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Glycerol-1-phosphate phosphohydrolase 1 (EC 3.1.3.21) ((DL)-glycerol-3-phosphatase 1) (Related to HOR2 protein 2)

 GPP1_YEAST              Reviewed;         250 AA.
P41277; D6VVM8; P38012;
01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
18-JUL-2018, entry version 163.
RecName: Full=Glycerol-1-phosphate phosphohydrolase 1 {ECO:0000305};
EC=3.1.3.21 {ECO:0000269|PubMed:8662716};
AltName: Full=(DL)-glycerol-3-phosphatase 1 {ECO:0000303|PubMed:8662716};
AltName: Full=Related to HOR2 protein 2 {ECO:0000303|PubMed:7500933};
Name=GPP1 {ECO:0000303|PubMed:8662716};
Synonyms=RHR2 {ECO:0000303|PubMed:7500933};
OrderedLocusNames=YIL053W {ECO:0000312|SGD:S000001315};
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [MRNA].
STRAIN=RS16;
PubMed=7500933; DOI=10.1007/BF00290358;
Hirayama T., Maeda T., Saito H., Shinozaki K.;
"Cloning and characterization of seven cDNAs for hyperosmolarity-
responsive (HOR) genes of Saccharomyces cerevisiae.";
Mol. Gen. Genet. 249:127-138(1995).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169870;
Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D.,
Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N.,
Harris D.E., Horsnell T., Hunt S., Jagels K., Jones M., Lye G.,
Moule S., Odell C., Pearson D., Rajandream M.A., Rice P., Rowley N.,
Skelton J., Smith V., Walsh S.V., Whitehead S., Barrell B.G.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome IX.";
Nature 387:84-87(1997).
[3]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[4]
PROTEIN SEQUENCE OF 86-97 AND 173-188.
STRAIN=ATCC 204508 / S288c;
PubMed=7895733; DOI=10.1002/elps.11501501210;
Garrels J.I., Futcher B., Kobayashi R., Latter G.I., Schwender B.,
Volpe T., Warner J.R., McLaughlin C.S.;
"Protein identifications for a Saccharomyces cerevisiae protein
database.";
Electrophoresis 15:1466-1486(1994).
[5]
PARTIAL PROTEIN SEQUENCE, FUNCTION, CATALYTIC ACTIVITY,
BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
PubMed=8662716; DOI=10.1074/jbc.271.23.13875;
Norbeck J., Paehlman A.-K., Akhtar N., Blomberg A., Adler L.;
"Purification and characterization of two isoenzymes of DL-glycerol-3-
phosphatase from Saccharomyces cerevisiae. Identification of the
corresponding GPP1 and GPP2 genes and evidence for osmotic regulation
of Gpp2p expression by the osmosensing mitogen-activated protein
kinase signal transduction pathway.";
J. Biol. Chem. 271:13875-13881(1996).
[6]
PROTEIN SEQUENCE OF 2-8.
STRAIN=ATCC 44827 / SKQ2N;
PubMed=9038161; DOI=10.1074/jbc.272.9.5544;
Norbeck J., Blomberg A.;
"Metabolic and regulatory changes associated with growth of
Saccharomyces cerevisiae in 1.4 M NaCl. Evidence for osmotic induction
of glycerol dissimilation via the dihydroxyacetone pathway.";
J. Biol. Chem. 272:5544-5554(1997).
[7]
IDENTIFICATION BY MASS SPECTROMETRY.
PubMed=9150920; DOI=10.1002/elps.1150180316;
Larsson T., Norbeck J., Karlsson H., Karlsson K.-A., Blomberg A.;
"Identification of two-dimensional gel electrophoresis resolved yeast
proteins by matrix-assisted laser desorption ionization mass
spectrometry.";
Electrophoresis 18:418-423(1997).
[8]
DISRUPTION PHENOTYPE.
PubMed=10931288; DOI=10.1046/j.1365-2958.2000.01955.x;
Siderius M., Van Wuytswinkel O., Reijenga K.A., Kelders M.,
Mager W.H.;
"The control of intracellular glycerol in Saccharomyces cerevisiae
influences osmotic stress response and resistance to increased
temperature.";
Mol. Microbiol. 36:1381-1390(2000).
