IPYR1_ARATH
ID IPYR1_ARATH Reviewed; 212 AA.
AC Q93V56; Q9MAM9;
DT 04-FEB-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Soluble inorganic pyrophosphatase 1 {ECO:0000303|PubMed:15135060};
DE EC=3.6.1.1 {ECO:0000269|Ref.9};
DE AltName: Full=Pyrophosphate phospho-hydrolase 1 {ECO:0000303|PubMed:15135060};
DE Short=PPase 1 {ECO:0000303|PubMed:15135060};
GN Name=PPA1 {ECO:0000303|PubMed:15135060};
GN OrderedLocusNames=At1g01050 {ECO:0000312|Araport:AT1G01050};
GN ORFNames=T25K16.5 {ECO:0000312|EMBL:AAL38377.1};
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 {ECO:0000312|EMBL:AAL15299.1};
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Fujita M., Mizukado S., Seki M., Shinozaki K., Mitsuda N., Takiguchi Y.,
RA Takagi M.;
RT "ORF cloning and analysis of Arabidopsis transcription factor genes.";
RL Submitted (MAR-2009) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=15135060; DOI=10.1016/j.febslet.2004.03.080;
RA Schulze S., Mant A., Kossmann J., Lloyd J.R.;
RT "Identification of an Arabidopsis inorganic pyrophosphatase capable of
RT being imported into chloroplasts.";
RL FEBS Lett. 565:101-105(2004).
RN [8]
RP SUBCELLULAR LOCATION.
RX PubMed=15610358; DOI=10.1111/j.1365-313x.2004.02281.x;
RA Koroleva O.A., Tomlinson M.L., Leader D., Shaw P., Doonan J.H.;
RT "High-throughput protein localization in Arabidopsis using Agrobacterium-
RT mediated transient expression of GFP-ORF fusions.";
RL Plant J. 41:162-174(2005).
RN [9]
RP FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES,
RP COFACTOR, ACTIVITY REGULATION, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Columbia;
RA Navarro-De la Sancha E., Coello-Coutino M.P., Valencia-Turcotte L.G.,
RA Hernandez-Dominguez E.E., Trejo-Yepes G., Rodriguez-Sotres R.;
RT "Characterization of two soluble inorganic pyrophosphatases from
RT Arabidopsis thaliana.";
RL Plant Sci. 172:796-807(2007).
RN [10]
RP FUNCTION.
RX PubMed=22566496; DOI=10.1104/pp.112.198309;
RA Meyer K., Stecca K.L., Ewell-Hicks K., Allen S.M., Everard J.D.;
RT "Oil and protein accumulation in developing seeds is influenced by the
RT expression of a cytosolic pyrophosphatase in Arabidopsis.";
RL Plant Physiol. 159:1221-1234(2012).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.93 ANGSTROMS) OF 33-212.
RA Grzechowiak M., Ruszkowski M., Sikorski M., Jaskolski M.;
RT "Crystal structure of Inorganic pyrophosphatase PPA1 from Arabidopsis
RT thaliana.";
RL Submitted (JUL-2013) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the irreversible hydrolysis of pyrophosphate (PPi)
CC to phosphate. The MgPPi(2-) complex binds to the enzyme only after a
CC free Mg(2+) ion has bound (Ref.9). No activity with glycerol-3-
CC phosphate, glucose-6-phosphate, p-nitrophenylphosphate, ADP, NADP(+),
CC NAD(+),NADH, NADPH or phosphoribosyl pyrophosphate as substrates
CC (Ref.9). Controls the equilibrium of gluconeogenic reactions in the
CC heterotrophic growth phase of early seedling establishment.
CC Determinates the rate of cytosolic glycolysis, providing carbon for
CC seed storage lipid accumulation (PubMed:22566496).
CC {ECO:0000269|PubMed:22566496, ECO:0000269|Ref.9}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=diphosphate + H2O = H(+) + 2 phosphate; Xref=Rhea:RHEA:24576,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:43474; EC=3.6.1.1; Evidence={ECO:0000269|Ref.9};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000269|Ref.9};
CC -!- ACTIVITY REGULATION: Inhibited by Zn(2+), Ca(2+), Ba(2+), Fe(2+),
CC Co(2+), Cu(2+), Eu(2+), Eu(3+) and Mn(2+). {ECO:0000269|Ref.9}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Note=kcat is 9.28 sec(-1) for pyrophosphate. {ECO:0000269|Ref.9};
CC -!- SUBUNIT: Monomer. {ECO:0000269|Ref.9}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:15610358}.
CC -!- TISSUE SPECIFICITY: Ubiquitous. Lower level of expression in ovary,
CC stigma and pollen. {ECO:0000303|Ref.9}.
CC -!- DEVELOPMENTAL STAGE: Expressed throughout plant development, with a
CC slight reduction during senescence. {ECO:0000303|Ref.9}.
CC -!- SIMILARITY: Belongs to the PPase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF26475.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC007323; AAF26475.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE27222.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM60177.1; -; Genomic_DNA.
DR EMBL; AY052717; AAK96621.1; -; mRNA.
DR EMBL; AY057668; AAL15299.1; -; mRNA.
DR EMBL; AY065201; AAL38377.1; -; mRNA.
DR EMBL; AY081555; AAM10117.1; -; mRNA.
DR EMBL; BT001144; AAN64535.1; -; mRNA.
DR EMBL; AY085015; AAM61573.1; -; mRNA.
DR EMBL; AK226833; BAE98927.1; -; mRNA.
DR EMBL; AB493418; BAH30256.1; -; mRNA.
DR PIR; C86141; C86141.
DR RefSeq; NP_001322481.1; NM_001331245.1.
DR RefSeq; NP_171613.1; NM_099987.4.
