YPC1/YBR183W Single Page Format

This page provides an alternative format to the SGD Locus Summary Page. Note that additional information may be available on or linked from the standard format SGD Locus Summary page.

Contents
Names and Identifiers

GO Annotations

Pathways

Summary Paragraph

Mutant Phenotypes

Interactions

Homologs

Protein Info (physical properties, transcript info)

PDB Homologs (protein structure info)

Motifs

Genome-wide Expression
(and other large-scale analyses)

Locus History (misc. notes)

Sequence Retrieval and Analysis

Map and Displays

Localization

Community Annotation

Literature Guide

Sequence Coordinates

ChrII: 596110 to 597060
CDS: 596110 - 597060

Click on map for expanded view

SGD ORF map GBrowse
SGD Locus Page

Names and Identifiers [TOP] [NEXT]
Standard Name Systematic Name Alias Feature Type SGDID

YPC1 YBR183W ORF, Verified S000000387

This name is reserved with SGD according to the Gene Naming Guidelines agreed upon by the yeast community.
Gene name reserved on: 1999-11-03. Gene name expires on 2000-11-03.
Description
Alkaline ceramidase that also has reverse (CoA-independent) ceramide synthase activity, catalyzes both breakdown and synthesis of phytoceramide; overexpression confers fumonisin B1 resistance

GO Annotations [TOP] [NEXT]
Molecular Function
Annotation(s) Reference(s) Evidence Assigned By
ceramidase activity Mao C, et al. (2000) Cloning and characterization of a Saccharomyces cerevisiae alkaline ceramidase with specificity for dihydroceramide. J Biol Chem 275(40):31369-78
       IDA : Inferred from Direct Assay
Assigned on 2002-11-01 SGD
hydrolase activity GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0378
Assigned on 2007-05-23 UniProtKB
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR008901
Assigned on 2007-05-23 UniProtKB
Biological Process
Annotation(s) Reference(s) Evidence Assigned By
ceramide biosynthetic process Schorling S, et al. (2001) Lag1p and Lac1p are essential for the Acyl-CoA-dependent ceramide synthase reaction in Saccharomyces cerevisae. Mol Biol Cell 12(11):3417-27
       IGI : Inferred from Genetic Interaction with SGD:LAG1, SGD:LAC1
Assigned on 2010-02-02 SGD
ceramide metabolic process Mao C, et al. (2000) Cloning and characterization of a Saccharomyces cerevisiae alkaline ceramidase with specificity for dihydroceramide. J Biol Chem 275(40):31369-78
       IMP : Inferred from Mutant Phenotype
Assigned on 2002-11-01 SGD
DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR008901
Assigned on 2007-05-23 UniProtKB
Cellular Component
Annotation(s) Reference(s) Evidence Assigned By
Golgi apparatus GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0333
Assigned on 2008-02-14 UniProtKB
Golgi membrane DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR008901
Assigned on 2009-06-17 UniProtKB
endoplasmic reticulum Mao C, et al. (2000) Cloning and characterization of a Saccharomyces cerevisiae alkaline ceramidase with specificity for dihydroceramide. J Biol Chem 275(40):31369-78
       IDA : Inferred from Direct Assay
Assigned on 2002-11-01 SGD
GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0256
Assigned on 2007-05-23 UniProtKB
endoplasmic reticulum membrane DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR008901
Assigned on 2009-06-17 UniProtKB
integral to membrane DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR008901
Assigned on 2007-05-23 UniProtKB
GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0812
Assigned on 2007-05-23 UniProtKB
GOA curators and UniProt curators (2007) Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping.
     IEA : Inferred from Electronic Annotation with EBI:SL-9909
Assigned on 2009-10-01 UniProtKB
membrane GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0472
Assigned on 2007-05-23 UniProtKB