[9]
INDUCTION.
PubMed=11113971;
DOI=10.1002/1097-0061(200012)16:16<1483::AID-YEA642>3.3.CO;2-B;
Costenoble R., Valadi H., Gustafsson L., Niklasson C., Franzen C.J.;
"Microaerobic glycerol formation in Saccharomyces cerevisiae.";
Yeast 16:1483-1495(2000).
[10]
FUNCTION, AND INDUCTION.
PubMed=11058591; DOI=10.1074/jbc.M007164200;
Pahlman A.K., Granath K., Ansell R., Hohmann S., Adler L.;
"The yeast glycerol 3-phosphatases Gpp1p and Gpp2p are required for
glycerol biosynthesis and differentially involved in the cellular
responses to osmotic, anaerobic, and oxidative stress.";
J. Biol. Chem. 276:3555-3563(2001).
[11]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[12]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[13]
INDUCTION.
PubMed=15066826; DOI=10.1128/AEM.70.4.2307-2317.2004;
Sonderegger M., Jeppsson M., Hahn-Hagerdal B., Sauer U.;
"Molecular basis for anaerobic growth of Saccharomyces cerevisiae on
xylose, investigated by global gene expression and metabolic flux
analysis.";
Appl. Environ. Microbiol. 70:2307-2317(2004).
[14]
SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-64, AND IDENTIFICATION BY
MASS SPECTROMETRY.
PubMed=15166219; DOI=10.1074/jbc.M404173200;
Zhou W., Ryan J.J., Zhou H.;
"Global analyses of sumoylated proteins in Saccharomyces cerevisiae.
Induction of protein sumoylation by cellular stresses.";
J. Biol. Chem. 279:32262-32268(2004).
[15]
FUNCTION.
PubMed=15113568; DOI=10.1016/j.ymben.2004.02.005;
Nguyen H.T., Dieterich A., Athenstaedt K., Truong N.H., Stahl U.,
Nevoigt E.;
"Engineering of Saccharomyces cerevisiae for the production of L-
glycerol 3-phosphate.";
Metab. Eng. 6:155-163(2004).
[16]
FUNCTION, AND INDUCTION.
PubMed=16358322; DOI=10.1002/yea.1307;
Granath K., Modig T., Forsmark A., Adler L., Liden G.;
"The YIG1 (YPL201c) encoded protein is involved in regulating
anaerobic glycerol metabolism in Saccharomyces cerevisiae.";
Yeast 22:1257-1268(2005).
[17]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=17287358; DOI=10.1073/pnas.0607084104;
Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
"Analysis of phosphorylation sites on proteins from Saccharomyces
cerevisiae by electron transfer dissociation (ETD) mass
spectrometry.";
Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
[18]
FUNCTION.
PubMed=18438874; DOI=10.1002/bit.21777;
Popp A., Nguyen H.T., Boulahya K., Bideaux C., Alfenore S.,
Guillouet S.E., Nevoigt E.;
"Fermentative production of L-glycerol 3-phosphate utilizing a
Saccharomyces cerevisiae strain with an engineered glycerol
biosynthetic pathway.";
Biotechnol. Bioeng. 100:497-505(2008).
[19]
INDUCTION.
PubMed=17425669; DOI=10.1111/j.1567-1364.2007.00234.x;
Wiebe M.G., Rintala E., Tamminen A., Simolin H., Salusjarvi L.,
Toivari M., Kokkonen J.T., Kiuru J., Ketola R.A., Jouhten P.,
Huuskonen A., Maaheimo H., Ruohonen L., Penttila M.;
"Central carbon metabolism of Saccharomyces cerevisiae in anaerobic,
oxygen-limited and fully aerobic steady-state conditions and following
a shift to anaerobic conditions.";
FEMS Yeast Res. 8:140-154(2008).
[20]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-90, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
[21]
INDUCTION.
PubMed=20803479; DOI=10.1002/yea.1819;
Bouwman J., Kiewiet J., Lindenbergh A., van Eunen K., Siderius M.,
Bakker B.M.;
"Metabolic regulation rather than de novo enzyme synthesis dominates
the osmo-adaptation of yeast.";
Yeast 28:43-53(2011).
