YSR3/YKR053C 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

ChrXI: 534923 to 533709
CDS: 534923 - 533709

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

YSR3 YKR053C LBP2 ORF, Verified S000001761

Description
Dihydrosphingosine 1-phosphate phosphatase, membrane protein involved in sphingolipid metabolism; has similarity to Lcb3p

GO Annotations [TOP] [NEXT]
Molecular Function
Annotation(s) Reference(s) Evidence Assigned By
catalytic activity DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR000326
Assigned on 2008-02-13 UniProtKB
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 2009-01-12 UniProtKB
sphingosine-1-phosphate phosphatase activity Zanolari B, et al. (2000) Sphingoid base synthesis requirement for endocytosis in Saccharomyces cerevisiae. EMBO J 19(12):2824-33
       IDA : Inferred from Direct Assay
Assigned on 2002-09-25 SGD
Biological Process
Annotation(s) Reference(s) Evidence Assigned By
lipid metabolic process GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0443
Assigned on 2009-10-01 UniProtKB
sphingolipid biosynthetic process Mao C and Obeid LM (2000) Yeast sphingosine-1-phosphate phosphatases: assay, expression, deletion, purification, and cellular localization by GFP tagging. Methods Enzymol 311:223-32
     TAS : Traceable Author Statement
Assigned on 2002-08-21 SGD
sphingolipid metabolic process GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0746
Assigned on 2009-01-12 UniProtKB
Cellular Component
Annotation(s) Reference(s) Evidence Assigned By
endoplasmic reticulum Mao C, et al. (1999) The dihydrosphingosine-1-phosphate phosphatases of Saccharomyces cerevisiae are important regulators of cell proliferation and heat stress responses. Biochem J 342 Pt 3():667-75
       IDA : Inferred from Direct Assay
Assigned on 2002-09-25 SGD
Pollack BP, et al. (1999) The human homologue of the yeast proteins Skb1 and Hsl7p interacts with Jak kinases and contains protein methyltransferase activity. J Biol Chem 274(44):31531-42
       IDA : Inferred from Direct Assay
Assigned on 2002-08-21 SGD
GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0256
Assigned on 2009-01-12 UniProtKB
integral to membrane 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 DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR000326
Assigned on 2009-01-12 UniProtKB
GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0472
Assigned on 2009-01-12 UniProtKB

Pathways [TOP] [NEXT]
sphingolipid metabolism

Summary Paragraph [TOP] [NEXT]
SUMMARY PARAGRAPH for YSR3/YKR053C for YSR3
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 forYSR3/YKR053C for YSR3
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. (1997) Identification and characterization of Saccharomyces cerevisiae dihydrosphingosine-1-phosphate phosphatase. J Biol Chem 272(45):28690-4

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for YSR3/YKR053C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for YSR3/YKR053C

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 MTIIQTV

C-term FTWTNLR

Length(aa) 404

MW(Da) 46,488

pI 7.62

Amino Acid Composition (full length)

GCG tools: PepPlot, Helical Wheel, PepStruct

Transcript Translation Calculations

Codon Bias 0.091

Codon Adaptation Index 0.125

Frequency of Optimal Codons 0.452

Hydropathicity of Protein 0.240

Aromaticity Score 0.146

10 20 30 40 50 | | | | | MTIIQTVTELGVTEDTIKVQMAPSGGKHLLADPGNHPAEHFESQMSWLRF QTRQYLTRFTDNQSDFVHSLQKKHRTPFRDVYFKYTSLMGSHMFYVIVLP MPVWLGYRDLTRDMIYVLGYSIYLSGYLKDYWCLPRPKSPPVDRITLSEY TTKEYGAPSSHSANATAVSLLFFWRICLSDTLVWPTKLLLLSLVIFYYLT LVFGRVYCGMHGMLDLFSGAAVGAICFFIRIWVVHALRNFQIGEHLWFPL LSVAWGLFILFNHVRPIDECPCFEDSVAFIGVVSGLDCSDWLTERYGWNL VCSRYASCGSKVFLRPLVGVASVIVWKDVISKTAVYTLLIKLLRFHDDRS EKVHFHNETSEEEECLLYSGVSKVEIVGRFLIYAGIPTTVFLLCPVFFTW TNLR*

Protein Structures from PDB: proteins of known structure with sequence similarity to YSR3/YKR053C, 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 Reference
YSR3 SGD (2007) Information without a citation in SGD

Mapping Notes
Date Note
1997-10-20 Edition 14: YSR3 has previously been called YSR2-1, but it should not be confused with LCB3/YSR2
Cherry JM, et al. (1997) Genetic and physical maps of Saccharomyces cerevisiae. Nature 387(6632 Suppl):67-73