Pathways [TOP] [NEXT]
sphingolipid metabolism

Summary Paragraph [TOP] [NEXT]
SUMMARY PARAGRAPH for YPC1/YBR183W for YPC1
About sphingolipid metabolism
Sphingolipids are essential components of the plasma membrane in all eukaryotic cells. S. cerevisiae cells make three complex sphingolipids: inositol-phosphoceramide (IPC), mannose-inositol-phosphoceramide (MIPC), and mannose-(inositol phosphate)2-ceramide (M(IP)2C)(1). In the yeast plasma membrane sphingolipids concentrate with ergosterol to form lipid rafts, specialized membrane microdomains implicated in a variety of cellular processes, including sorting of membrane proteins and lipids, as well as organizing and regulating signaling cascades (2). Intermediates in sphingolipid biosynthesis have been shown to play important roles as signaling molecules and growth regulators. Sphingolipid long chain bases (LCBs), dihydrosphingosine (DHS) and phytosphingosine (PHS), have been implicated as secondary messengers in signaling pathways that regulate heat stress response (3, 4). Other intermediates, phytoceramide and long-chain base phosphates (LCBPs), have been shown to be components of the tightly-controlled ceramide/LCBP rheostat, which regulates cell growth (5). Since phosphoinositol-containing sphingolipids are unique to fungi, the sphingolipid biosynthesis pathway is considered a target for antifungal drugs (6, 7).
Last Updated: 2007-10-05

Basic References [TOP]
BASIC INFORMATION REFERENCES forYPC1/YBR183W for YPC1
1) Dickson RC and Lester RL (2002) Sphingolipid functions in Saccharomyces cerevisiae. Biochim Biophys Acta 1583(1):13-25

2) Bagnat M and Simons K (2002) Lipid rafts in protein sorting and cell polarity in budding yeast Saccharomyces cerevisiae. Biol Chem 383(10):1475-80

3) Jenkins GM, et al. (1997) Involvement of yeast sphingolipids in the heat stress response of Saccharomyces cerevisiae. J Biol Chem 272(51):32566-72

4) Ferguson-Yankey SR, et al. (2002) Mutant analysis reveals complex regulation of sphingolipid long chain base phosphates and long chain bases during heat stress in yeast. Yeast 19(7):573-86

5) Kobayashi SD and Nagiec MM (2003) Ceramide/long-chain base phosphate rheostat in Saccharomyces cerevisiae: regulation of ceramide synthesis by Elo3p and Cka2p. Eukaryot Cell 2(2):284-94

6) Nagiec MM, et al. (1997) Sphingolipid synthesis as a target for antifungal drugs. Complementation of the inositol phosphorylceramide synthase defect in a mutant strain of Saccharomyces cerevisiae by the AUR1 gene. J Biol Chem 272(15):9809-17

7) Sugimoto Y, et al. (2004) IPC synthase as a useful target for antifungal drugs. Curr Drug Targets Infect Disord 4(4):311-22

8) Mao C, et al. (2000) Cloning of an alkaline ceramidase from Saccharomyces cerevisiae. An enzyme with reverse (CoA-independent) ceramide synthase activity. J Biol Chem 275(10):6876-84

9) Mao C, et al. (2000) Cloning and characterization of a Saccharomyces cerevisiae alkaline ceramidase with specificity for dihydroceramide. J Biol Chem 275(40):31369-78

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for YPC1/YBR183W

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for YPC1/YBR183W

Homologs [TOP] [NEXT]

Comparison Resources

Physical Properties and Transcript Information: predicted from sequence [TOP] [NEXT]
Protein Sequence Calculations
from Predicted Full length Translation

N-term MGIFRWN

C-term IEVKKEK

Length(aa) 316

MW(Da) 36,419

pI 8.35

Amino Acid Composition (full length)

GCG tools: PepPlot, Helical Wheel, PepStruct

Transcript Translation Calculations

Codon Bias 0.069

Codon Adaptation Index 0.116

Frequency of Optimal Codons 0.448

Hydropathicity of Protein 0.317

Aromaticity Score 0.152

10 20 30 40 50 | | | | | MGIFRWNYPESSVPGVWGETTSTIDWCEENYVVSPYIAEWSNTLTNSVFI LSAIYTTYSAYKNKLEKRFLLIGFGYGLVGVGSWLFHMTLKYRFQLLDEL PMIYAMCIPTWSLVCEAKEALLNGDNHKKVPLFEQIFIGVIIGLAVTTAS ILYVIYKNVDIHQILFGVQIVVVAATAGSLTYRYVHDPLAKRNLKASMAL GAILFLSGYISWLLDIHYCSFWVHVRRSILALPLGVLLEPHGWWHILTGM GIYFYIVSLEHLRVITLNVSCNYQFIWRWKVFPELIWKGRKPSTRYSLEL FGPYVEDQSIEVKKEK*

Protein Structures from PDB: proteins of known structure with sequence similarity to YPC1/YBR183W, based on Smith-Waterman analysis. [TOP] [NEXT]
No protein structure information available.

