PDF1_SCHPO
ID PDF1_SCHPO Reviewed; 622 AA.
AC O59747;
DT 02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2012, sequence version 2.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=Palmitoyl-protein thioesterase-dolichyl pyrophosphate phosphatase fusion 1;
DE Contains:
DE RecName: Full=Palmitoyl-protein thioesterase {ECO:0000250|UniProtKB:P45478, ECO:0000303|PubMed:15075260};
DE Short=PPT {ECO:0000250|UniProtKB:P45478};
DE EC=3.1.2.22;
DE AltName: Full=Palmitoyl-protein hydrolase {ECO:0000250|UniProtKB:P45478};
DE Contains:
DE RecName: Full=Dolichyldiphosphatase {ECO:0000250|UniProtKB:P53223};
DE EC=3.6.1.43;
DE AltName: Full=Dolichyl pyrophosphate phosphatase {ECO:0000250|UniProtKB:P53223, ECO:0000303|PubMed:15075260};
DE Flags: Precursor;
GN Name=pdf1; Synonyms=yhc1 {ECO:0000312|PomBase:SPBC530.12c};
GN ORFNames=SPBC530.12c;
OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC Schizosaccharomyces.
OX NCBI_TaxID=284812;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=11859360; DOI=10.1038/nature724;
RA Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA Nurse P.;
RT "The genome sequence of Schizosaccharomyces pombe.";
RL Nature 415:871-880(2002).
RN [2]
RP REVISION OF GENE MODEL.
RX PubMed=21511999; DOI=10.1126/science.1203357;
RA Rhind N., Chen Z., Yassour M., Thompson D.A., Haas B.J., Habib N.,
RA Wapinski I., Roy S., Lin M.F., Heiman D.I., Young S.K., Furuya K., Guo Y.,
RA Pidoux A., Chen H.M., Robbertse B., Goldberg J.M., Aoki K., Bayne E.H.,
RA Berlin A.M., Desjardins C.A., Dobbs E., Dukaj L., Fan L., FitzGerald M.G.,
RA French C., Gujja S., Hansen K., Keifenheim D., Levin J.Z., Mosher R.A.,
RA Mueller C.A., Pfiffner J., Priest M., Russ C., Smialowska A., Swoboda P.,
RA Sykes S.M., Vaughn M., Vengrova S., Yoder R., Zeng Q., Allshire R.,
RA Baulcombe D., Birren B.W., Brown W., Ekwall K., Kellis M., Leatherwood J.,
RA Levin H., Margalit H., Martienssen R., Nieduszynski C.A., Spatafora J.W.,
RA Friedman N., Dalgaard J.Z., Baumann P., Niki H., Regev A., Nusbaum C.;
RT "Comparative functional genomics of the fission yeasts.";
RL Science 332:930-936(2011).
RN [3] {ECO:0000305}
RP FUNCTION, SUBCELLULAR LOCATION, CLEAVAGE, MUTAGENESIS OF SER-125; ASP-245;
RP 322-THR--ASN-622; ARG-363; ARG-373 AND HIS-497, AND DISRUPTION PHENOTYPE.
RX PubMed=15075260; DOI=10.1128/ec.3.2.302-310.2004;
RA Cho S.K., Hofmann S.L.;
RT "pdf1, a palmitoyl protein thioesterase 1 ortholog in Schizosaccharomyces
RT pombe: a yeast model of infantile Batten disease.";
RL Eukaryot. Cell 3:302-310(2004).
RN [4] {ECO:0000305}
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=16823372; DOI=10.1038/nbt1222;
RA Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S.,
RA Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S.,
RA Yoshida M.;
RT "ORFeome cloning and global analysis of protein localization in the fission
RT yeast Schizosaccharomyces pombe.";
RL Nat. Biotechnol. 24:841-847(2006).
CC -!- FUNCTION: Essential protein. Removes thioester-linked fatty acyl groups
CC such as palmitate from modified cysteine residues in proteins or
CC peptides during vacuolar degradation. Required for efficient N-
CC glycosylation. Necessary for maintaining optimal levels of dolichol-
CC linked oligosaccharides. {ECO:0000250|UniProtKB:P45478,
CC ECO:0000250|UniProtKB:P53223, ECO:0000269|PubMed:15075260}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + S-hexadecanoyl-L-cysteinyl-[protein] = H(+) +
CC hexadecanoate + L-cysteinyl-[protein]; Xref=Rhea:RHEA:19233,
CC Rhea:RHEA-COMP:10131, Rhea:RHEA-COMP:11032, ChEBI:CHEBI:7896,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:29950,
CC ChEBI:CHEBI:74151; EC=3.1.2.22;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a dolichyl diphosphate + H2O = a dolichyl phosphate + H(+) +
CC phosphate; Xref=Rhea:RHEA:14385, Rhea:RHEA-COMP:9517, Rhea:RHEA-
CC COMP:9529, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:57497, ChEBI:CHEBI:57683; EC=3.6.1.43;
CC Evidence={ECO:0000250|UniProtKB:P53223};
CC -!- SUBCELLULAR LOCATION: Vacuole {ECO:0000255}. Endoplasmic reticulum
CC membrane {ECO:0000255}; Multi-pass membrane protein {ECO:0000255}.
