GDE1 glycerophosphocholine phosphodiesterase [Saccharomyces cerevisiae S288C] - Gene

Summary

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Gene symbol: GDE1
Gene description: glycerophosphocholine phosphodiesterase
Primary source: FungiDB:YPL110C
Locus tag: YPL110C
See related: SGD:S000006031; AllianceGenome:SGD:S000006031; VEuPathDB:YPL110C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables glycerophosphocholine phosphodiesterase activity. Involved in glycerophospholipid catabolic process. Located in cytoplasm. Orthologous to human GPCPD1 (glycerophosphocholine phosphodiesterase 1). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See GDE1 in Genome Data Viewer

Location:: chromosome: XVI

Exon count:: 1

Sequence:: Chromosome: XVI; NC_001148.4 (341068..344739, complement)

Chromosome XVI - NC_001148.4 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001148.4

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

in contrast to ypl206c, ypl110c does not use GroPCho for growth
Title: Glycerophosphocholine catabolism as a new route for choline formation for phosphatidylcholine synthesis by the Kennedy pathway.
YPL110c and the Git1p permease are required for growth on glycerophosphocholine
Title: Glycerophosphocholine-dependent growth requires Gde1p (YPL110c) and Git1p in Saccharomyces cerevisiae.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables glycerophosphocholine phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info
enables glycerophosphocholine phosphodiesterase activity	IEA Inferred from Electronic Annotation more info
enables glycerophosphocholine phosphodiesterase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables glycerophosphoinositol glycerophosphodiesterase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables phosphoric diester hydrolase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in glycerophospholipid catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in glycerophospholipid catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lipid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in phosphate-containing compound metabolic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	HDA more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: glycerophosphocholine phosphodiesterase

NP_015215.1

EC 3.1.4.2

Glycerophosphocholine (GroPCho) phosphodiesterase; hydrolyzes GroPCho to choline and glycerolphosphate, for use as a phosphate source and as a precursor for phosphocholine synthesis; may interact with ribosomes

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001148.4 Reference assembly

Range

341068..344739 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001183924.1 → NP_015215.1 TPA: glycerophosphocholine phosphodiesterase [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_015215.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W3Q7, Q02979

UniProtKB/TrEMBL

B3LKW3, C7GJ64, N1NX43

Conserved Domains (5) summary

cd08606
Location:871 → 1219

GDPD_YPL110cp_fungi; Glycerophosphodiester phosphodiesterase domain of Saccharomyces cerevisiae YPL110cp and similar proteins

COG0666
Location:361 → 594

ANKYR; Ankyrin repeat [Signal transduction mechanisms]

COG5408
Location:1 → 300

COG5408; SPX domain-containing protein [Signal transduction mechanisms]

sd00045
Location:540 → 569

ANK; ANK repeat [structural motif]

pfam12796
Location:508 → 603

Ank_2; Ankyrin repeats (3 copies)