AT1G05630-MONOMER; -.
BioCyc; MetaCyc:AT1G05630-MONOMER; -.
BRENDA; 3.1.3.36; 399.
BRENDA; 3.1.3.56; 399.
Reactome; R-ATH-1660499; Synthesis of PIPs at the plasma membrane.
Reactome; R-ATH-1855183; Synthesis of IP2, IP, and Ins in the cytosol.
Reactome; R-ATH-1855204; Synthesis of IP3 and IP4 in the cytosol.
PRO; PR:Q9SYK4; -.
Proteomes; UP000006548; Chromosome 1.
ExpressionAtlas; Q9SYK4; baseline and differential.
Genevisible; Q9SYK4; AT.
GO; GO:0005634; C:nucleus; IDA:TAIR.
GO; GO:0052659; F:inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity; IEA:UniProtKB-EC.
GO; GO:0052658; F:inositol-1,4,5-trisphosphate 5-phosphatase activity; IDA:TAIR.
GO; GO:0004445; F:inositol-polyphosphate 5-phosphatase activity; IEA:UniProtKB-EC.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0010252; P:auxin homeostasis; IMP:TAIR.
GO; GO:0009630; P:gravitropism; IMP:UniProtKB.
GO; GO:0046855; P:inositol phosphate dephosphorylation; IDA:TAIR.
GO; GO:0010087; P:phloem or xylem histogenesis; IMP:TAIR.
GO; GO:0046856; P:phosphatidylinositol dephosphorylation; IEA:InterPro.
GO; GO:0009846; P:pollen germination; IGI:UniProtKB.
GO; GO:0009737; P:response to abscisic acid; IMP:TAIR.
GO; GO:0009637; P:response to blue light; IMP:TAIR.
GO; GO:0009743; P:response to carbohydrate; IMP:TAIR.
GO; GO:0007584; P:response to nutrient; IMP:TAIR.
GO; GO:0009611; P:response to wounding; IEP:TAIR.
GO; GO:0048364; P:root development; IMP:TAIR.
GO; GO:0010182; P:sugar mediated signaling pathway; IMP:TAIR.
Gene3D; 2.130.10.10; -; 2.
Gene3D; 3.60.10.10; -; 1.
InterPro; IPR036691; Endo/exonu/phosph_ase_sf.
InterPro; IPR005135; Endo/exonuclease/phosphatase.
InterPro; IPR000300; IPPc.
InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
InterPro; IPR001680; WD40_repeat.
Pfam; PF03372; Exo_endo_phos; 1.
SMART; SM00128; IPPc; 1.
SMART; SM00320; WD40; 4.
SUPFAM; SSF56219; SSF56219; 2.
1: Evidence at protein level;
Alternative splicing; Complete proteome; Hydrolase; Isopeptide bond;
Magnesium; Metal-binding; Nucleus; Reference proteome; Repeat;
Ubl conjugation; WD repeat.
CHAIN 1 1136 Type I inositol polyphosphate 5-
phosphatase 13.
/FTId=PRO_0000359743.
REPEAT 147 185 WD 1.
REPEAT 205 244 WD 2.
REPEAT 259 297 WD 3.
REPEAT 436 475 WD 4.
REPEAT 515 552 WD 5.
REGION 782 798 Catalytic 1.
{ECO:0000250|UniProtKB:Q84MA2}.
REGION 861 876 Catalytic 2.
{ECO:0000250|UniProtKB:Q84MA2}.
CROSSLNK 940 940 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in ubiquitin).
{ECO:0000250|UniProtKB:O80560}.
VAR_SEQ 750 750 A -> AAGMVPYLFLSCSLGFSTYLFWLLYSSGLPWALSL
(in isoform 2). {ECO:0000305}.
/FTId=VSP_036161.
CONFLICT 739 739 V -> I (in Ref. 3; CAC82096).
{ECO:0000305}.
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


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