GPP1_ARATH
ID GPP1_ARATH Reviewed; 298 AA.
AC F4JTE7; Q8GW23; Q8L8P9; Q9SW01;
DT 13-NOV-2013, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 72.
DE RecName: Full=(DL)-glycerol-3-phosphatase 1, mitochondrial {ECO:0000303|PubMed:17136424};
DE EC=3.1.3.21 {ECO:0000269|PubMed:17136424};
DE AltName: Full=5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase {ECO:0000305|PubMed:27490826};
DE Short=AtGpp1/PyrP3 {ECO:0000303|PubMed:27490826};
DE EC=3.1.3.104 {ECO:0000269|PubMed:27490826};
DE AltName: Full=5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate phosphatase {ECO:0000305|PubMed:27490826};
DE Short=ARPP phosphatase {ECO:0000305|PubMed:27490826};
DE AltName: Full=Glycerol-1-phosphatase 1 {ECO:0000303|PubMed:17136424};
DE Short=AtGPP1 {ECO:0000303|PubMed:17136424};
DE AltName: Full=Haloacid dehalogenase-like hydrolase domain-containing protein GPP1 {ECO:0000303|PubMed:17136424};
DE Flags: Precursor;
GN Name=GPP1 {ECO:0000303|PubMed:17136424};
GN Synonyms=PYRP3 {ECO:0000303|PubMed:27490826};
GN OrderedLocusNames=At4g25840 {ECO:0000312|Araport:AT4G25840};
GN ORFNames=F14M19.120 {ECO:0000312|EMBL:CAB39605.1};
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(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].
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 15-298.
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 50-298.
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 [6]
RP BIOPHYSICOCHEMICAL PROPERTIES, CATALYTIC ACTIVITY, TISSUE SPECIFICITY,
RP SUBCELLULAR LOCATION, AND FUNCTION.
RX PubMed=17136424; DOI=10.1007/s11103-006-9104-0;
RA Caparros-Martin J.A., Reiland S., Koechert K., Cutanda M.C.,
RA Culianez-Macia F.A.;
RT "Arabidopsis thaliana AtGppl and AtGpp2: two novel low molecular weight
RT phosphatases involved in plant glycerol metabolism.";
RL Plant Mol. Biol. 63:505-517(2007).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBCELLULAR LOCATION.
RX PubMed=27490826; DOI=10.1111/tpj.13291;
RA Sa N., Rawat R., Thornburg C., Walker K.D., Roje S.;
RT "Identification and characterization of the missing phosphatase on the
RT riboflavin biosynthesis pathway in Arabidopsis thaliana.";
RL Plant J. 88:705-716(2016).
CC -!- FUNCTION: Acts as a glycerol-3-phosphatase with higher
CC stereospecificity for L-glycerol-3-phosphate than DL-glycerol-3-
CC phosphate (PubMed:17136424). Can also dephosphorylate in vitro 5-amino-
CC 6-(5-phospho-D-ribitylamino)uracil, also known as ARPP
CC (PubMed:27490826). {ECO:0000269|PubMed:17136424,
CC ECO:0000269|PubMed:27490826}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + sn-glycerol 1-phosphate = glycerol + phosphate;
CC Xref=Rhea:RHEA:46084, ChEBI:CHEBI:15377, ChEBI:CHEBI:17754,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57685; EC=3.1.3.21;
CC Evidence={ECO:0000269|PubMed:17136424};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + sn-glycerol 3-phosphate = glycerol + phosphate;
CC Xref=Rhea:RHEA:66372, ChEBI:CHEBI:15377, ChEBI:CHEBI:17754,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57597; EC=3.1.3.21;
CC Evidence={ECO:0000269|PubMed:17136424};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-amino-6-(5-phospho-D-ribitylamino)uracil + H2O = 5-amino-6-
CC (D-ribitylamino)uracil + phosphate; Xref=Rhea:RHEA:25197,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15934, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:58421; EC=3.1.3.104;
CC Evidence={ECO:0000269|PubMed:27490826};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=5.2 mM for DL-glycerol-3-phosphate {ECO:0000269|PubMed:17136424};
CC Vmax=3 nmol/min/mg enzyme toward DL-glycerol-3-phosphate
CC {ECO:0000269|PubMed:17136424};
CC pH dependence:
CC Optimum pH is 7.0. {ECO:0000269|PubMed:17136424};
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:27490826}.