CC -!- PTM: Proteolytically cleaved, possibly by krp1.
CC {ECO:0000269|PubMed:15075260}.
CC -!- DISRUPTION PHENOTYPE: Cells show lethality and the
CC dolichyldiphosphatase domain alone can rescue the lethal phenotype, but
CC the growth rate of these cells is slower than in wild-type cells. Cells
CC containing wild-type palmitoyl-protein thioesterase (PPT) and
CC inactivated dolichyldiphosphatase reverse the growth retardation
CC phenotype. Cells containing no functional copy of palmitoyl-protein
CC thioesterase are viable, but abnormally sensitive to sodium
CC orthovanadate and elevated external pH. These sensitivities are
CC reversed when the cells are transformed with plasmid containing wild-
CC type PPT and an inactivating mutation in the dolichyldiphosphatase
CC domain. {ECO:0000269|PubMed:15075260}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the palmitoyl-protein
CC thioesterase family. {ECO:0000255}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the
CC dolichyldiphosphatase family. {ECO:0000255}.
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DR EMBL; CU329671; CAA19178.2; -; Genomic_DNA.
DR PIR; T40528; T40528.
DR RefSeq; NP_595325.2; NM_001021232.2.
DR AlphaFoldDB; O59747; -.
DR SMR; O59747; -.
DR BioGRID; 277420; 3.
DR STRING; 4896.SPBC530.12c.1; -.
DR ESTHER; schpo-SPBC530.12C; Palmitoyl-protein_thioesterase.
DR MaxQB; O59747; -.
DR PaxDb; O59747; -.
DR EnsemblFungi; SPBC530.12c.1; SPBC530.12c.1:pep; SPBC530.12c.
DR GeneID; 2540904; -.
DR KEGG; spo:SPBC530.12c; -.
DR PomBase; SPBC530.12c; pdf1.
DR VEuPathDB; FungiDB:SPBC530.12c; -.
DR eggNOG; KOG2541; Eukaryota.
DR eggNOG; KOG3146; Eukaryota.
DR HOGENOM; CLU_439507_0_0_1; -.
DR InParanoid; O59747; -.
DR OMA; MQFGGQV; -.
DR BRENDA; 3.1.2.22; 5613.
DR Reactome; R-SPO-446199; Synthesis of Dolichyl-phosphate.
DR PRO; PR:O59747; -.
DR Proteomes; UP000002485; Chromosome II.
DR GO; GO:0005783; C:endoplasmic reticulum; HDA:PomBase.
DR GO; GO:0030176; C:integral component of endoplasmic reticulum membrane; IBA:GO_Central.
DR GO; GO:0043231; C:intracellular membrane-bounded organelle; IBA:GO_Central.
DR GO; GO:0005773; C:vacuole; IEA:UniProtKB-SubCell.
DR GO; GO:0047874; F:dolichyldiphosphatase activity; IBA:GO_Central.
DR GO; GO:0008474; F:palmitoyl-(protein) hydrolase activity; ISO:PomBase.
DR GO; GO:0008610; P:lipid biosynthetic process; IBA:GO_Central.
DR GO; GO:0006487; P:protein N-linked glycosylation; IBA:GO_Central.
DR GO; GO:0030148; P:sphingolipid biosynthetic process; ISO:PomBase.
DR CDD; cd03382; PAP2_dolichyldiphosphatase; 1.
DR Gene3D; 3.40.50.1820; -; 1.
DR InterPro; IPR029058; AB_hydrolase.
DR InterPro; IPR039667; Dolichyldiphosphatase_PAP2.
DR InterPro; IPR039666; Dolpp1/Cax4.
DR InterPro; IPR036938; P_Acid_Pase_2/haloperoxi_sf.
DR InterPro; IPR000326; P_Acid_Pase_2/haloperoxidase.