Standard Name	Reference
YSR3	SGD (2007) Information without a citation in SGD

Date	Note
1997-10-20	Edition 14: YSR3 has previously been called YSR2-1, but it should not be confused with LCB3/YSR2 *Cherry JM, et al.* (1997)** Genetic and physical maps of Saccharomyces cerevisiae. Nature 387(6632 Suppl):67-73

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

YKR053C SGD Systematic Sequence

853927 NCBI: Gene ID

NP_012979.1 NCBI: RefSeq protein version ID

NP_012979.1 NCBI: RefSeq protein version ID

6322906 NCBI: NCBI protein GI

Sequence from other databases
Sequence ID	Source
YKR053C	SGD Systematic Sequence
853927	NCBI: Gene ID
NP_012979.1	NCBI: RefSeq protein version ID
NP_012979.1	NCBI: RefSeq protein version ID
6322906	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
27 curated references; 0 references not yet curated
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
DeLuna A, et al. (2008) Exposing the fitness contribution of duplicated genes. Nat Genet 40(5):676-81
         |GDH1 |GDH3 |ITR1 |ITR2 |LCB3 |NDE1 |NDE2
Reviews
Dickson RC (2008) Thematic Review Series: Sphingolipids. New insights into sphingolipid metabolism and function in budding yeast. J Lipid Res 49(5):909-21
       |AUR1 |CSG2 |CSH1 |DPL1 |FEN1 |IFA38 |IPT1 |ISC1 |LCB1 |LCB2 |LCB3 |LCB4 |LCB5 |LIP1 |MORE
RNA Levels and Processing
Regulation of
Guo N, et al. (2008) Global gene expression profile of Saccharomyces cerevisiae induced by dictamnine. Yeast 25(9):631-41
       |ADE1 |ADE12 |ADE13 |ADE16 |ADE17 |ADE2 |ADE4 |ADE5,7 |ADE6 |ADE8 |ADY2 |APT1 |CBF1 |CIS3 |MORE
Reviews
Cowart LA and Obeid LM (2007) Yeast sphingolipids: recent developments in understanding biosynthesis, regulation, and function. Biochim Biophys Acta 1771(3):421-31
       |AUR1 |CSG2 |CSH1 |DPL1 |FEN1 |ISC1 |LAC1 |LAG1 |LCB1 |LCB2 |LCB3 |LCB4 |LCB5 |SUR1 |MORE
DNA/RNA Sequence Features
Ferreira TC, et al. (2007) The yeast genome may harbor hypoxia response elements (HRE). Comp Biochem Physiol C Toxicol Pharmacol 146(1-2):255-63
       |AFT1 |ALD6 |ARO9 |ASC1 |ATM1 |BUD7 |CIS3 |CTF19 |CWP1 |DAN1 |EXG1 |GIT1 |GLY1 |GPA2 |MORE
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 |YPC1
Reviews
Dickson RC, et al. (2006) Functions and metabolism of sphingolipids in Saccharomyces cerevisiae. Prog Lipid Res 45(6):447-65
       |ARV1 |AUR1 |CSH1 |DPL1 |FEN1 |IPT1 |LCB1 |LCB2 |LCB3 |LCB4 |LCB5 |NCR1 |PKH1 |PKH2 |MORE
Reviews
Riezman H (2006) Organization and functions of sphingolipid biosynthesis in yeast. Biochem Soc Trans 34(3):367-369
       |AUR1 |CSG2 |DPL1 |IPT1 |LAC1 |LAG1 |LCB1 |LCB2 |LCB3 |LCB4 |LCB5 |LIP1 |SUR1 |SUR2 |MORE
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
RNA Levels and Processing
Regulation of
Lai LC, et al. (2005) Dynamical remodeling of the transcriptome during short-term anaerobiosis in Saccharomyces cerevisiae: differential response and role of Msn2 and/or Msn4 and other factors in galactose and glucose media. Mol Cell Biol 25(10):4075-91
         |AAC1 |ADE1 |ADE12 |ADE17 |ADE4 |AFR1 |AIM17 |AIM3 |AKR1 |AKR2 |ALA1 |ALD5 |ARE1 |ARN1 |MORE
Genomic expression study
RNA Levels and Processing
Regulation of
Parveen M, et al. (2004) Response of Saccharomyces cerevisiae to a monoterpene: evaluation of antifungal potential by DNA microarray analysis. J Antimicrob Chemother 54(1):46-55
               |AAD6 |ADH5 |ADH7 |ADY2 |AGA2 |AMS1 |ARG1 |ARN2 |ATF2 |ATX1 |BCK1 |BFR1 |BSC1 |BUD7 |MORE
Non-Fungal Related Genes/Proteins
Reviews
Saba JD and Hla T (2004) Point-counterpoint of sphingosine 1-phosphate metabolism. Circ Res 94(6):724-34
           |LCB3 |LCB4 |LCB5
RNA Levels and Processing
Regulation of
Sirisattha S, et al. (2004) Toxicity of anionic detergents determined by Saccharomyces cerevisiae microarray analysis. Water Res 38(1):61-70
