YOS9/YDR057W 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: 565926 to 567554
CDS: 565926 - 567554

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

YOS9 YDR057W ORF, Verified S000002464

Description
ER quality-control lectin; integral subunit of the HRD ligase; binds to glycans with terminal alpha-1,6 linked mannose on misfolded N-glycosylated proteins and participates in targeting proteins to ERAD; member of the OS-9 protein family

GO Annotations [TOP] [NEXT]
Molecular Function
Annotation(s) Reference(s) Evidence Assigned By
oligosaccharide binding Quan EM, et al. (2008) Defining the glycan destruction signal for endoplasmic reticulum-associated degradation. Mol Cell 32(6):870-7
       IDA : Inferred from Direct Assay
Assigned on 2009-10-30 SGD
sugar binding Szathmary R, et al. (2005) Yos9 protein is essential for degradation of misfolded glycoproteins and may function as lectin in ERAD. Mol Cell 19(6):765-75
         ISS : Inferred from Sequence or structural Similarity
IMP : Inferred from Mutant Phenotype
Assigned on 2005-12-09 SGD
Biological Process
Annotation(s) Reference(s) Evidence Assigned By
ER-associated protein catabolic process Szathmary R, et al. (2005) Yos9 protein is essential for degradation of misfolded glycoproteins and may function as lectin in ERAD. Mol Cell 19(6):765-75
         IMP : Inferred from Mutant Phenotype
Assigned on 2005-12-09 SGD
Bhamidipati A, et al. (2005) Exploration of the Topological Requirements of ERAD Identifies Yos9p as a Lectin Sensor of Misfolded Glycoproteins in the ER Lumen. Mol Cell 19(6):741-51
       IMP : Inferred from Mutant Phenotype
Assigned on 2005-12-09 SGD
Kim W, et al. (2005) Yos9p detects and targets misfolded glycoproteins for ER-associated degradation. Mol Cell 19(6):753-64
       IMP : Inferred from Mutant Phenotype
Assigned on 2005-12-09 SGD
Cellular Component
Annotation(s) Reference(s) Evidence Assigned By
colocalizes_with Hrd1p ubiquitin ligase ERAD-L complex Carvalho P, et al. (2006) Distinct ubiquitin-ligase complexes define convergent pathways for the degradation of ER proteins. Cell 126(2):361-73
       IPI : Inferred from Physical Interaction with SGD:HRD3
Assigned on 2008-02-06 SGD
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 2009-10-01 UniProtKB
endoplasmic reticulum lumen Kim W, et al. (2005) Yos9p detects and targets misfolded glycoproteins for ER-associated degradation. Mol Cell 19(6):753-64
       IDA : Inferred from Direct Assay
Assigned on 2007-01-30 SGD
luminal surveillance complex Denic V, et al. (2006) A luminal surveillance complex that selects misfolded glycoproteins for ER-associated degradation. Cell 126(2):349-59
       IDA : Inferred from Direct Assay
Assigned on 2008-02-06 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 forYOS9/YDR057W for YOS9
1) Buschhorn BA, et al. (2004) A genome-wide screen identifies Yos9p as essential for ER-associated degradation of glycoproteins. FEBS Lett 577(3):422-6

2) Szathmary R, et al. (2005) Yos9 protein is essential for degradation of misfolded glycoproteins and may function as lectin in ERAD. Mol Cell 19(6):765-75

3) Bhamidipati A, et al. (2005) Exploration of the Topological Requirements of ERAD Identifies Yos9p as a Lectin Sensor of Misfolded Glycoproteins in the ER Lumen. Mol Cell 19(6):741-51

4) Kim W, et al. (2005) Yos9p detects and targets misfolded glycoproteins for ER-associated degradation. Mol Cell 19(6):753-64

5) Gauss R, et al. (2006) A complex of Yos9p and the HRD ligase integrates endoplasmic reticulum quality control into the degradation machinery. Nat Cell Biol 8(8):849-54

6) Quan EM, et al. (2008) Defining the glycan destruction signal for endoplasmic reticulum-associated degradation. Mol Cell 32(6):870-7

7) Friedmann E, et al. (2002) YOS9, the putative yeast homolog of a gene amplified in osteosarcomas, is involved in the endoplasmic reticulum (ER)-Golgi transport of GPI-anchored proteins. J Biol Chem 277(38):35274-81

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for YOS9/YDR057W

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for YOS9/YDR057W

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 MQAKIIY

C-term FIEHDEL

Length(aa) 542

MW(Da) 61,257

pI 4.33

Amino Acid Composition (full length)

