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SHR3/YDL212W 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   ChrIV: 78427 to 79059 CDS: 78427 - 79059 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
SHR3	YDL212W	APF1	ORF, Verified	S000002371
Description
Endoplasmic reticulum packaging chaperone, required for incorporation of amino acid permeases into COPII coated vesicles for transport to the cell surface

GO Annotations [TOP] [NEXT]
Molecular Function Annotation(s) Reference(s) Evidence Assigned By unfolded protein binding Gilstring CF, et al. (1999) Shr3p mediates specific COPII coatomer-cargo interactions required for the packaging of amino acid permeases into ER-derived transport vesicles. Mol Biol Cell 10(11):3549-65        IMP : Inferred from Mutant Phenotype IPI : Inferred from Physical Interaction Assigned on 2002-07-26 SGD Kota J and Ljungdahl PO (2005) Specialized membrane-localized chaperones prevent aggregation of polytopic proteins in the ER. J Cell Biol 168(1):79-88        IMP : Inferred from Mutant Phenotype Assigned on 2008-07-31 SGD
Biological Process Annotation(s) Reference(s) Evidence Assigned By ER to Golgi vesicle-mediated transport Gilstring CF, et al. (1999) Shr3p mediates specific COPII coatomer-cargo interactions required for the packaging of amino acid permeases into ER-derived transport vesicles. Mol Biol Cell 10(11):3549-65        IPI : Inferred from Physical Interaction IGI : Inferred from Genetic Interaction Assigned on 2002-07-26 SGD amine transport Huttenhower C and Troyanskaya OG (2009) Prediction of Gene Ontology annotations by integrating high-throughput datasets    RCA : Reviewed Computational Analysis Assigned on 2009-08-06 bioPIXIE_MEFIT organic acid transport Huttenhower C and Troyanskaya OG (2009) Prediction of Gene Ontology annotations by integrating high-throughput datasets    RCA : Reviewed Computational Analysis Assigned on 2009-08-06 bioPIXIE_MEFIT peptidyl-amino acid modification Huttenhower C and Troyanskaya OG (2009) Prediction of Gene Ontology annotations by integrating high-throughput datasets    RCA : Reviewed Computational Analysis Assigned on 2009-08-06 bioPIXIE_MEFIT protein folding Kota J and Ljungdahl PO (2005) Specialized membrane-localized chaperones prevent aggregation of polytopic proteins in the ER. J Cell Biol 168(1):79-88        IMP : Inferred from Mutant Phenotype Assigned on 2005-07-08 SGD protein transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0653 Assigned on 2007-05-23 UniProtKB transmembrane transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0811 Assigned on 2009-10-01 UniProtKB transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0813 Assigned on 2007-05-23 UniProtKB
Cellular Component Annotation(s) Reference(s) Evidence Assigned By endoplasmic reticulum 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 integral to endoplasmic reticulum membrane Ljungdahl PO, et al. (1992) SHR3: a novel component of the secretory pathway specifically required for localization of amino acid permeases in yeast. Cell 71(3):463-78        IDA : Inferred from Direct Assay ISS : Inferred from Sequence or structural Similarity Assigned on 2002-07-26 SGD Kota J and Ljungdahl PO (2005) Specialized membrane-localized chaperones prevent aggregation of polytopic proteins in the ER. J Cell Biol 168(1):79-88        IDA : Inferred from Direct Assay Assigned on 2005-07-08 SGD 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 mating projection tip Narayanaswamy R, et al. (2009) Systematic Definition of Protein Constituents along the Major Polarization Axis Reveals an Adaptive Reuse of the Polarization Machinery in Pheromone-Treated Budding Yeast. J Proteome Res 8(1):6-19        IDA : Inferred from Direct Assay Assigned on 2008-12-19 SGD 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]
No pathways available

Summary Paragraph [TOP] [NEXT]
No summary paragraph available

Basic References [TOP]

