LSF2_ARATH
ID LSF2_ARATH Reviewed; 282 AA.
AC Q9SRK5; Q8LBS6;
DT 16-MAY-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=Phosphoglucan phosphatase LSF2, chloroplastic;
DE EC=3.1.3.- {ECO:0000269|PubMed:22100529, ECO:0000269|PubMed:23832589, ECO:0000269|PubMed:26231210};
DE AltName: Full=Phosphoglucan phosphatase like sex Four2 {ECO:0000303|PubMed:22100529, ECO:0000303|PubMed:23832589};
DE AltName: Full=Protein LIKE SEX4 2 {ECO:0000303|PubMed:23832589};
DE Flags: Precursor;
GN Name=LSF2; OrderedLocusNames=At3g10940; ORFNames=F9F8.24;
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Shinn P., Chen H., Kim C.J., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
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 [5]
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 [6]
RP FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, TISSUE SPECIFICITY,
RP INDUCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=22100529; DOI=10.1105/tpc.111.092155;
RA Santelia D., Koetting O., Seung D., Schubert M., Thalmann M., Bischof S.,
RA Meekins D.A., Lutz A., Patron N., Gentry M.S., Allain F.H., Zeeman S.C.;
RT "The phosphoglucan phosphatase like sex Four2 dephosphorylates starch at
RT the C3-position in Arabidopsis.";
RL Plant Cell 23:4096-4111(2011).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ARG-157; CYS-193;
RP 194-SER--GLY-198 AND PHE-261, MOTIF, AND ACTIVE SITE.
RX PubMed=26231210; DOI=10.1074/jbc.m115.658203;
RA Meekins D.A., Raththagala M., Auger K.D., Turner B.D., Santelia D.,
RA Koetting O., Gentry M.S., Vander Kooi C.W.;
RT "Mechanistic insights into glucan phosphatase activity against polyglucan
RT substrates.";
RL J. Biol. Chem. 290:23361-23370(2015).
RN [8] {ECO:0007744|PDB:4KYQ, ECO:0007744|PDB:4KYR}
RP X-RAY CRYSTALLOGRAPHY (1.64 ANGSTROMS) OF 79-282 IN COMPLEX WITH THE
RP SUBSTRATE ANALOGS MALTOHEXAOSE AND PHOSPHATE, FUNCTION, CATALYTIC ACTIVITY,
RP ACTIVE SITE, AND MUTAGENESIS OF TYR-83; TYR-85; TYR-135; TRP-136; ARG-153;
RP MET-155; ARG-157; PHE-162; TRP-180; CYS-193; LYS-245; PHE-261 AND GLU-268.
RX PubMed=23832589; DOI=10.1105/tpc.113.112706;
RA Meekins D.A., Guo H.F., Husodo S., Paasch B.C., Bridges T.M., Santelia D.,
RA Kotting O., Vander Kooi C.W., Gentry M.S.;
RT "Structure of the Arabidopsis glucan phosphatase like sex four2 reveals a
RT unique mechanism for starch dephosphorylation.";
RL Plant Cell 25:2302-2314(2013).
CC -!- FUNCTION: Starch-associated phosphoglucan phosphatase that selectively
CC dephosphorylates the glucan C3 position. Probably participates in the
CC regulation of starch degradation. {ECO:0000269|PubMed:22100529,
CC ECO:0000269|PubMed:23832589, ECO:0000269|PubMed:26231210}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:22100529}.
CC -!- TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:22100529}.
CC -!- INDUCTION: Expressed with a circadian rhythm showing a peak at the end
CC of the day and then decreasing to reach the lowest levels at the end of
CC the night. {ECO:0000269|PubMed:22100529}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions, but starch of mutant plants contains high levels of C3-
CC bound phosphate. {ECO:0000269|PubMed:22100529}.
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DR EMBL; AC009991; AAF01527.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE74980.1; -; Genomic_DNA.
DR EMBL; BT024510; ABD19691.1; -; mRNA.
DR EMBL; AK226225; BAE98389.1; -; mRNA.
DR EMBL; AY087019; AAM64580.1; -; mRNA.
DR RefSeq; NP_566383.1; NM_111931.3.
DR PDB; 4KYQ; X-ray; 1.64 A; A=79-282.
DR PDB; 4KYR; X-ray; 2.30 A; A=79-282.
DR PDBsum; 4KYQ; -.
DR PDBsum; 4KYR; -.
DR AlphaFoldDB; Q9SRK5; -.
DR SMR; Q9SRK5; -.
DR STRING; 3702.AT3G10940.1; -.
DR PaxDb; Q9SRK5; -.
DR PRIDE; Q9SRK5; -.
DR ProteomicsDB; 238804; -.
DR EnsemblPlants; AT3G10940.1; AT3G10940.1; AT3G10940.
DR GeneID; 820265; -.
DR Gramene; AT3G10940.1; AT3G10940.1; AT3G10940.
DR KEGG; ath:AT3G10940; -.
DR Araport; AT3G10940; -.
