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protein coding gene - pdf1 (SPBC530.12c) - palmitoyl protein thioesterase/ dolichol pyrophosphate phosphatase fusion protein Pdf1

Gene summary

Standard name
pdf1
Systematic ID
SPBC530.12c
Product
palmitoyl protein thioesterase/ dolichol pyrophosphate phosphatase fusion protein Pdf1
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
yhc1
UniProt ID
O59747
ORFeome ID
36/36F01
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome II: 820804..823168 reverse strand

Annotation

PBO:0003353 - 3.1.2.22

PBO:0000522 - 3.6.1.-

Complementation

PBO:0003352 - functionally complemented by human PPT1

References:

Disease association

MONDO:0002561 - lysosomal storage disease

References:

MONDO:0005066 - metabolic disease

References:

MONDO:0005071 - nervous system disorder

References:

MONDO:0009744 - neuronal ceroid lipofuscinosis 1

References:

MONDO:0008767 - neuronal ceroid lipofuscinosis 3

References:

GO biological process

GO:0008610 - lipid biosynthetic process

References:

GO:0006487 - protein N-linked glycosylation

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GO cellular component

GO:0005783 - endoplasmic reticulum

References:

GO:0005789 - endoplasmic reticulum membrane

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GO molecular function

GO:0047874 - dolichyldiphosphatase activity

References:

GO:0008474 - palmitoyl-(protein) hydrolase activity

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Genome organisation

PBO:0000228 - domain combination not observed in other organisms

PBO:0000229 - tandem fusion protein

References:

Modification

MOD:00689 - disulfide crosslinked residues

References:

MOD:00006 - N-glycosylated residue

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MOD:01148 - ubiquitinylated lysine

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Protein sequence feature

SO:0100011 - cleaved_peptide_region

References:

SO:0000418 - signal_peptide

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SO:0001812 - transmembrane_helix

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Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0001669 - abolished protein processing during vegetative growth

References:

Genotypes:

FYPO:0001422 - decreased protein processing during vegetative growth

References:

Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

References:

Genotypes:

FYPO:0000311 - inviable after spore germination with normal, unseptated germ tube morphology

References:

Genotypes:

FYPO:0002151 - inviable spore

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Genotypes:

FYPO:0002061 - inviable vegetative cell population

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Genotypes:

FYPO:0001357 - normal vegetative cell population growth

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Genotypes:

FYPO:0000723 - sensitive to alkalinity

References:

Genotypes:

FYPO:0003656 - sensitive to vanadate

References:

Genotypes:

Taxonomic conservation

PBO:0011065 - conserved in eukaryotes

PBO:0011071 - conserved in eukaryotes only

PBO:0011064 - conserved in fungi

PBO:0011069 - conserved in metazoa

PBO:0011070 - conserved in vertebrates

PBO:0006222 - predominantly single copy (one to one)

Warnings

PBO:0000070 - gene structure updated

References:

Protein features

IDNameInterPro nameDB name
PF01569PAP2PAP2/HPOPfam
PF02089Palm_thioestPfam
cd03382PAP2_dolichyldiphosphataseDolichyldiphosphatase_PAP2CDD
SM00014acidPPcPAP2/HPOSMART
G3DSA:1.20.144.10CATH-Gene3D
G3DSA:3.40.50.1820AB_hydrolase_foldCATH-Gene3D
SSF48317PAP2/HPO_sfSUPERFAMILY
SSF53474AB_hydrolase_foldSUPERFAMILY
PTHR11247PANTHER
Transmembrane alpha helixDeepTMHMM
Signal PeptideSignal-Peptide-DeepTMHMM

Orthologs

References / Literature

PMID:37970674 - SUMOylation regulates Lem2 function in centromere clustering and silencing.
Strachan J et al. J Cell Sci 2023 Dec 01;136(23)
PMID:23163955 - Analysis of stress-induced duplex destabilization (SIDD) properties of replication origins, genes and intergenes in the fission yeast, Schizosaccharomyces pombe.
Yadav MP et al. BMC Res Notes 2012 Nov 19;5:643
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:23101633 - Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells.
Marguerat S et al. Cell 2012 Oct 26;151(3):671-83
GO_REF:0000024 - Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.
PMID:22633491 - Mapping N-glycosylation sites across seven evolutionarily distant species reveals a divergent substrate proteome despite a common core machinery.
Zielinska DF et al. Mol Cell 2012 May 25;46(4):542-8
PMID:15075260 - pdf1, a palmitoyl protein thioesterase 1 Ortholog in Schizosaccharomyces pombe: a yeast model of infantile Batten disease.
Cho SK et al. Eukaryot Cell 2004 Apr;3(2):302-10
PMID:30824696 - Systematic analysis reveals the prevalence and principles of bypassable gene essentiality.
Li J et al. Nat Commun 2019 Mar 01;10(1):1002
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:20473289 - Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.
Kim DU et al. Nat Biotechnol 2010 Jun;28(6):617-623
PMID:33109728 - High-Throughput Identification of Nuclear Envelope Protein Interactions in Schizosaccharomyces pombe Using an Arrayed Membrane Yeast-Two Hybrid Library.
Varberg JM et al. G3 (Bethesda) 2020 Dec 03;10(12):4649-4663
PMID:11152613 - Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
Krogh A et al. J Mol Biol 2001 Jan 19;305(3):567-80
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
PMID:23697806 - A genome-wide resource of cell cycle and cell shape genes of fission yeast.
Hayles J et al. Open Biol 2013 May 22;3(5):130053
PMID:40015273 - A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin.
Skribbe M et al. Mol Cell 2025 Feb 19;
PMID:16823372 - ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.
Matsuyama A et al. Nat Biotechnol 2006 Jul;24(7):841-7
PB_REF:0000003 - Disease Association Curation
PMID:36408920 - UniProt: the Universal Protein Knowledgebase in 2023.
UniProt Consortium Nucleic Acids Res 2023 Jan 06;51(D1):D523-D531