[22]
UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-64 AND LYS-144, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22106047; DOI=10.1002/pmic.201100166;
Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
"Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
Proteomics 12:236-240(2012).
[23]
X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
Midwest center for structural genomics (MCSG);
"The crystal structure of an isoform of DL-glycerol-3-phosphatase,
Rhr2p from Saccharomyces cerevisiae.";
Submitted (FEB-2009) to the PDB data bank.
-!- FUNCTION: Major isoform of glycerol-1-phosphate phosphohydrolase
involved in glycerol biosynthesis. Plays a role in osmoadaptation
and required for adaptation to anaerobic conditions.
{ECO:0000269|PubMed:11058591, ECO:0000269|PubMed:15113568,
ECO:0000269|PubMed:16358322, ECO:0000269|PubMed:18438874,
ECO:0000269|PubMed:8662716}.
-!- CATALYTIC ACTIVITY: Glycerol 1-phosphate + H(2)O = glycerol +
phosphate. {ECO:0000269|PubMed:8662716}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000305|PubMed:8662716};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=3.1 mM for (DL)-glycerol 3-phosphate
{ECO:0000269|PubMed:8662716};
Vmax=49 umol/min/mg enzyme {ECO:0000269|PubMed:8662716};
pH dependence:
Optimum pH is 6.5. {ECO:0000269|PubMed:8662716};
-!- SUBUNIT: Monomer. {ECO:0000269|PubMed:8662716}.
-!- INTERACTION:
P10591:SSA1; NbExp=3; IntAct=EBI-7829, EBI-8591;
P10592:SSA2; NbExp=2; IntAct=EBI-7829, EBI-8603;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
Nucleus {ECO:0000269|PubMed:14562095}.
-!- INDUCTION: In response to both anaerobic and osmotic stress.
Expression seems to be under the control of YIG1.
{ECO:0000269|PubMed:11058591, ECO:0000269|PubMed:11113971,
ECO:0000269|PubMed:15066826, ECO:0000269|PubMed:16358322,
ECO:0000269|PubMed:17425669, ECO:0000269|PubMed:20803479}.
-!- DISRUPTION PHENOTYPE: Leads to osmosensitivity.
{ECO:0000269|PubMed:10931288}.
-!- MISCELLANEOUS: Present with 193000 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. DOG/GPP
family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=CAA86169.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; D50471; BAA09060.1; -; mRNA.
EMBL; Z38060; CAA86169.1; ALT_INIT; Genomic_DNA.
EMBL; BK006942; DAA08494.1; -; Genomic_DNA.
PIR; S48426; S48426.
RefSeq; NP_012211.2; NM_001179403.1.
PDB; 2QLT; X-ray; 1.60 A; A=1-250.
PDBsum; 2QLT; -.
ProteinModelPortal; P41277; -.
SMR; P41277; -.
BioGrid; 34937; 151.
DIP; DIP-4713N; -.
IntAct; P41277; 30.
MINT; P41277; -.
STRING; 4932.YIL053W; -.
iPTMnet; P41277; -.
MaxQB; P41277; -.
PaxDb; P41277; -.
PRIDE; P41277; -.
TopDownProteomics; P41277; -.
EnsemblFungi; YIL053W; YIL053W; YIL053W.
GeneID; 854758; -.
KEGG; sce:YIL053W; -.
EuPathDB; FungiDB:YIL053W; -.
SGD; S000001315; GPP1.
GeneTree; ENSGT00530000065392; -.
HOGENOM; HOG000248341; -.
InParanoid; P41277; -.
KO; K06116; -.
OMA; VVERSWC; -.
OrthoDB; EOG092C47K9; -.
BioCyc; MetaCyc:YIL053W-MONOMER; -.
BioCyc; YEAST:YIL053W-MONOMER; -.
BRENDA; 3.1.3.21; 984.
EvolutionaryTrace; P41277; -.
PRO; PR:P41277; -.
Proteomes; UP000002311; Chromosome IX.
GO; GO:0005737; C:cytoplasm; IDA:SGD.
GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
GO; GO:0000121; F:glycerol-1-phosphatase activity; IDA:SGD.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0006114; P:glycerol biosynthetic process; IMP:SGD.
GO; GO:0006970; P:response to osmotic stress; TAS:SGD.