CC -!- TISSUE SPECIFICITY: Ubiquitous with highest expression in siliques.
CC Mainly restricted to the meristem of immature flower and vascular
CC elements of the root, shoot, leave, siliqua and developing embryo (at
CC the protein level). {ECO:0000269|PubMed:17136424}.
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. DOG/GPP
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAC43699.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAB39605.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAB79439.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AL049480; CAB39605.1; ALT_INIT; Genomic_DNA.
DR EMBL; AL161564; CAB79439.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP002687; AEE85121.1; -; Genomic_DNA.
DR EMBL; AY088882; AAM67188.1; -; mRNA.
DR EMBL; AK119129; BAC43699.1; ALT_INIT; mRNA.
DR EMBL; BT005264; AAO63328.1; -; mRNA.
DR PIR; T04238; T04238.
DR RefSeq; NP_567731.1; NM_118717.3.
DR AlphaFoldDB; F4JTE7; -.
DR SMR; F4JTE7; -.
DR STRING; 3702.AT4G25840.1; -.
DR PaxDb; F4JTE7; -.
DR PRIDE; F4JTE7; -.
DR ProteomicsDB; 220619; -.
DR EnsemblPlants; AT4G25840.1; AT4G25840.1; AT4G25840.
DR GeneID; 828690; -.
DR Gramene; AT4G25840.1; AT4G25840.1; AT4G25840.
DR KEGG; ath:AT4G25840; -.
DR Araport; AT4G25840; -.
DR TAIR; locus:2117512; AT4G25840.
DR eggNOG; KOG2914; Eukaryota.
DR HOGENOM; CLU_045011_13_0_1; -.
DR InParanoid; F4JTE7; -.
DR OMA; DSERVYT; -.
DR OrthoDB; 1510544at2759; -.
DR PRO; PR:F4JTE7; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; F4JTE7; baseline and differential.
DR Genevisible; F4JTE7; AT.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0043726; F:5-amino-6-(5-phosphoribitylamino)uracil phosphatase activity; IEA:RHEA.
DR GO; GO:0000121; F:glycerol-1-phosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0043136; F:glycerol-3-phosphatase activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016791; F:phosphatase activity; IBA:GO_Central.
DR GO; GO:0016311; P:dephosphorylation; IDA:UniProtKB.
DR GO; GO:0006114; P:glycerol biosynthetic process; IMP:UniProtKB.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IEA:UniProtKB-KW.
DR CDD; cd07529; HAD_AtGPP-like; 1.
DR Gene3D; 1.10.150.240; -; 1.
DR Gene3D; 3.40.50.1000; -; 1.
DR InterPro; IPR045228; Gpp1/Gpp2-like.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006439; HAD-SF_hydro_IA.
DR InterPro; IPR041492; HAD_2.
DR InterPro; IPR023214; HAD_sf.
DR InterPro; IPR023198; PGP-like_dom2.
DR Pfam; PF13419; HAD_2; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01509; HAD-SF-IA-v3; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Magnesium; Metal-binding; Mitochondrion; Reference proteome;
KW Riboflavin biosynthesis; Transit peptide.
FT TRANSIT 1..46
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 47..298
FT /note="(DL)-glycerol-3-phosphatase 1, mitochondrial"
FT /id="PRO_0000424317"
FT ACT_SITE 77
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT ACT_SITE 79
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 77
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 79
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 242
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT CONFLICT 58
FT /note="N -> D (in Ref. 3; AAM67188)"
FT /evidence="ECO:0000305"
FT CONFLICT 263
FT /note="S -> P (in Ref. 3; AAM67188)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 298 AA; 33071 MW; 72508B3036A95DE7 CRC64;
MLTTPTRFVA LRIPFRSSNK IPISIAPSPK VFPRKPVIRV PASLRFVATM STPAAAVNAT
VTVTDAGRGS ITHVIFDMDG LLLDTEKFYT EVQEKILARY NKTFDWSLKA KMMGRKAIEA
ARLFVDESGI SDSLSAEDFI VERESMLQDL FPTSDLMPGA SRLLRHLHGK GIPICIATGT
HTRHFDLKTQ RHRELFSLMH HVVRGDDPEV KEGKPAPDGF LAASRRFEDG PVDPRKVLVF
EDAPSGVQAA KNAGMNVIMV PDSRLDKSYC NVADQVLASL LDFKPEEWGL PSFQDSHN
