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Protein

Palmitoyl-protein thioesterase-dolichyl pyrophosphate phosphatase fusion 1

Gene

pdf1

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Essential protein. Removes thioester-linked fatty acyl groups such as palmitate from modified cysteine residues in proteins or peptides during vacuolar degradation. Required for efficient N-glycosylation. Necessary for maintaining optimal levels of dolichol-linked oligosaccharides.By similarity1 Publication

Catalytic activityi

Palmitoyl-[protein] + H2O = palmitate + [protein].
Dolichyl diphosphate + H2O = dolichyl phosphate + phosphate.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei125 – 1251By similarity
Active sitei245 – 2451By similarity
Active sitei298 – 2981By similarity
Sitei373 – 3731Crucial for post-translational processingBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Enzyme and pathway databases

BRENDAi3.1.2.22. 5613.
ReactomeiR-SPO-75876. Synthesis of very long-chain fatty acyl-CoAs.

Protein family/group databases

ESTHERischpo-SPBC530.12C. Palmitoyl-protein_thioesterase.

Names & Taxonomyi

Protein namesi
Recommended name:
Palmitoyl-protein thioesterase-dolichyl pyrophosphate phosphatase fusion 1
Cleaved into the following 2 chains:
Palmitoyl-protein thioesterase1 PublicationBy similarity (EC:3.1.2.22)
Short name:
PPTBy similarity
Alternative name(s):
Palmitoyl-protein hydrolaseBy similarity
DolichyldiphosphataseBy similarity (EC:3.6.1.43)
Alternative name(s):
Dolichyl pyrophosphate phosphatase1 PublicationBy similarity
Gene namesi
Name:pdf1
Synonyms:yhc1Imported
ORF Names:SPBC530.12c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:SPBC530.12c.
PomBaseiSPBC530.12c. pdf1.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini25 – 405381LumenalSequence analysisAdd
BLAST
Transmembranei406 – 42621HelicalSequence analysisAdd
BLAST
Topological domaini427 – 4282CytoplasmicSequence analysis
Transmembranei429 – 44921HelicalSequence analysisAdd
BLAST
Topological domaini450 – 48839LumenalSequence analysisAdd
BLAST
Transmembranei489 – 51123HelicalSequence analysisAdd
BLAST
Topological domaini512 – 5198CytoplasmicSequence analysis
Transmembranei520 – 54021HelicalSequence analysisAdd
BLAST
Topological domaini541 – 55212LumenalSequence analysisAdd
BLAST
Transmembranei553 – 57321HelicalSequence analysisAdd
BLAST
Topological domaini574 – 62249CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane, Vacuole

Pathology & Biotechi

Disruption phenotypei

Cells show lethality and the dolichyldiphosphatase domain alone can rescue the lethal phenotype, but the growth rate of these cells is slower than in wild-type cells. Cells containing wild-type palmitoyl-protein thioesterase (PPT) and inactivated dolichyldiphosphatase reverse the growth retardation phenotype. Cells containing no functional copy of palmitoyl-protein thioesterase are viable, but abnormally sensitive to sodium orthovanadate and elevated external pH. These sensitivities are reversed when the cells are transformed with plasmid containing wild-type PPT and an inactivating mutation in the dolichyldiphosphatase domain.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi125 – 1251S → A: Sensitive to vanadate and elevation of external pH. 1 Publication
Mutagenesisi245 – 2451D → A: Sensitive to vanadate and elevation of external pH. 1 Publication
Mutagenesisi322 – 622301Missing : Lethal. 1 PublicationAdd
BLAST
Mutagenesisi363 – 3631R → A: No prevention of cleavage of the linker domain, but increases the ratio of the unprocessed from the processed form. 1 Publication
Mutagenesisi373 – 3731R → A: Abolished cleavage of the linker domain. 1 Publication
Mutagenesisi497 – 4971H → A: Lethal. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini? – 622DolichyldiphosphatasePRO_0000349154
Signal peptidei1 – 2424Sequence analysisAdd
BLAST
Chaini25 – 622598Palmitoyl-protein thioesterase-dolichyl pyrophosphate phosphatase fusion 1PRO_0000349152Add
BLAST
Chaini25 – ?Palmitoyl-protein thioesterasePRO_0000349153

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi106 ↔ 138By similarity
Glycosylationi223 – 2231N-linked (GlcNAc...)Sequence analysis
Glycosylationi260 – 2601N-linked (GlcNAc...)Sequence analysis
Glycosylationi396 – 3961N-linked (GlcNAc...)Sequence analysis

Post-translational modificationi

Proteolytically cleaved, possibly by krp1.1 Publication

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

MaxQBiO59747.

Interactioni

Protein-protein interaction databases

MINTiMINT-4675865.

Family & Domainsi

Sequence similaritiesi

In the N-terminal section; belongs to the palmitoyl-protein thioesterase family.Sequence analysis
In the C-terminal section; belongs to the dolichyldiphosphatase family.Sequence analysis

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

InParanoidiO59747.
KOiK01074.
OrthoDBiEOG7TF7KS.