Gene3D; 1.10.150.240; -; 1.
Gene3D; 3.40.50.1000; -; 2.
InterPro; IPR036412; HAD-like_sf.
InterPro; IPR006439; HAD-SF_hydro_IA.
InterPro; IPR023214; HAD_sf.
InterPro; IPR023198; PGP-like_dom2.
SUPFAM; SSF56784; SSF56784; 1.
TIGRFAMs; TIGR01509; HAD-SF-IA-v3; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Direct protein sequencing;
Hydrolase; Isopeptide bond; Magnesium; Metal-binding; Nucleus;
Phosphoprotein; Reference proteome; Ubl conjugation.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:9038161}.
CHAIN 2 250 Glycerol-1-phosphate phosphohydrolase 1.
/FTId=PRO_0000087560.
ACT_SITE 18 18 Nucleophile. {ECO:0000250}.
ACT_SITE 20 20 Proton donor. {ECO:0000250}.
METAL 18 18 Magnesium. {ECO:0000250}.
METAL 20 20 Magnesium. {ECO:0000250}.
METAL 179 179 Magnesium. {ECO:0000250}.
MOD_RES 90 90 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
CROSSLNK 64 64 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO);
alternate. {ECO:0000269|PubMed:15166219}.
CROSSLNK 64 64 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in ubiquitin);
alternate. {ECO:0000244|PubMed:22106047}.
CROSSLNK 144 144 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in ubiquitin).
{ECO:0000244|PubMed:22106047}.
CONFLICT 91 91 I -> IK (in Ref. 4; AA sequence).
{ECO:0000305}.
STRAND 6 17 {ECO:0000244|PDB:2QLT}.
TURN 21 23 {ECO:0000244|PDB:2QLT}.
HELIX 27 38 {ECO:0000244|PDB:2QLT}.
HELIX 46 52 {ECO:0000244|PDB:2QLT}.
HELIX 58 65 {ECO:0000244|PDB:2QLT}.
HELIX 67 69 {ECO:0000244|PDB:2QLT}.
HELIX 72 80 {ECO:0000244|PDB:2QLT}.
HELIX 82 86 {ECO:0000244|PDB:2QLT}.
HELIX 96 104 {ECO:0000244|PDB:2QLT}.
HELIX 108 110 {ECO:0000244|PDB:2QLT}.
STRAND 111 114 {ECO:0000244|PDB:2QLT}.
HELIX 119 129 {ECO:0000244|PDB:2QLT}.
STRAND 135 138 {ECO:0000244|PDB:2QLT}.
HELIX 140 142 {ECO:0000244|PDB:2QLT}.
HELIX 151 159 {ECO:0000244|PDB:2QLT}.
HELIX 169 171 {ECO:0000244|PDB:2QLT}.
STRAND 174 180 {ECO:0000244|PDB:2QLT}.
HELIX 181 189 {ECO:0000244|PDB:2QLT}.
STRAND 193 201 {ECO:0000244|PDB:2QLT}.
HELIX 203 206 {ECO:0000244|PDB:2QLT}.
STRAND 212 217 {ECO:0000244|PDB:2QLT}.
HELIX 218 220 {ECO:0000244|PDB:2QLT}.
STRAND 221 223 {ECO:0000244|PDB:2QLT}.
TURN 228 231 {ECO:0000244|PDB:2QLT}.
STRAND 232 238 {ECO:0000244|PDB:2QLT}.
STRAND 241 243 {ECO:0000244|PDB:2QLT}.
TURN 245 248 {ECO:0000244|PDB:2QLT}.
SEQUENCE 250 AA; 27947 MW; 9494B158A937413C CRC64;
MPLTTKPLSL KINAALFDVD GTIIISQPAI AAFWRDFGKD KPYFDAEHVI HISHGWRTYD
AIAKFAPDFA DEEYVNKLEG EIPEKYGEHS IEVPGAVKLC NALNALPKEK WAVATSGTRD
MAKKWFDILK IKRPEYFITA NDVKQGKPHP EPYLKGRNGL GFPINEQDPS KSKVVVFEDA
PAGIAAGKAA GCKIVGIATT FDLDFLKEKG CDIIVKNHES IRVGEYNAET DEVELIFDDY
LYAKDDLLKW


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