DR TAIR; locus:2085542; AT3G10940.
DR eggNOG; KOG1716; Eukaryota.
DR HOGENOM; CLU_085882_0_0_1; -.
DR InParanoid; Q9SRK5; -.
DR OMA; PYEYHHE; -.
DR OrthoDB; 865142at2759; -.
DR PhylomeDB; Q9SRK5; -.
DR PRO; PR:Q9SRK5; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SRK5; baseline and differential.
DR Genevisible; Q9SRK5; AT.
DR GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
DR GO; GO:0019203; F:carbohydrate phosphatase activity; IDA:UniProtKB.
DR GO; GO:0008138; F:protein tyrosine/serine/threonine phosphatase activity; IEA:InterPro.
DR GO; GO:2001070; F:starch binding; IDA:UniProtKB.
DR GO; GO:0050308; F:sugar-phosphatase activity; IDA:TAIR.
DR GO; GO:0046838; P:phosphorylated carbohydrate dephosphorylation; IDA:UniProtKB.
DR GO; GO:0006470; P:protein dephosphorylation; IEA:InterPro.
DR GO; GO:0005983; P:starch catabolic process; IDA:UniProtKB.
DR CDD; cd14526; DSP_laforin-like; 1.
DR Gene3D; 3.90.190.10; -; 1.
DR InterPro; IPR045204; DSP_laforin-like.
DR InterPro; IPR000340; Dual-sp_phosphatase_cat-dom.
DR InterPro; IPR029021; Prot-tyrosine_phosphatase-like.
DR InterPro; IPR000387; Tyr_Pase_dom.
DR InterPro; IPR020422; TYR_PHOSPHATASE_DUAL_dom.
DR Pfam; PF00782; DSPc; 1.
DR SMART; SM00195; DSPc; 1.
DR SUPFAM; SSF52799; SSF52799; 1.
DR PROSITE; PS50056; TYR_PHOSPHATASE_2; 1.
DR PROSITE; PS50054; TYR_PHOSPHATASE_DUAL; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Chloroplast; Hydrolase; Plastid;
KW Protein phosphatase; Reference proteome; Transit peptide.
FT TRANSIT 1..61
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 62..282
FT /note="Phosphoglucan phosphatase LSF2, chloroplastic"
FT /id="PRO_0000417335"
FT DOMAIN 92..249
FT /note="Tyrosine-protein phosphatase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00160"
FT MOTIF 193..199
FT /note="Glucan phosphatase signature motif CXAGXGR"
FT /evidence="ECO:0000305|PubMed:26231210"
FT ACT_SITE 193
FT /note="Phosphocysteine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00160,
FT ECO:0000305|PubMed:26231210"
FT BINDING 83
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23832589,
FT ECO:0007744|PDB:4KYR"
FT BINDING 153..156
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23832589,
FT ECO:0007744|PDB:4KYR"
FT BINDING 161
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23832589,
FT ECO:0007744|PDB:4KYR"
FT BINDING 177..180
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23832589,
FT ECO:0007744|PDB:4KYR"
FT BINDING 194..199
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23832589,
FT ECO:0007744|PDB:4KYR"
FT BINDING 230
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23832589,
FT ECO:0007744|PDB:4KYR"
FT BINDING 245
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23832589,
FT ECO:0007744|PDB:4KYR"
FT BINDING 251
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23832589,
FT ECO:0007744|PDB:4KYR"
FT BINDING 259..263
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23832589,
FT ECO:0007744|PDB:4KYR"
FT BINDING 268
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23832589,
FT ECO:0007744|PDB:4KYR"
FT MUTAGEN 83
FT /note="Y->A: Decreases starch C3 dephosphorylation. No
FT effect on phosphatase activity with p-nitrophenyl
FT phosphate."
FT /evidence="ECO:0000269|PubMed:23832589"
FT MUTAGEN 85
FT /note="Y->A: Nearly abolishes starch C3 dephosphorylation.
FT No effect on phosphatase activity with p-nitrophenyl
FT phosphate."
FT /evidence="ECO:0000269|PubMed:23832589"
FT MUTAGEN 135
FT /note="Y->A: Decreases starch C3 dephosphorylation. No
FT effect on phosphatase activity with p-nitrophenyl
FT phosphate."
FT /evidence="ECO:0000269|PubMed:23832589"
FT MUTAGEN 136
FT /note="W->A: Abolishes starch C3 dephosphorylation. No
FT effect on phosphatase activity with p-nitrophenyl
FT phosphate."
FT /evidence="ECO:0000269|PubMed:23832589"
FT MUTAGEN 153
FT /note="R->A: Decreases starch C3 dephosphorylation. No
FT effect on phosphatase activity with p-nitrophenyl
FT phosphate."
FT /evidence="ECO:0000269|PubMed:23832589"
FT MUTAGEN 155
FT /note="M->A: Decreases starch C3 dephosphorylation. No
FT effect on phosphatase activity with p-nitrophenyl
FT phosphate."