Genome-wide Expression and Other Large-Scale Analyses [TOP] [NEXT]

Functional Analysis
You can also search multiple datasets simultaneously using Expression Connection for expression studies or Function Junction for other large scale analyses.

Locus History (misc. notes) [TOP] [NEXT]
Nomenclature History
Standard Name Date Standardized Reference
YPC1 2000-03-28 SGD (2007) Information without a citation in SGD

Standard Name	Date Standardized	Reference
YPC1	2000-03-28	SGD (2007) Information without a citation in SGD

Sequence Retrieval [TOP] [NEXT]
Sequence Type Output Format

Genomic DNA GCG | FASTA | NoHeader

Genomic DNA with 1 kb up and downstream GCG | FASTA | NoHeader

DNA coding sequence
(without introns, without flanking regions) GCG | FASTA | NoHeader

Protein Translation of ORF GCG | FASTA | NoHeader

6-Frame Translation(with Restriction Map) GCG

Restriction Fragment Sizes GCG

Sequence Analysis Tools
Sequence from other databases

Sequence ID Source

YBR183W SGD Systematic Sequence

852481 NCBI: Gene ID

NP_009742.1 NCBI: RefSeq protein version ID

NP_009742.1 NCBI: RefSeq protein version ID

6319660 NCBI: NCBI protein GI

Sequence from other databases
Sequence ID	Source
YBR183W	SGD Systematic Sequence
852481	NCBI: Gene ID
NP_009742.1	NCBI: RefSeq protein version ID
NP_009742.1	NCBI: RefSeq protein version ID
6319660	NCBI: NCBI protein GI

Map and Displays [TOP] [NEXT]
Physical, Genetic Maps: Chromosomal Feature Map GBrowse Combined Physical and Genetic Map Genetic Distance vs. Physical Distance Ratios
Similarity Viewers: Synteny Viewer Genomic Stripe View SAGE Results Map

Localization [TOP] [NEXT]

Localization Resources

Community Annotation [TOP] [NEXT]
No community annotation available.