BASIC INFORMATION REFERENCES forSHR3/YDL212W for SHR3 1) Grenson M and Hennaut C (1971) Mutation affecting activity of several distinct amino acid transport systems in Saccharomyces cerevisiae. J Bacteriol 105(2):477-82            2) Ljungdahl PO, et al. (1992) SHR3: a novel component of the secretory pathway specifically required for localization of amino acid permeases in yeast. Cell 71(3):463-78        3) Gilstring CF, et al. (1999) Shr3p mediates specific COPII coatomer-cargo interactions required for the packaging of amino acid permeases into ER-derived transport vesicles. Mol Biol Cell 10(11):3549-65        4) Kuehn MJ, et al. (1996) Amino acid permeases require COPII components and the ER resident membrane protein Shr3p for packaging into transport vesicles in vitro. J Cell Biol 135(3):585-95

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for SHR3/YDL212W

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for SHR3/YDL212W

Homologs [TOP] [NEXT]
Comparison Resources PSI-BLAST Results Ashbya Homologs (AGD) BLASTN vs. fungi BLASTP at NCBI BLASTP vs. fungi Candida Homologs (CGD) Candida Homologs (CandidaDB) Fungal Alignment Fungal Orthogroups Repository Ortholog Search (P-POD) PhylomeDB Synteny Viewer Yeast Gene Order Browser (YGOB) eukarYotic OrtholoGY (YOGY)

Physical Properties and Transcript Information: predicted from sequence [TOP] [NEXT]
Protein Sequence Calculations from Predicted Full length Translation N-term MFSYSDF C-term KRKNAKK Length(aa) 210 MW(Da) 23,512 pI 8.07 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias 0.219   Codon Adaptation Index 0.239   Frequency of Optimal Codons 0.542   Hydropathicity of Protein 0.074   Aromaticity Score 0.110	10 20 30 40 50 | | | | | MFSYSDFCSIGTAMILSATTFLMGVFFSNMPYDYHLLFNPNSTQEHFDLA LRHYQILHETPLPVIVTLCVVAGIGLVGGTIKVFKPNPELQMFEYCSLGL YVLAICVFLTNVKTGIDCSVSHNWGEVTENQGLAVIASSNIILLVMFAGV IILQIGLWYSNWDLQKRLKEFYAQEEREAANAGKKTEKVDNAKKNDNKSK GAQKRKNAKK*

Protein Structures from PDB: proteins of known structure with sequence similarity to SHR3/YDL212W, based on Smith-Waterman analysis. [TOP] [NEXT]
No protein structure information available.

Genome-wide Expression and Other Large-Scale Analyses [TOP] [NEXT]
Functional Analysis Expression Connection Summary Cell cycle and metabolic oscillation Cell cycle transcript profile Cyclebase Genevestigator GermOnline SPELL Microarray Search YGAC Triples Yeast Microarray Global Viewer YeastFunc	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
SHR3	Ljungdahl PO, et al. (1992) SHR3: a novel component of the secretory pathway specifically required for localization of amino acid permeases in yeast. Cell 71(3):463-78

Alias Name(s)	Reference
APF1	Grenson M and Hennaut C (1971) Mutation affecting activity of several distinct amino acid transport systems in Saccharomyces cerevisiae. J Bacteriol 105(2):477-82

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 BLASTP BLASTN Design Primers FASTA aa FASTA nt Restriction Fragment Map Restriction Fragment Sizes Six-Frame Translation

Sequence from other databases
Sequence ID	Source
YDL212W	SGD Systematic Sequence
851314	NCBI: Gene ID
NP_010069.1	NCBI: RefSeq protein version ID
NP_010069.1	NCBI: RefSeq protein version ID
6319989	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 YeastRC Localization (Seattle) YGAC Triples YeastGFP DB (UCSF) at SGD