GCG tools: PepPlot, Helical Wheel, PepStruct

Transcript Translation Calculations

Codon Bias -0.022

Codon Adaptation Index 0.117

Frequency of Optimal Codons 0.412

Hydropathicity of Protein -0.376

Aromaticity Score 0.083

10 20 30 40 50 | | | | | MQAKIIYALSAISALIPLGSSLLAPIEDPIVSNKYLISYIDEDDWSDRIL QNQSVMNSGYIVNMGDDLECFIQNASTQLNDVLEDSNEHSNSEKTALLTK TLNQGVKTIFDKLNERCIFYQAGFWIYEYCPGIEFVQFHGRVNTKTGEIV NRDESLVYRLGKPKANVEEREFELLYDDVGYYISEIIGSGDICDVTGAER MVEIQYVCGGSNSGPSTIQWVRETKICVYEAQVTIPELCNLELLAKNEDQ KNASPILCRMPAKSKIGSNSIDLITKYEPIFLGSGIYFLRPFNTDERDKL MVTDNAMSNWDEITETYYQKFGNAINKMLSLRLVSLPNGHILQPGDSCVW LAEVVDMKDRFQTTLSLNILNSQRAEIFFNKTFTFNEDNGNFLSYKIGDH GESTELGQITHSNKADINTAEIRSDEYLINTDNELFLRISKEIAEVKELL NEIVSPHEMEVIFENMRNQPNNDFELALMNKLKSSLNDDNKVEQINNARM DDDESTSHTTRDIGEAGSQTTGNTESEVTNVAAGVFIEHDEL*

Protein Structures from PDB: proteins of known structure with sequence similarity to YOS9/YDR057W, 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
YOS9 Friedmann E, et al. (2002) YOS9, the putative yeast homolog of a gene amplified in osteosarcomas, is involved in the endoplasmic reticulum (ER)-Golgi transport of GPI-anchored proteins. J Biol Chem 277(38):35274-81

Standard Name	Reference
YOS9	*Friedmann E, et al.* (2002)** YOS9, the putative yeast homolog of a gene amplified in osteosarcomas, is involved in the endoplasmic reticulum (ER)-Golgi transport of GPI-anchored proteins. J Biol Chem 277(38):35274-81

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

YDR057W SGD Systematic Sequence

851627 NCBI: Gene ID

NP_010342.1 NCBI: RefSeq protein version ID

NP_010342.1 NCBI: RefSeq protein version ID

6320262 NCBI: NCBI protein GI

Sequence from other databases
Sequence ID	Source
YDR057W	SGD Systematic Sequence
851627	NCBI: Gene ID
NP_010342.1	NCBI: RefSeq protein version ID
NP_010342.1	NCBI: RefSeq protein version ID
6320262	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]
Protein Details
Topic Research Highlight Reference Contributor
Protein Function/Process Description: The ER lumenal protein Yos9p is required for both release of DHFR and degradation of multiple ERAD substrates. Yos9p forms a complex with substrates and has a sugar binding pocket that is essential for its ERAD function. Nonetheless, substrate recognition persists even when the sugar binding site is mutated or CPY* is unglycosylated. These and other considerations suggest that Yos9p plays a critical role in the bipartite recognition of terminally misfolded glycoproteins. Bhamidipati A, et al. (2005) Exploration of the Topological Requirements of ERAD Identifies Yos9p as a Lectin Sensor of Misfolded Glycoproteins in the ER Lumen. Mol Cell 19(6):741-51
Maya Schuldiner
2005-12-09