Literature Guide: papers categorized by topic. [TOP]
Topics Reference Other Genes Addressed
18 curated references; 0 references not yet curated
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Cerantola V, et al. (2009) Aureobasidin A arrests growth of yeast cells through both ceramide intoxication and deprivation of essential inositolphosphorylceramides. Mol Microbiol 71(6):1523-37
     |AUR1 |LAC1 |LAG1 |YDC1
Genetic Interactions
Mutants/Phenotypes
Regulatory Role
Strains/Constructs
Villa NY, et al. (2009) Sphingolipids function as downstream effectors of a fungal PAQR. Mol Pharmacol 75(4):866-75
     |FET3 |IZH2 |NRG1 |NRG2 |PKH1 |PKH2 |TPK2 |YDC1
Regulation of
Transcription
Ye Y, et al. (2009) Gaining insight into the response logic of Saccharomyces cerevisiae to heat shock by combining expression profiles with metabolic pathways. Biochem Biophys Res Commun 385(3):357-62
       |ADH6 |ADH7 |AFT1 |ARA1 |ATH1 |CRD1 |DPL1 |FHL1 |GCY1 |GDB1 |GLC3 |GLG1 |GLG2 |GPH1 |MORE
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Mousley CJ, et al. (2008) Trans-Golgi network and endosome dynamics connect ceramide homeostasis with regulation of the unfolded protein response and TOR signaling in yeast. Mol Biol Cell 19(11):4785-803
       |CKI1 |GSG1 |ISC1 |KES1 |PIK1 |PPN1 |SEC14 |SNC1 |SNC2 |STT4 |SUI2 |TLG2
Cross-species Expression
Genetic Interactions
Mutants/Phenotypes
Non-Fungal Related Genes/Proteins
Strains/Constructs
Pata MO, et al. (2008) Molecular cloning and characterization of OsCDase, a ceramidase enzyme from rice. Plant J 55(6):1000-9
       |YDC1
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Cerantola V, et al. (2007) Yeast sphingolipids do not need to contain very long chain fatty acids. Biochem J 401(1):205-216
       |LAC1 |LAG1 |LIP1 |YDC1
Mutants/Phenotypes
Hirasawa T, et al. (2007) Identification of target genes conferring ethanol stress tolerance to Saccharomyces cerevisiae based on DNA microarray data analysis. J Biotechnol 131(1):34-44
       |IRC15 |SOH1 |TAT2 |TRP1 |TRP2 |TRP3 |TRP4 |TRP5
Reviews
Kihara A, et al. (2007) Metabolism and biological functions of two phosphorylated sphingolipids, sphingosine 1-phosphate and ceramide 1-phosphate. Prog Lipid Res 46(2):126-44
         |DPL1 |LAC1 |LAG1 |LCB1 |LCB2 |LCB3 |LCB4 |LCB5 |LIP1 |SUR2 |TSC10 |TSC3 |YDC1 |YSR3
Cross-species Expression
Mutants/Phenotypes
Non-Fungal Related Genes/Proteins
Galadari S, et al. (2006) Identification of a novel amidase motif in neutral ceramidase. Biochem J 393(Pt 3):687-95
       |YDC1
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Gaigg B, et al. (2005) Synthesis of sphingolipids with very long chain fatty acids but not ergosterol is required for routing of newly synthesized plasma membrane ATPase to the cell surface of yeast. J Biol Chem 280(23):22515-22
       |ACB1 |ACC1 |ARE1 |ARE2 |AYR1 |CSG2 |DPL1 |ELO1 |ERG24 |ERG3 |ERG4 |ERG5 |FEN1 |HEM1 |MORE
Function/Process
Mutants/Phenotypes
Strains/Constructs
Proszynski TJ, et al. (2005) A genome-wide visual screen reveals a role for sphingolipids and ergosterol in cell surface delivery in yeast. Proc Natl Acad Sci U S A 102(50):17981-6
       |AYR1 |BUD27 |CCZ1 |CHS5 |ERG4 |ERG6 |FAB1 |GIM3 |KES1 |LCB1 |MCH5 |MON1 |OPI9 |PAC10 |MORE
Function/Process
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Jiang JC, et al. (2004) Suppressor analysis points to the subtle role of the LAG1 ceramide synthase gene in determining yeast longevity. Exp Gerontol 39(7):999-1009
       |LAC1 |LAG1 |YDC1
Regulation of
Transcription
Zhang W, et al. (2003) Microarray analyses of the metabolic responses of Saccharomyces cerevisiae to organic solvent dimethyl sulfoxide. J Ind Microbiol Biotechnol 30(1):57-69
         |AAH1 |ABP140 |ACS2 |ADE1 |ADE12 |ADE17 |ADE4 |ADE8 |ADH2 |ADH4 |ADH5 |ADK1 |ADO1 |ALD3 |MORE
Reviews
Funato K, et al. (2002) Biosynthesis and trafficking of sphingolipids in the yeast Saccharomyces cerevisiae. Biochemistry 41(51):15105-14
     |ACB1 |AUR1 |CCC2 |CSG2 |DPL1 |ELO1 |FEN1 |FMP45 |IFA38 |IPT1 |ISC1 |LAC1 |LAG1 |LCB1 |MORE
Function/Process
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Schorling S, et al. (2001) Lag1p and Lac1p are essential for the Acyl-CoA-dependent ceramide synthase reaction in Saccharomyces cerevisae. Mol Biol Cell 12(11):3417-27
       |LAC1 |LAG1 |YDC1
Function/Process
Mutants/Phenotypes
Strains/Constructs
de Groot PW, et al. (2001) A genomic approach for the identification and classification of genes involved in cell wall formation and its regulation in Saccharomyces cerevisiae. Comp Funct Genomics 2(3):124-42
             |AAD4 |AIM22 |ALG12 |ALK2 |ARE2 |ARG2 |ARP5 |ASI2 |ATG4 |ATG9 |AVL9 |AVT1 |AVT4 |BFA1 |MORE
Function/Process
Fungal Related Genes/Proteins
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Substrates/Ligands/Cofactors
Mao C, et al. (2000) Cloning and characterization of a Saccharomyces cerevisiae alkaline ceramidase with specificity for dihydroceramide. J Biol Chem 275(40):31369-78
       |YDC1
Function/Process
Mutants/Phenotypes
Strains/Constructs
Substrates/Ligands/Cofactors
Mao C, et al. (2000) Cloning of an alkaline ceramidase from Saccharomyces cerevisiae. An enzyme with reverse (CoA-independent) ceramide synthase activity. J Biol Chem 275(10):6876-84

Return to SGD

SGD^tm pages Database Copyright © 1997-2010 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied. The SGD project at Stanford University is supported by a Genome Research Resource Grant from the US National Human Genome Research Institute, part of the US National Institutes of Health.