DR PDB; 4LUG; X-ray; 1.93 A; A/B=33-212.
DR PDB; 5LS0; X-ray; 1.83 A; A/B=30-208.
DR PDBsum; 4LUG; -.
DR PDBsum; 5LS0; -.
DR AlphaFoldDB; Q93V56; -.
DR SMR; Q93V56; -.
DR IntAct; Q93V56; 3.
DR STRING; 3702.AT1G01050.1; -.
DR iPTMnet; Q93V56; -.
DR PaxDb; Q93V56; -.
DR PRIDE; Q93V56; -.
DR ProteomicsDB; 248488; -.
DR EnsemblPlants; AT1G01050.1; AT1G01050.1; AT1G01050.
DR EnsemblPlants; AT1G01050.2; AT1G01050.2; AT1G01050.
DR GeneID; 839579; -.
DR Gramene; AT1G01050.1; AT1G01050.1; AT1G01050.
DR Gramene; AT1G01050.2; AT1G01050.2; AT1G01050.
DR KEGG; ath:AT1G01050; -.
DR Araport; AT1G01050; -.
DR TAIR; locus:2200965; AT1G01050.
DR eggNOG; KOG1626; Eukaryota.
DR HOGENOM; CLU_073198_2_1_1; -.
DR InParanoid; Q93V56; -.
DR OMA; HDLDIGA; -.
DR OrthoDB; 1429691at2759; -.
DR PhylomeDB; Q93V56; -.
DR BRENDA; 3.6.1.1; 399.
DR PRO; PR:Q93V56; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q93V56; baseline and differential.
DR Genevisible; Q93V56; AT.
DR GO; GO:0005737; C:cytoplasm; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0005654; C:nucleoplasm; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
DR GO; GO:0004427; F:inorganic diphosphatase activity; IDA:TAIR.
DR GO; GO:0000287; F:magnesium ion binding; IBA:GO_Central.
DR GO; GO:0042546; P:cell wall biogenesis; IMP:TAIR.
DR GO; GO:0019915; P:lipid storage; IMP:TAIR.
DR GO; GO:0006796; P:phosphate-containing compound metabolic process; IBA:GO_Central.
DR GO; GO:2000904; P:regulation of starch metabolic process; IMP:TAIR.
DR GO; GO:0005985; P:sucrose metabolic process; IDA:TAIR.
DR CDD; cd00412; pyrophosphatase; 1.
DR Gene3D; 3.90.80.10; -; 1.
DR HAMAP; MF_00209; Inorganic_PPase; 1.
DR InterPro; IPR008162; Pyrophosphatase.
DR InterPro; IPR036649; Pyrophosphatase_sf.
DR PANTHER; PTHR10286; PTHR10286; 1.
DR Pfam; PF00719; Pyrophosphatase; 1.
DR SUPFAM; SSF50324; SSF50324; 1.
DR PROSITE; PS00387; PPASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Hydrolase; Magnesium; Metal-binding;
KW Reference proteome.
FT CHAIN 1..212
FT /note="Soluble inorganic pyrophosphatase 1"
FT /id="PRO_0000431795"
FT ACT_SITE 84
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P00817"
FT BINDING 62
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P9WI55"
FT BINDING 76
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P9WI55"
FT BINDING 88
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P9WI55"
FT BINDING 98
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P0A7A9"
FT BINDING 103
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P0A7A9"
FT BINDING 103
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P0A7A9"
FT BINDING 135
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P0A7A9"
FT BINDING 172
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P9WI55"
FT TURN 35..38
FT /evidence="ECO:0007829|PDB:5LS0"
FT TURN 43..47
FT /evidence="ECO:0007829|PDB:5LS0"
FT STRAND 48..55
FT /evidence="ECO:0007829|PDB:5LS0"
FT STRAND 61..65
FT /evidence="ECO:0007829|PDB:5LS0"
FT TURN 67..69
FT /evidence="ECO:0007829|PDB:5LS0"
FT STRAND 72..77
FT /evidence="ECO:0007829|PDB:5LS0"
FT STRAND 79..81
FT /evidence="ECO:0007829|PDB:5LS0"
FT STRAND 85..90
FT /evidence="ECO:0007829|PDB:5LS0"
FT STRAND 103..107
FT /evidence="ECO:0007829|PDB:5LS0"
FT STRAND 117..126
FT /evidence="ECO:0007829|PDB:5LS0"
FT STRAND 128..130
FT /evidence="ECO:0007829|PDB:5LS0"
FT STRAND 137..142
FT /evidence="ECO:0007829|PDB:5LS0"
FT TURN 146..150
FT /evidence="ECO:0007829|PDB:5LS0"
FT HELIX 154..156
FT /evidence="ECO:0007829|PDB:5LS0"
FT HELIX 159..171
FT /evidence="ECO:0007829|PDB:5LS0"
FT HELIX 174..176
FT /evidence="ECO:0007829|PDB:5LS0"
FT STRAND 180..182
FT /evidence="ECO:0007829|PDB:5LS0"
FT HELIX 188..204
FT /evidence="ECO:0007829|PDB:5LS0"
SQ SEQUENCE 212 AA; 24484 MW; F4581A52CCAB7190 CRC64;
MSEETKDNQR LQRPAPRLNE RILSSLSRRS VAAHPWHDLE IGPGAPQIFN VVVEITKGSK
VKYELDKKTG LIKVDRILYS SVVYPHNYGF VPRTLCEDND PIDVLVIMQE PVLPGCFLRA
RAIGLMPMID QGEKDDKIIA VCVDDPEYKH YTDIKELPPH RLSEIRRFFE DYKKNENKEV
AVNDFLPSES AVEAIQYSMD LYAEYILHTL RR