           |ATX1 |CMK2 |CRS5 |DIA1 |GPX1 |GRE2 |GRX1 |GRX2 |GRX6 |GTT2 |GYP8 |HSP12 |HSP26 |HYR1 |MORE
Regulation of
Transcription
Agarwal AK, et al. (2003) Genome-wide expression profiling of the response to polyene, pyrimidine, azole, and echinocandin antifungal agents in Saccharomyces cerevisiae. J Biol Chem 278(37):34998-5015
         |AGA1 |AMS1 |ATF2 |AUS1 |BAG7 |BAP2 |BAP3 |CRH1 |CTR1 |CWP1 |CYB5 |DAN1 |DAN4 |ELO1 |MORE
Reviews
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
       |AUR1 |CSG2 |IPT1 |LAC1 |LAG1 |LCB1 |LCB2 |LCB3 |LCB4 |LCB5 |SUR1 |SUR2 |TSC10
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
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Techniques and Reagents
Kim S, et al. (2000) Accumulation of phosphorylated sphingoid long chain bases results in cell growth inhibition in Saccharomyces cerevisiae. Genetics 156(4):1519-29
       |DPL1 |LCB3 |LCB4 |LCB5 |SUR2
Alias
Fungal Related Genes/Proteins
Non-Fungal Related Genes/Proteins
Mandala SM, et al. (2000) Molecular cloning and characterization of a lipid phosphohydrolase that degrades sphingosine-1- phosphate and induces cell death. Proc Natl Acad Sci U S A 97(14):7859-64
       |LCB3
Function/Process
Substrates/Ligands/Cofactors
Techniques and Reagents
Mao C and Obeid LM (2000) Yeast sphingosine-1-phosphate phosphatases: assay, expression, deletion, purification, and cellular localization by GFP tagging. Methods Enzymol 311:223-32
     |LCB3
Function/Process
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Zanolari B, et al. (2000) Sphingoid base synthesis requirement for endocytosis in Saccharomyces cerevisiae. EMBO J 19(12):2824-33
       |ACT1 |LCB1 |LCB3 |LCB4 |LCB5 |SLA2
Alias
Function/Process
Mutants/Phenotypes
Strains/Constructs
Dickson RC and Lester RL (1999) Metabolism and selected functions of sphingolipids in the yeast Saccharomyces cerevisiae. Biochim Biophys Acta 1438(3):305-21
       |AUR1 |CSG2 |DPL1 |ERG2 |FAS2 |FEN1 |IPT1 |LCB1 |LCB2 |LCB3 |LCB4 |LCB5 |MSN2 |MSN4 |MORE
Cell Cycle Phase Involved
Cellular Location
Function/Process
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Mao C, et al. (1999) The dihydrosphingosine-1-phosphate phosphatases of Saccharomyces cerevisiae are important regulators of cell proliferation and heat stress responses. Biochem J 342 Pt 3():667-75
       |LCB3
RNA Levels and Processing
Regulation of
ter Linde JJ, et al. (1999) Genome-wide transcriptional analysis of aerobic and anaerobic chemostat cultures of Saccharomyces cerevisiae. J Bacteriol 181(24):7409-13
             |AAC3 |ADH2 |ADY2 |AGP1 |ANB1 |ARO10 |CIT3 |CLD1 |CTA1 |CYB2 |DAN1 |DIP5 |FDH1 |FDH2 |MORE
Reviews
Daum G, et al. (1998) Biochemistry, cell biology and molecular biology of lipids of Saccharomyces cerevisiae. Yeast 14(16):1471-510
       |ACC1 |ACP1 |AUR1 |CDS1 |CEM1 |CHO1 |CHO2 |CKI1 |CPT1 |CRD1 |CSG2 |DPL1 |DPP1 |EPT1 |MORE
DNA/RNA Sequence Features
Function/Process
Fungal Related Genes/Proteins
Genetic Interactions
Protein Sequence Features
Mandala SM, et al. (1998) Sphingoid base 1-phosphate phosphatase: a key regulator of sphingolipid metabolism and stress response. Proc Natl Acad Sci U S A 95(1):150-5
       |LCB3
Alias
Cellular Location
Function/Process
Fungal Related Genes/Proteins
Mutants/Phenotypes
Protein Physical Properties
Strains/Constructs
Substrates/Ligands/Cofactors
Mao C, et al. (1997) Identification and characterization of Saccharomyces cerevisiae dihydrosphingosine-1-phosphate phosphatase. J Biol Chem 272(45):28690-4
       |LCB3
Fungal Related Genes/Proteins
Mutants/Phenotypes
Strains/Constructs
Qie L, et al. (1997) Identification of a Saccharomyces gene, LCB3, necessary for incorporation of exogenous long chain bases into sphingolipids. J Biol Chem 272(26):16110-7
       |LCB3

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