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

Literature Guide: papers categorized by topic. [TOP]
Topics	Reference	Other Genes Addressed
38 curated references; 0 references not yet curated
Genetic Interactions	Kim JH, et al. (2009) The unfolded protein response is necessary but not sufficient to compensate for defects in disulfide isomerization. J Biol Chem 284(16):10400-8	|ALG8 |APM3 |APS3 |ARL1 |AVL9 |CCZ1 |CDC50 |COG8 |EPS1 |ERV41 |ERV46 |EUG1 |FLD1 |GCS1 |MORE
Cellular Location	Narayanaswamy R, et al. (2009) Systematic Definition of Protein Constituents along the Major Polarization Axis Reveals an Adaptive Reuse of the Polarization Machinery in Pheromone-Treated Budding Yeast. J Proteome Res 8(1):6-19	|ABP1 |ABP140 |AIM21 |AIP1 |ARK1 |BCK1 |BEM1 |BEM3 |BNI1 |BOI1 |BSP1 |BUD6 |BZZ1 |CAP1 |MORE
Mutants/Phenotypes Strains/Constructs	Breslow DK, et al. (2008) A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat Methods 5(8):711-8	|AAR2 |ABD1 |ABF1 |ACC1 |ACP1 |ADE13 |AFG2 |ALA1 |ALG1 |ALG13 |ALG14 |ALG2 |ALG7 |ALR1 |MORE
Cellular Location Computational analysis	Qi Y, et al. (2008) Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. Genome Res 18(12):1991-2004	|AAH1 |ADA2 |AGE1 |AGE2 |AIM29 |ALG3 |ALG5 |ALG6 |ALG8 |ALG9 |ANP1 |ARL3 |ARP3 |ARP4 |MORE
Fungal Related Genes/Proteins	Biswas S, et al. (2007) Environmental Sensing and Signal Transduction Pathways Regulating Morphopathogenic Determinants of Candida albicans. Microbiol Mol Biol Rev 71(2):348-76	|BCY1 |CAP1 |CDC4 |CLN1 |CLN3 |CYC8 |CYR1 |GAP1 |GAS1 |GCN2 |GCN4 |GPA2 |GPR1 |MEP2 |MORE
Function/Process Genetic Interactions Mutants/Phenotypes Strains/Constructs Substrates/Ligands/Cofactors	Kota J, et al. (2007) Membrane chaperone Shr3 assists in folding amino acid permeases preventing precocious ERAD. J Cell Biol 176(5):617-28	|AGP1 |GAP1 |GNP1 |HRD1 |PEP4 |SSM4 |UBC6 |UBC7
Genetic Interactions Mutants/Phenotypes Strains/Constructs	Kota J, et al. (2007) Ssh4, Rcr2 and Rcr1 Affect Plasma Membrane Transporter Activity in Saccharomyces cerevisiae. Genetics 175(4):1681-94	|GAP1 |RCR1 |RCR2 |SSH4 |TAT2
Protein Physical Properties	White MA, et al. (2007) Characteristics affecting expression and solubilization of yeast membrane proteins. J Mol Biol 365(3):621-36	|ALG1 |ALG7 |APQ12 |AQY1 |ARE2 |ATG9 |ATP4 |BET1 |BIG1 |BOS1 |BRR6 |CAX4 |CHO1 |COS7 |MORE
Cross-species Expression Fungal Related Genes/Proteins Genetic Interactions Mutants/Phenotypes	Erpapazoglou Z, et al. (2006) The product of the SHR3 orthologue of Aspergillus nidulans has restricted range of amino acid transporter targets. Fungal Genet Biol 43(4):222-33
Fungal Related Genes/Proteins Mutants/Phenotypes	Snoek IS and Steensma HY (2006) Why does Kluyveromyces lactis not grow under anaerobic conditions? Comparison of essential anaerobic genes of Saccharomyces cerevisiae with the Kluyveromyces lactis genome. FEMS Yeast Res 6(3):393-403	|ACP1 |ARB1 |ARG82 |ARH1 |ARV1 |ATM1 |BTS1 |BUR6 |CAB2 |CAX4 |CDC40 |CNM67 |CTF4 |DBP7 |MORE
RNA Levels and Processing Regulation of	Tanaka F, et al. (2006) Functional genomic analysis of commercial baker's yeast during initial stages of model dough-fermentation. Food Microbiol 23(8):717-28	|ACE2 |ACO1 |ACS1 |ACS2 |ACT1 |ADH1 |ADH2 |ADH5 |ADK1 |AIM38 |ALD2 |ALG8 |ARG1 |ARG3 |MORE