FT /evidence="ECO:0000269|PubMed:23832589"
FT MUTAGEN 157
FT /note="R->A: Decreases starch binding and starch C3
FT dephosphorylation. Moderate decrease of phosphatase
FT activity with soluble substrates; when associated with A-
FT 261. Nearly abolishes activity with water-insoluble starch;
FT when associated with A-261."
FT /evidence="ECO:0000269|PubMed:26231210"
FT MUTAGEN 162
FT /note="F->A: Decreases starch C3 dephosphorylation. No
FT effect on phosphatase activity with p-nitrophenyl
FT phosphate."
FT /evidence="ECO:0000269|PubMed:23832589"
FT MUTAGEN 180
FT /note="W->A: Decreases starch C3 dephosphorylation. No
FT effect on phosphatase activity with p-nitrophenyl
FT phosphate."
FT /evidence="ECO:0000269|PubMed:23832589"
FT MUTAGEN 193
FT /note="C->S: Abolishes phosphatase activity."
FT /evidence="ECO:0000269|PubMed:23832589,
FT ECO:0000269|PubMed:26231210"
FT MUTAGEN 194..198
FT /note="SAGLG->TTGFD: Abolishes glucan phosphatase
FT activity."
FT /evidence="ECO:0000269|PubMed:26231210"
FT MUTAGEN 245
FT /note="K->A: Decreases starch C3 dephosphorylation. No
FT effect on phosphatase activity with p-nitrophenyl
FT phosphate."
FT /evidence="ECO:0000269|PubMed:23832589"
FT MUTAGEN 261
FT /note="F->A: Strongly decreases starch binding and starch
FT C3 dephosphorylation. Moderate decrease of phosphatase
FT activity with soluble substrates; when associated with A-
FT 157. Nearly abolishes activity with water-insoluble starch;
FT when associated with A-157."
FT /evidence="ECO:0000269|PubMed:23832589,
FT ECO:0000269|PubMed:26231210"
FT MUTAGEN 268
FT /note="E->A: Decreases starch C3 dephosphorylation. No
FT effect on phosphatase activity with p-nitrophenyl
FT phosphate."
FT /evidence="ECO:0000269|PubMed:23832589"
FT CONFLICT 38..39
FT /note="RF -> SL (in Ref. 5; AAM64580)"
FT /evidence="ECO:0000305"
FT STRAND 80..83
FT /evidence="ECO:0007829|PDB:4KYR"
FT HELIX 87..89
FT /evidence="ECO:0007829|PDB:4KYQ"
FT STRAND 93..97
FT /evidence="ECO:0007829|PDB:4KYQ"
FT STRAND 100..103
FT /evidence="ECO:0007829|PDB:4KYQ"
FT HELIX 109..119
FT /evidence="ECO:0007829|PDB:4KYQ"
FT STRAND 121..126
FT /evidence="ECO:0007829|PDB:4KYQ"
FT HELIX 130..136
FT /evidence="ECO:0007829|PDB:4KYQ"
FT HELIX 140..149
FT /evidence="ECO:0007829|PDB:4KYQ"
FT STRAND 153..156
FT /evidence="ECO:0007829|PDB:4KYQ"
FT HELIX 164..184
FT /evidence="ECO:0007829|PDB:4KYQ"
FT STRAND 186..192
FT /evidence="ECO:0007829|PDB:4KYQ"
FT STRAND 194..198
FT /evidence="ECO:0007829|PDB:4KYQ"
FT HELIX 199..211
FT /evidence="ECO:0007829|PDB:4KYQ"
FT HELIX 216..226
FT /evidence="ECO:0007829|PDB:4KYQ"
FT HELIX 233..244
FT /evidence="ECO:0007829|PDB:4KYQ"
FT HELIX 248..250
FT /evidence="ECO:0007829|PDB:4KYR"
FT HELIX 253..255
FT /evidence="ECO:0007829|PDB:4KYQ"
FT TURN 258..261
FT /evidence="ECO:0007829|PDB:4KYQ"
FT HELIX 266..278
FT /evidence="ECO:0007829|PDB:4KYQ"
FT TURN 279..281
FT /evidence="ECO:0007829|PDB:4KYQ"
SQ SEQUENCE 282 AA; 32087 MW; BDB1A93855C98849 CRC64;
MSVIGSKSCI FSVARYTREN EKSSCFTSIN KKSSLDLRFP RNLAGVSCKF SGENPGTNGV
SLSSKNKMED YNTAMKRLMR SPYEYHHDLG MNYTLIRDEL IVGSQPQKPE DIDHLKQEQN
VAYILNLQQD KDIEYWGIDL DSIVRRCKEL GIRHMRRPAK DFDPLSLRSQ LPKAVSSLEW
AVSEGKGRVY VHCSAGLGRA PGVSIAYMYW FCDMNLNTAY DTLVSKRPCG PNKGAIRGAT
YDLAKNDPWK EPFESLPENA FEDIADWERK LIQERVRALR GT