Family and domain databases

Gene3Di1.20.144.10. 1 hit.
3.40.50.1820. 1 hit.
InterProiIPR029058. AB_hydrolase.
IPR000326. P_Acid_Pase_2/haloperoxidase.
IPR002472. Palm_thioest.
[Graphical view]
PfamiPF02089. Palm_thioest. 1 hit.
PF01569. PAP2. 1 hit.
[Graphical view]
SMARTiSM00014. acidPPc. 1 hit.
[Graphical view]
SUPFAMiSSF48317. SSF48317. 1 hit.
SSF53474. SSF53474. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O59747-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLSCSSFLIF FLFSWVLLPM KSFAIPIISL DKVRLAINDG ASEQLPVVIW
60 70 80 90 100
HGLGDTPTSF TLTEVSQRVQ KLTKGAVYAI RVGDNEFEDI KAGYLGKLED
110 120 130 140 150
QLDEVCDLIG NEDSLSNGFY ALGLSQGGLF LRALAQTCDA AKIRSLITLG
160 170 180 190 200
SPHSGINTIP GCSPTNLICK AVVHSILGLG IWHSWIQNHV VQAQYYRTEK
210 220 230 240 250
QYDKYLENNK FLTHLNNEVL HDNYTRNIEK LKELDNLVAV SFERDDIVEP
260 270 280 290 300
PYSTGFGWIN ETTGENIEME DFVLYESLGL KDLVNQGKLE TISFPGRHLQ
310 320 330 340 350
MRWGDFDALV LKYFKDEKEE KTELEESTRP SNFLSTYFVS PLVSAIDGTV
360 370 380 390 400
DYLHGKSLFP EKRNFKELTM RKRSIVTPED SEEVYPYISE FVAASNVSEE
410 420 430 440 450
KGPKSFANLA FITIFSHFFY HIDDMWRSTL GLFSLIPQII GIIYLTVMFT
460 470 480 490 500
GRELDTFMQF GGQVVNEFIN YVVKVSLKYP RPADIEYGVG YGMPSSHSQF
510 520 530 540 550
MGFFSAYMIA WDYKYRRSQC FSMLSFAKYA IYLTLSTFVC SSRYLLDFHY
560 570 580 590 600
LTQVVYGYMI GFGVGLFWVY LVGKLRSLGV TKWLLSLPPL QFFYIKDTIP
610 620
HSKDNHKRQW LESKQFKNQK SN
Length:622
Mass (Da):71,196
Last modified:October 3, 2012 - v2
Checksum:i48FFF42EFCAD1962
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329671 Genomic DNA. Translation: CAA19178.2.
PIRiT40528.
RefSeqiNP_595325.2. NM_001021232.2.

Genome annotation databases

EnsemblFungiiSPBC530.12c.1; SPBC530.12c.1:pep; SPBC530.12c.
GeneIDi2540904.
KEGGispo:SPBC530.12c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329671 Genomic DNA. Translation: CAA19178.2.
PIRiT40528.
RefSeqiNP_595325.2. NM_001021232.2.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

MINTiMINT-4675865.

Protein family/group databases

ESTHERischpo-SPBC530.12C. Palmitoyl-protein_thioesterase.

Proteomic databases

MaxQBiO59747.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPBC530.12c.1; SPBC530.12c.1:pep; SPBC530.12c.
GeneIDi2540904.
KEGGispo:SPBC530.12c.

Organism-specific databases

EuPathDBiFungiDB:SPBC530.12c.
PomBaseiSPBC530.12c. pdf1.

Phylogenomic databases

InParanoidiO59747.
KOiK01074.
OrthoDBiEOG7TF7KS.

Enzyme and pathway databases

BRENDAi3.1.2.22. 5613.
ReactomeiR-SPO-75876. Synthesis of very long-chain fatty acyl-CoAs.

Miscellaneous databases

PROiO59747.

Family and domain databases

Gene3Di1.20.144.10. 1 hit.
3.40.50.1820. 1 hit.
InterProiIPR029058. AB_hydrolase.
IPR000326. P_Acid_Pase_2/haloperoxidase.
IPR002472. Palm_thioest.
[Graphical view]
PfamiPF02089. Palm_thioest. 1 hit.
PF01569. PAP2. 1 hit.
[Graphical view]
SMARTiSM00014. acidPPc. 1 hit.
[Graphical view]
SUPFAMiSSF48317. SSF48317. 1 hit.
SSF53474. SSF53474. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  2. "Comparative functional genomics of the fission yeasts."
    Rhind N., Chen Z., Yassour M., Thompson D.A., Haas B.J., Habib N., Wapinski I., Roy S., Lin M.F., Heiman D.I., Young S.K., Furuya K., Guo Y., Pidoux A., Chen H.M., Robbertse B., Goldberg J.M., Aoki K.
    , Bayne E.H., Berlin A.M., Desjardins C.A., Dobbs E., Dukaj L., Fan L., FitzGerald M.G., French C., Gujja S., Hansen K., Keifenheim D., Levin J.Z., Mosher R.A., Mueller C.A., Pfiffner J., Priest M., Russ C., Smialowska A., Swoboda P., Sykes S.M., Vaughn M., Vengrova S., Yoder R., Zeng Q., Allshire R., Baulcombe D., Birren B.W., Brown W., Ekwall K., Kellis M., Leatherwood J., Levin H., Margalit H., Martienssen R., Nieduszynski C.A., Spatafora J.W., Friedman N., Dalgaard J.Z., Baumann P., Niki H., Regev A., Nusbaum C.
    Science 332:930-936(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVISION OF GENE MODEL.
  3. "pdf1, a palmitoyl protein thioesterase 1 ortholog in Schizosaccharomyces pombe: a yeast model of infantile Batten disease."
    Cho S.K., Hofmann S.L.
    Eukaryot. Cell 3:302-310(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, CLEAVAGE, MUTAGENESIS OF SER-125; ASP-245; 322-THR--ASN-622; ARG-363; ARG-373 AND HIS-497, DISRUPTION PHENOTYPE.
  4. "ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe."
    Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S., Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S., Yoshida M.
    Nat. Biotechnol. 24:841-847(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiPDF1_SCHPO
AccessioniPrimary (citable) accession number: O59747
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 2, 2008
Last sequence update: October 3, 2012
Last modified: July 6, 2016
This is version 101 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.