DR PANTHER; PTHR11247:SF1; PTHR11247:SF1; 1.
DR Pfam; PF01569; PAP2; 1.
DR SMART; SM00014; acidPPc; 1.
DR SUPFAM; SSF48317; SSF48317; 1.
DR SUPFAM; SSF53474; SSF53474; 1.
PE 1: Evidence at protein level;
KW Disulfide bond; Endoplasmic reticulum; Glycoprotein; Hydrolase; Membrane;
KW Reference proteome; Signal; Transmembrane; Transmembrane helix; Vacuole.
FT SIGNAL 1..24
FT /evidence="ECO:0000255"
FT CHAIN 25..622
FT /note="Palmitoyl-protein thioesterase-dolichyl
FT pyrophosphate phosphatase fusion 1"
FT /id="PRO_0000349152"
FT CHAIN 25..?
FT /note="Palmitoyl-protein thioesterase"
FT /id="PRO_0000349153"
FT CHAIN ?..622
FT /note="Dolichyldiphosphatase"
FT /id="PRO_0000349154"
FT TOPO_DOM 25..405
FT /note="Lumenal"
FT /evidence="ECO:0000255"
FT TRANSMEM 406..426
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 427..428
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 429..449
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 450..488
FT /note="Lumenal"
FT /evidence="ECO:0000255"
FT TRANSMEM 489..511
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 512..519
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 520..540
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 541..552
FT /note="Lumenal"
FT /evidence="ECO:0000255"
FT TRANSMEM 553..573
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 574..622
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT ACT_SITE 125
FT /evidence="ECO:0000250"
FT ACT_SITE 245
FT /evidence="ECO:0000250"
FT ACT_SITE 298
FT /evidence="ECO:0000250"
FT SITE 373
FT /note="Crucial for post-translational processing"
FT /evidence="ECO:0000250"
FT CARBOHYD 223
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 260
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 396
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT DISULFID 106..138
FT /evidence="ECO:0000250"
FT MUTAGEN 125
FT /note="S->A: Sensitive to vanadate and elevation of
FT external pH."
FT /evidence="ECO:0000269|PubMed:15075260"
FT MUTAGEN 245
FT /note="D->A: Sensitive to vanadate and elevation of
FT external pH."
FT /evidence="ECO:0000269|PubMed:15075260"
FT MUTAGEN 322..622
FT /note="Missing: Lethal."
FT /evidence="ECO:0000269|PubMed:15075260"
FT MUTAGEN 363
FT /note="R->A: No prevention of cleavage of the linker
FT domain, but increases the ratio of the unprocessed from the
FT processed form."
FT /evidence="ECO:0000269|PubMed:15075260"
FT MUTAGEN 373
FT /note="R->A: Abolished cleavage of the linker domain."
FT /evidence="ECO:0000269|PubMed:15075260"
FT MUTAGEN 497
FT /note="H->A: Lethal."
FT /evidence="ECO:0000269|PubMed:15075260"
SQ SEQUENCE 622 AA; 71196 MW; 48FFF42EFCAD1962 CRC64;
MLSCSSFLIF FLFSWVLLPM KSFAIPIISL DKVRLAINDG ASEQLPVVIW HGLGDTPTSF
TLTEVSQRVQ KLTKGAVYAI RVGDNEFEDI KAGYLGKLED QLDEVCDLIG NEDSLSNGFY
ALGLSQGGLF LRALAQTCDA AKIRSLITLG SPHSGINTIP GCSPTNLICK AVVHSILGLG
IWHSWIQNHV VQAQYYRTEK QYDKYLENNK FLTHLNNEVL HDNYTRNIEK LKELDNLVAV
SFERDDIVEP PYSTGFGWIN ETTGENIEME DFVLYESLGL KDLVNQGKLE TISFPGRHLQ
MRWGDFDALV LKYFKDEKEE KTELEESTRP SNFLSTYFVS PLVSAIDGTV DYLHGKSLFP
EKRNFKELTM RKRSIVTPED SEEVYPYISE FVAASNVSEE KGPKSFANLA FITIFSHFFY
HIDDMWRSTL GLFSLIPQII GIIYLTVMFT GRELDTFMQF GGQVVNEFIN YVVKVSLKYP
RPADIEYGVG YGMPSSHSQF MGFFSAYMIA WDYKYRRSQC FSMLSFAKYA IYLTLSTFVC
SSRYLLDFHY LTQVVYGYMI GFGVGLFWVY LVGKLRSLGV TKWLLSLPPL QFFYIKDTIP
HSKDNHKRQW LESKQFKNQK SN
