D89S2_ARATH
ID D89S2_ARATH Reviewed; 367 AA.
AC Q949P3; Q7XJS9; Q8LCJ8;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Damage-control phosphatase At2g17340 {ECO:0000303|PubMed:27322068};
DE EC=3.1.3.- {ECO:0000269|PubMed:27322068};
DE AltName: Full=Sugar phosphates phosphatase At2g17340 {ECO:0000303|PubMed:27322068};
GN OrderedLocusNames=At2g17340; ORFNames=F5J6.10;
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=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
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 ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [6]
RP FUNCTION, DOMAIN, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES,
RP ACTIVITY REGULATION, COFACTOR, AND MUTAGENESIS OF ASP-220; ASN-221 AND
RP ASP-256.
RX PubMed=27322068; DOI=10.1038/nchembio.2108;
RA Huang L., Khusnutdinova A., Nocek B., Brown G., Xu X., Cui H., Petit P.,
RA Flick R., Zallot R., Balmant K., Ziemak M.J., Shanklin J.,
RA de Crecy-Lagard V., Fiehn O., Gregory J.F. III, Joachimiak A.,
RA Savchenko A., Yakunin A.F., Hanson A.D.;
RT "A family of metal-dependent phosphatases implicated in metabolite damage-
RT control.";
RL Nat. Chem. Biol. 12:621-627(2016).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 2-367, AND SUBUNIT.
RX PubMed=16511115; DOI=10.1107/s1744309105017690;
RA Bitto E., Bingman C.A., Allard S.T.M., Wesenberg G.E., Phillips G.N. Jr.;
RT "The structure at 1.7A resolution of the protein product of the At2g17340
RT gene from Arabidopsis thaliana.";
RL Acta Crystallogr. F 61:630-635(2005).
CC -!- FUNCTION: Metal-dependent phosphatase with probable damage-control
CC functions (PubMed:27322068). Shows phosphatase activity against several
CC substrates, including sugar phosphates and p-nitrophenyl
CC phosphate(pNPP) (PubMed:27322068). Prefers sugar phosphate substrates,
CC including the extremely potent glycating agents ribose-5-phosphate and
CC erythrose-4-phosphate (PubMed:27322068). {ECO:0000269|PubMed:27322068}.
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:27322068};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:27322068};
CC Note=Phosphatase activity is strongly promoted by several divalent
CC cations but is it suggested that Mn(2+) and possibly Ni(2+) represent
CC biologically relevant metal ion cofactors for damage-control
CC phosphatases. {ECO:0000269|PubMed:27322068};
CC -!- ACTIVITY REGULATION: Activity is strongly promoted by Co(2+), Ni(2+),
CC Mg(2+), Cu(2+) and Mn(2+) (PubMed:27322068). Activity is inhibited by
CC EDTA (PubMed:27322068). {ECO:0000269|PubMed:27322068}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=418 uM for p-nitrophenylphosphate {ECO:0000269|PubMed:27322068};
CC KM=70 uM for ribose 5-phosphate {ECO:0000269|PubMed:27322068};
CC KM=90 uM for 2-desoxyribose 5-phosphate
CC {ECO:0000269|PubMed:27322068};
CC Note=kcat is 1.68 sec(-1) with p-nitrophenylphosphate as substrate.
CC kcat is 0.94 sec(-1) with ribose 5-phosphate as substrate. kcat is
CC 1.1 sec(-1) with 2-desoxyribose 5-phosphate as substrate.
CC {ECO:0000269|PubMed:27322068};
CC -!- SUBUNIT: Multimer. {ECO:0000305|PubMed:16511115}.
CC -!- DOMAIN: Subfamily II proteins have an EGMGR motif about 50 residues
CC from the C-terminus (Probable). This motif lies near the metal-binding
CC residues in the putative substrate-binding cleft 2 (Probable).
CC Subfamily II proteins occur only in eukaryotes, in two forms: as a
CC stand-alone unit in plants, and as a C-terminal domain of pantothenate
CC kinases in plants, animals, and chytrid fungi (Probable).
CC {ECO:0000305|PubMed:27322068}.
CC -!- SIMILARITY: Belongs to the damage-control phosphatase family.
CC Phosphopantetheine phosphatase II subfamily. {ECO:0000305}.
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DR EMBL; CP002685; AEC06614.1; -; Genomic_DNA.
DR EMBL; AY096682; AAM20316.1; -; mRNA.
DR EMBL; AY050977; AAK93654.1; -; mRNA.
DR EMBL; AY086556; AAM63619.1; -; mRNA.
DR PIR; A84551; A84551.
DR RefSeq; NP_565412.1; NM_127289.4.
DR PDB; 1XFI; X-ray; 1.70 A; A=2-367.
DR PDB; 2Q40; X-ray; 1.70 A; A=2-367.
DR PDBsum; 1XFI; -.
DR PDBsum; 2Q40; -.
DR AlphaFoldDB; Q949P3; -.
DR SMR; Q949P3; -.
DR STRING; 3702.AT2G17340.1; -.
DR iPTMnet; Q949P3; -.
DR PaxDb; Q949P3; -.
DR PRIDE; Q949P3; -.
DR ProteomicsDB; 234590; -.
DR DNASU; 816241; -.
DR EnsemblPlants; AT2G17340.1; AT2G17340.1; AT2G17340.
DR GeneID; 816241; -.
DR Gramene; AT2G17340.1; AT2G17340.1; AT2G17340.