Literature Guide: papers categorized by topic. [TOP]
Topics Reference Other Genes Addressed
19 curated references; 1 references not yet curated
Not yet curated Hosokawa N, et al. (2010) The role of MRH domain-containing lectins in ERAD. Glycobiology
     |HMLALPHA1 |HRD1 |HRD3 |MATALPHA1
Reviews
Hoseki J, et al. (2010) Mechanism and components of endoplasmic reticulum-associated degradation. J Biochem 147(1):19-25
       |CDC48 |DER1 |HRD1 |HRD3 |KAR2 |SSM4 |UBX2 |USA1
Reviews
Yoshida Y and Tanaka K (2010) Lectin-like ERAD players in ER and cytosol. Biochim Biophys Acta 1800(2):172-180
       |MNL1 |PNG1
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Clerc S, et al. (2009) Htm1 protein generates the N-glycan signal for glycoprotein degradation in the endoplasmic reticulum. J Cell Biol 184(1):159-72
           |ALG12 |ALG3 |ALG8 |ALG9 |MNL1 |MNS1 |PDI1 |PRC1 |ROT2
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Jonikas MC, et al. (2009) Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum. Science 323(5922):1693-7
       |AIM27 |ALG12 |ALG3 |ALG5 |ALG6 |ALG8 |ALG9 |CUE1 |DER1 |DIE2 |EMC1 |EMC2 |EMC4 |EMC6 |MORE
Mutants/Phenotypes
Protein-protein Interactions
Strains/Constructs
Sato BK, et al. (2009) Misfolded membrane proteins are specifically recognized by the transmembrane domain of the Hrd1p ubiquitin ligase. Mol Cell 34(2):212-22
       |CDC48 |DER1 |HMG2 |HRD1 |HRD3 |PDR5 |SEC61 |UBX2 |USA1
Protein-protein Interactions
Goder V, et al. (2008) The ER-associated degradation component Der1p and its homolog Dfm1p are contained in complexes with distinct cofactors of the ATPase Cdc48p. FEBS Lett 582(11):1575-80
       |CDC48 |DER1 |DFM1 |HRD1 |HRD3 |KAR2 |NPL4 |SHP1 |UBX2 |UBX7 |UFD1 |USA1
Reviews
Jigami Y (2008) Yeast glycobiology and its application. Biosci Biotechnol Biochem 72(3):637-48
       |ALG1 |ALG11 |ALG12 |ALG13 |ALG14 |ALG2 |ALG3 |ALG5 |ALG6 |ALG7 |ALG8 |ALG9 |ANP1 |CWH41 |MORE
Function/Process
Mutants/Phenotypes
Protein Processing/Modification/Regulation
Strains/Constructs
Substrates/Ligands/Cofactors
Quan EM, et al. (2008) Defining the glycan destruction signal for endoplasmic reticulum-associated degradation. Mol Cell 32(6):870-7
       |ALG12 |ALG9 |MNL1
Protein-protein Interactions
Ng W, et al. (2007) Characterization of the proteasome interaction with the Sec61 channel in the endoplasmic reticulum. J Cell Sci 120(Pt 4):682-91
         |CDC48 |CUE1 |HRD1 |KAR2 |RPT1 |RPT3 |RPT5 |RPT6 |SBH1 |SEC61 |SEC62 |SEC63 |SEC72 |SSH1 |MORE
Protein-protein Interactions
Carvalho P, et al. (2006) Distinct ubiquitin-ligase complexes define convergent pathways for the degradation of ER proteins. Cell 126(2):361-73
       |CDC48 |CUE1 |DER1 |HRD1 |HRD3 |IRE1 |NPL4 |SSM4 |UBC7 |UBX2 |USA1
Function/Process
Mutants/Phenotypes
Protein Sequence Features
Protein-protein Interactions
Strains/Constructs
Substrates/Ligands/Cofactors
Denic V, et al. (2006) A luminal surveillance complex that selects misfolded glycoproteins for ER-associated degradation. Cell 126(2):349-59
       |CDC48 |EMP47 |HRD1 |HRD3 |KAR2 |UBX2
Cellular Location
Function/Process
Protein-protein Interactions
Gauss R, et al. (2006) A complex of Yos9p and the HRD ligase integrates endoplasmic reticulum quality control into the degradation machinery. Nat Cell Biol 8(8):849-54
         |HRD1 |HRD3
Function/Process
Mutants/Phenotypes
Non-Fungal Related Genes/Proteins
Protein Physical Properties
Protein Sequence Features
Regulatory Role
Strains/Constructs
Substrates/Ligands/Cofactors
Bhamidipati A, et al. (2005) Exploration of the Topological Requirements of ERAD Identifies Yos9p as a Lectin Sensor of Misfolded Glycoproteins in the ER Lumen. Mol Cell 19(6):741-51
       |DER1 |HRD1 |MNL1 |MNS1
Non-Fungal Related Genes/Proteins
Hellauer K, et al. (2005) Large-scale analysis of genes that alter sensitivity to the anticancer drug tirapazamine in Saccharomyces cerevisiae. Mol Pharmacol 68(5):1365-75
       |AGP3 |BNR1 |CAF40 |CMR1 |DNL4 |DPL1 |EKI1 |ERV41 |FYV10 |KNS1 |NCP1 |PAF1 |PUS4 |RAD18 |MORE
Function/Process
Genetic Interactions
Mutants/Phenotypes
Protein Physical Properties
Protein Sequence Features
Strains/Constructs
Kim W, et al. (2005) Yos9p detects and targets misfolded glycoproteins for ER-associated degradation. Mol Cell 19(6):753-64
       |CUE1 |DER1 |MNL1
Function/Process
Fungal Related Genes/Proteins
Mutants/Phenotypes
Non-Fungal Related Genes/Proteins
Protein Sequence Features
Regulatory Role
Strains/Constructs
Substrates/Ligands/Cofactors
Szathmary R, et al. (2005) Yos9 protein is essential for degradation of misfolded glycoproteins and may function as lectin in ERAD. Mol Cell 19(6):765-75
         |ALG12 |ALG3 |ALG9 |MNL1 |MNS1 |PRC1
Cellular Location
Function/Process
Mutants/Phenotypes
Buschhorn BA, et al. (2004) A genome-wide screen identifies Yos9p as essential for ER-associated degradation of glycoproteins. FEBS Lett 577(3):422-6
     |MNL1
Cellular Location
Function/Process
Genetic Interactions
Mutants/Phenotypes
Non-Fungal Related Genes/Proteins
Protein-protein Interactions
Strains/Constructs
Substrates/Ligands/Cofactors
Friedmann E, et al. (2002) YOS9, the putative yeast homolog of a gene amplified in osteosarcomas, is involved in the endoplasmic reticulum (ER)-Golgi transport of GPI-anchored proteins. J Biol Chem 277(38):35274-81
       |COG3 |GAS1 |MKC7
Disease Gene Related
Non-Fungal Related Genes/Proteins
Su YA, et al. (1996) Complete sequence analysis of a gene (OS-9) ubiquitously expressed in human tissues and amplified in sarcomas. Mol Carcinog 15(4):270-5

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