Function/Process Mutants/Phenotypes Protein Sequence Features Regulatory Role	Kota J and Ljungdahl PO (2005) Specialized membrane-localized chaperones prevent aggregation of polytopic proteins in the ER. J Cell Biol 168(1):79-88	|CHS7 |GAP1 |GSF2 |PHO86
Protein-protein Interactions	Miller JP, et al. (2005) Large-scale identification of yeast integral membrane protein interactions. Proc Natl Acad Sci U S A 102(34):12123-8	|ARV1 |EMP24 |EMP46 |EMP47 |ERD1 |ERD2 |ERG11 |ERP5 |ERV29 |ERV41 |MST27 |PHO84 |PHO88 |SEC61 |MORE
Fungal Related Genes/Proteins	Sims AH, et al. (2005) Transcriptome analysis of recombinant protein secretion by Aspergillus nidulans and the unfolded-protein response in vivo. Appl Environ Microbiol 71(5):2737-47	|BCH2 |EPT1 |INO1 |KAR2 |NCE102 |RPT3 |SEC27 |SEC63 |SEC65 |SEC72 |SLC1 |SRP54 |UBA1
Fungal Related Genes/Proteins	Martinez P and Ljungdahl PO (2004) An ER packaging chaperone determines the amino acid uptake capacity and virulence of Candida albicans. Mol Microbiol 51(2):371-84
Cellular Location Protein Physical Properties	Kim H, et al. (2003) Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and predictions. J Biol Chem 278(12):10208-13	|AQY1 |ASG7 |ATO2 |AVT6 |CDC1 |ECM7 |ERP2 |ERV15 |FCY2 |FLD1 |HHY1 |IZH4 |MEP1 |MUP1 |MORE
Cellular Location Function/Process Mutants/Phenotypes	Opekarova M, et al. (2002) Phosphatidyl ethanolamine is essential for targeting the arginine transporter Can1p to the plasma membrane of yeast. Biochim Biophys Acta 1564(1):9-13	|ANP1 |CAN1 |HXT1 |MAL6 |PMA1 |URA4
Function/Process Mutants/Phenotypes Strains/Constructs	Gilstring CF and Ljungdahl PO (2000) A method for determining the in vivo topology of yeast polytopic membrane proteins demonstrates that Gap1p fully integrates into the membrane independently of Shr3p. J Biol Chem 275(40):31488-95	|GAP1
Fungal Related Genes/Proteins Genetic Interactions Mutants/Phenotypes Protein Sequence Features Strains/Constructs	Martinez P and Ljungdahl PO (2000) The SHR3 homologue from S. pombe demonstrates a conserved function of ER packaging chaperones. J Cell Sci 113 Pt 23():4351-62
Cellular Location Function/Process Genetic Interactions Mutants/Phenotypes Protein-protein Interactions Strains/Constructs	Gilstring CF, et al. (1999) Shr3p mediates specific COPII coatomer-cargo interactions required for the packaging of amino acid permeases into ER-derived transport vesicles. Mol Biol Cell 10(11):3549-65	|GAL2 |GAP1 |PMA1 |SAR1 |SEC12 |SEC13 |SEC23 |SEC24 |SEC31 |SEC61
Function/Process Substrates/Ligands/Cofactors	Klasson H, et al. (1999) Ssy1p and Ptr3p are plasma membrane components of a yeast system that senses extracellular amino acids. Mol Cell Biol 19(8):5405-16	|CAR1 |DIP5 |GAP1 |GNP1 |PTR2 |PTR3 |SSY1
Cellular Location	Wang Q and Chang A (1999) Eps1, a novel PDI-related protein involved in ER quality control in yeast. EMBO J 18(21):5972-82	|EPS1 |GAS1 |KAR2 |PDI1 |PMA1 |UBC6
Mutants/Phenotypes Other Features Strains/Constructs	Fujimura H (1998) Molecular cloning of Saccharomyces cerevisiae MLF4/SSH4 gene which confers the immunosuppressant leflunomide resistance. Biochem Biophys Res Commun 246(2):378-81	|SSH4
Function/Process Protein Physical Properties	Kuehn MJ, et al. (1998) COPII-cargo interactions direct protein sorting into ER-derived transport vesicles. Nature 391(6663):187-90	|BET1 |EMP24 |KAR2 |SAR1 |SEC23