DR KEGG; ath:AT2G17340; -.
DR Araport; AT2G17340; -.
DR TAIR; locus:2827544; AT2G17340.
DR eggNOG; KOG4584; Eukaryota.
DR HOGENOM; CLU_039785_0_0_1; -.
DR InParanoid; Q949P3; -.
DR OMA; KACTIPY; -.
DR OrthoDB; 865329at2759; -.
DR PhylomeDB; Q949P3; -.
DR EvolutionaryTrace; Q949P3; -.
DR PRO; PR:Q949P3; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q949P3; baseline and differential.
DR Genevisible; Q949P3; AT.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:InterPro.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004594; F:pantothenate kinase activity; IBA:GO_Central.
DR GO; GO:0015937; P:coenzyme A biosynthetic process; IBA:GO_Central.
DR Gene3D; 1.20.1700.10; -; 1.
DR InterPro; IPR036075; ARMT-1-like_metal-bd_sf.
DR InterPro; IPR002791; ARMT1-like_metal-bd.
DR InterPro; IPR016949; At2g17340.
DR InterPro; IPR035073; At2g17340_3_helix_bundle.
DR InterPro; IPR004567; Type_II_PanK.
DR PANTHER; PTHR12280; PTHR12280; 1.
DR Pfam; PF01937; ARMT1-like_dom; 1.
DR PIRSF; PIRSF030210; UCP030210; 1.
DR SUPFAM; SSF111321; SSF111321; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Hydrolase; Manganese; Metal-binding; Nickel;
KW Reference proteome.
FT CHAIN 1..367
FT /note="Damage-control phosphatase At2g17340"
FT /id="PRO_0000220602"
FT MOTIF 318..322
FT /note="Subfamily II EGMGR motif"
FT /evidence="ECO:0000305|PubMed:27322068"
FT BINDING 220
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q04371"
FT BINDING 221
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q04371"
FT BINDING 256
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q04371"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT MUTAGEN 220
FT /note="D->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT MUTAGEN 221
FT /note="N->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT MUTAGEN 256
FT /note="D->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:27322068"
FT CONFLICT 259
FT /note="C -> H (in Ref. 4; AAM63619)"
FT /evidence="ECO:0000305"
FT TURN 18..20
FT /evidence="ECO:0007829|PDB:1XFI"
FT STRAND 23..26
FT /evidence="ECO:0007829|PDB:2Q40"
FT HELIX 40..50
FT /evidence="ECO:0007829|PDB:1XFI"
FT HELIX 53..61
FT /evidence="ECO:0007829|PDB:1XFI"
FT HELIX 69..89
FT /evidence="ECO:0007829|PDB:1XFI"
FT HELIX 93..95
FT /evidence="ECO:0007829|PDB:1XFI"
FT HELIX 100..113
FT /evidence="ECO:0007829|PDB:1XFI"
FT HELIX 121..143
FT /evidence="ECO:0007829|PDB:1XFI"
FT HELIX 148..164
FT /evidence="ECO:0007829|PDB:1XFI"
FT HELIX 183..186
FT /evidence="ECO:0007829|PDB:1XFI"
FT STRAND 196..198
FT /evidence="ECO:0007829|PDB:1XFI"
FT HELIX 200..208
FT /evidence="ECO:0007829|PDB:1XFI"
FT STRAND 214..218
FT /evidence="ECO:0007829|PDB:1XFI"
FT HELIX 224..228
FT /evidence="ECO:0007829|PDB:1XFI"
FT HELIX 230..239
FT /evidence="ECO:0007829|PDB:1XFI"
FT STRAND 243..251
FT /evidence="ECO:0007829|PDB:1XFI"
FT HELIX 259..269
FT /evidence="ECO:0007829|PDB:1XFI"
FT STRAND 284..288
FT /evidence="ECO:0007829|PDB:1XFI"
FT STRAND 293..295
FT /evidence="ECO:0007829|PDB:1XFI"
FT HELIX 303..309
FT /evidence="ECO:0007829|PDB:1XFI"
FT STRAND 313..319
FT /evidence="ECO:0007829|PDB:1XFI"
FT HELIX 320..323
FT /evidence="ECO:0007829|PDB:1XFI"
FT STRAND 333..341
FT /evidence="ECO:0007829|PDB:1XFI"
FT HELIX 345..351
FT /evidence="ECO:0007829|PDB:1XFI"
FT STRAND 358..363
FT /evidence="ECO:0007829|PDB:1XFI"
SQ SEQUENCE 367 AA; 40858 MW; A9A204EA1ADF699A CRC64;
MESDSEMVPF PQLPMPIENN YRACTIPYRF PSDDPKKATP NEISWINVFA NSIPSFKKRA
ESDITVPDAP ARAEKFAERY AGILEDLKKD PESHGGPPDG ILLCRLREQV LRELGFRDIF
KKVKDEENAK AISLFPQVVS LSDAIEDDGK RLENLVRGIF AGNIFDLGSA QLAEVFSRDG
MSFLASCQNL VPRPWVIDDL ENFQAKWINK SWKKAVIFVD NSGADIILGI LPFARELLRR
GAQVVLAANE LPSINDITCT ELTEILSQLK DENGQLLGVD TSKLLIANSG NDLPVIDLSR
VSQELAYLSS DADLVIVEGM GRGIETNLYA QFKCDSLKIG MVKHLEVAEF LGGRLYDCVF
KFNEVQS