DNA/RNA Sequence Features Mapping Strains/Constructs	Bahr A, et al. (1997) The nucleotide sequence of a 39 kb segment of yeast chromosome IV: 12 new open reading frames, nine known genes and one genes for Gly-tRNA. Yeast 13(2):163-9	|ACK1 |ASF2 |GDH2 |GGC1 |HEM3 |MGT1 |NHP2 |UGA4 |YDL206W |YDL211C
Function/Process Mutants/Phenotypes	Matijekova A and Sychrova H (1997) Biogenesis of Candida albicans Can1 permease expressed in Saccharomyces cerevisiae. FEBS Lett 408(1):89-93	|CAN1 |LYP1 |SEC1
Mutants/Phenotypes	Palkova Z, et al. (1997) Ammonia mediates communication between yeast colonies. Nature 390(6659):532-6
Genetic Interactions	Wright MB, et al. (1997) Potassium transport by amino acid permeases in Saccharomyces cerevisiae. J Biol Chem 272(21):13647-52	|BAP2 |BAP3 |HIP1 |HIS4 |TRK1 |TRK2
Other Features	Chianelli MS, et al. (1996) Isolation of a trifluoroleucine-resistant mutant of Saccharomyces cerevisiae deficient in both high- and low-affinity L-leucine transport. Cell Mol Biol (Noisy-le-grand) 42(6):847-57	|AAT1 |GAP1 |LET1 |LET2 |LUP1
Function/Process	Gilstring CF, et al. (1996) SHR3 function is linked to cOPII mediated ER vesicle formation. Folia Microbiol (Praha) 41(1):93	|HIP1 |SEC13 |SEC3
Function/Process Mutants/Phenotypes Regulatory Role Strains/Constructs	Kuehn MJ, et al. (1996) Amino acid permeases require COPII components and the ER resident membrane protein Shr3p for packaging into transport vesicles in vitro. J Cell Biol 135(3):585-95	|GAP1 |HIP1 |PMA1 |SAR1 |SEC13 |SEC23
Other Features	Matejckova A and Sychrova H (1996) Properties of Candida albicans CAN1 permease expressed in Saccharomyces cerevisiae. Folia Microbiol (Praha) 41(1):107-9	|CAN1 |LYP1 |SEC1
Mutants/Phenotypes Other Features Techniques and Reagents	Rentsch D, et al. (1996) Salt stress-induced proline transporters and salt stress-repressed broad specificity amino acid permeases identified by suppression of a yeast amino acid permease-targeting mutant. Plant Cell 8(8):1437-46
Reviews	Sophianopoulou V and Diallinas G (1995) Amino acid transporters of lower eukaryotes: regulation, structure and topogenesis. FEMS Microbiol Rev 16(1):53-75	|AUA1 |CAN1 |DAL5 |DAL80 |DAL81 |FUR4 |GAP1 |GCN4 |GLN3 |GNP1 |HIP1 |LYP1 |NPR1 |PUT4 |MORE
Cellular Location Function/Process Genetic Interactions Mutants/Phenotypes Strains/Constructs	Horak J and Kotyk A (1993) Functional analysis of apf1 mutation causing defective amino acid transport in Saccharomyces cerevisiae. Biochem Mol Biol Int 29(5):907-12
Mutants/Phenotypes	Gimeno CJ, et al. (1992) Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: regulation by starvation and RAS. Cell 68(6):1077-90	|RAS2 |RSR1
Cellular Location DNA/RNA Sequence Features Function/Process Genetic Interactions Mapping Mutants/Phenotypes Protein Sequence Features Strains/Constructs	Ljungdahl PO, et al. (1992) SHR3: a novel component of the secretory pathway specifically required for localization of amino acid permeases in yeast. Cell 71(3):463-78	|GCN4
Alias Mutants/Phenotypes Strains/Constructs	Grenson M and Hennaut C (1971) Mutation affecting activity of several distinct amino acid transport systems in Saccharomyces cerevisiae. J Bacteriol 105(2):477-82

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