HRD3/YLR207W 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

ChrXII: 556790 to 559291
CDS: 556790 - 559291

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

HRD3 YLR207W ORF, Verified S000004197

Description
Resident protein of the ER membrane that plays a central role in ER-associated protein degradation (ERAD), forms HRD complex with Hrd1p and ERAD determinants that engages in lumen to cytosol communication and coordination of ERAD events

GO Annotations [TOP] [NEXT]
Molecular Function
Annotation(s) Reference(s) Evidence Assigned By
binding DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR011990
Assigned on 2007-05-23 UniProtKB
contributes_to ubiquitin-protein ligase activity Gardner RG, et al. (2001) In vivo action of the HRD ubiquitin ligase complex: mechanisms of endoplasmic reticulum quality control and sterol regulation. Mol Cell Biol 21(13):4276-91
       IDA : Inferred from Direct Assay
Assigned on 2008-08-14 SGD
Biological Process
Annotation(s) Reference(s) Evidence Assigned By
ER-associated protein catabolic process Haynes CM, et al. (2002) An HRD/DER-independent ER quality control mechanism involves Rsp5p-dependent ubiquitination and ER-Golgi transport. J Cell Biol 158(1):91-101
       IDA : Inferred from Direct Assay
Assigned on 2002-08-01 SGD
Cellular Component
Annotation(s) Reference(s) Evidence Assigned By
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
       IDA : Inferred from Direct Assay
Assigned on 2008-02-06 SGD
Hrd1p ubiquitin ligase ERAD-M complex Carvalho P, et al. (2006) Distinct ubiquitin-ligase complexes define convergent pathways for the degradation of ER proteins. Cell 126(2):361-73
       IDA : Inferred from Direct Assay
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 2008-02-14 UniProtKB
endoplasmic reticulum membrane Gauss R, et al. (2006) The Hrd1p ligase complex forms a linchpin between ER-lumenal substrate selection and Cdc48p recruitment. EMBO J 25(9):1827-35
       IPI : Inferred from Physical Interaction with SGD:HRD1, SGD:DER1
Assigned on 2006-08-03 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-9904
Assigned on 2009-10-01 UniProtKB
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 forHRD3/YLR207W for HRD3
1) Gardner RG, et al. (2000) Endoplasmic reticulum degradation requires lumen to cytosol signaling. Transmembrane control of Hrd1p by Hrd3p. J Cell Biol 151(1):69-82

2) Hampton RY, et al. (1996) Role of 26S proteasome and HRD genes in the degradation of 3-hydroxy-3-methylglutaryl-CoA reductase, an integral endoplasmic reticulum membrane protein. Mol Biol Cell 7(12):2029-44

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for HRD3/YLR207W

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for HRD3/YLR207W

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 MITLLLY

C-term NVQIFAI

Length(aa) 833

MW(Da) 95,480

pI 6.59

Amino Acid Composition (full length)

GCG tools: PepPlot, Helical Wheel, PepStruct

Transcript Translation Calculations

Codon Bias 0.094

Codon Adaptation Index 0.142

Frequency of Optimal Codons 0.461

Hydropathicity of Protein -0.453

Aromaticity Score 0.116

10 20 30 40 50 | | | | | MITLLLYLCVICNAIVLIRADSIADPWPEARHLLNTIAKSRDPMKEAAME PNADEFVGFYVPMDYSPRNEEKNYQSIWQNEITDSQRHIYELLVQSSEQF NNSEATYTLSQIHLWSQYNFPHNMTLAHKYLEKFNDLTHFTNHSAIFDLA VMYATGGCASGNDQTVIPQDSAKALLYYQRAAQLGNLKAKQVLAYKYYSG FNVPRNFHKSLVLYRDIAEQLRKSYSRDEWDIVFPYWESYNVRISDFESG LLGKGLNSVPSSTVRKRTTRPDIGSPFIAQVNGVQMTLQIEPMGRFAFNG NDGNINGDEDDEDASERRIIRIYYAALNDYKGTYSQSRNCERAKNLLELT YKEFQPHVDNLDPLQVFYYVRCLQLLGHMYFTGEGSSKPNIHMAEEILTT SLEISRRAQGPIGRACIDLGLINQYITNNISQAISYYMKAMKTQANNGIV EFQLSKLATSFPEEKIGDPFNLMETAYLNGFIPAIYEFAVMIESGMNSKS SVENTAYLFKTFVDKNEAIMAPKLRTAFAALINDRSEVALWAYSQLAEQG YETAQVSAAYLMYQLPYEFEDPPRTTDQRKTLAISYYTRAFKQGNIDAGV VAGDIYFQMQNYSKAMALYQGAALKYSIQAIWNLGYMHEHGLGVNRDFHL AKRYYDQVSEHDHRFYLASKLSVLKLHLKSWLTWITREKVNYWKPSSPLN PNEDTQHSKTSWYKQLTKILQRMRHKEDSDKAAEDSHKHRTVVQNGANHR GDDQEEASEILGFQMEDLVTMGCILGIFLLSILMSTLAARRGWNVRFNGA QLNANGNRQQEQQQQQQAQGPPGWDFNVQIFAI*

Protein Structures from PDB: proteins of known structure with sequence similarity to HRD3/YLR207W, 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
HRD3 Hampton RY, et al. (1996) Role of 26S proteasome and HRD genes in the degradation of 3-hydroxy-3-methylglutaryl-CoA reductase, an integral endoplasmic reticulum membrane protein. Mol Biol Cell 7(12):2029-44

Standard Name	Reference
HRD3	*Hampton RY, et al.* (1996)** Role of 26S proteasome and HRD genes in the degradation of 3-hydroxy-3-methylglutaryl-CoA reductase, an integral endoplasmic reticulum membrane protein. Mol Biol Cell 7(12):2029-44

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

YLR207W SGD Systematic Sequence

850904 NCBI: Gene ID

NP_013308.1 NCBI: RefSeq protein version ID

NP_013308.1 NCBI: RefSeq protein version ID

6323236 NCBI: NCBI protein GI

Sequence from other databases
Sequence ID	Source
YLR207W	SGD Systematic Sequence
850904	NCBI: Gene ID
NP_013308.1	NCBI: RefSeq protein version ID
NP_013308.1	NCBI: RefSeq protein version ID
6323236	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
38 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 |MATALPHA1 |YOS9
Reviews
Hoseki J, et al. (2010) Mechanism and components of endoplasmic reticulum-associated degradation. J Biochem 147(1):19-25
       |CDC48 |DER1 |HRD1 |KAR2 |SSM4 |UBX2 |USA1 |YOS9
Mutants/Phenotypes
Strains/Constructs
Garza RM, et al. (2009) In vitro analysis of Hrd1p-mediated retrotranslocation of its multispanning membrane substrate 3-hydroxy-3-methylglutaryl (HMG)-CoA reductase. J Biol Chem 284(22):14710-22
       |CDC48 |DER1 |DFM1 |DSK2 |HMG2 |HRD1 |RAD23 |RPN1 |UBC7 |UBX2
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 |PDR5 |SEC61 |UBX2 |USA1 |YOS9
Non-Fungal Related Genes/Proteins
Spork S, et al. (2009) An unusual ERAD-like complex is targeted to the apicoplast of Plasmodium falciparum. Eukaryot Cell 8(8):1134-45
       |CDC48 |DER1 |HRD1 |NPL4 |RPL40A |RPL40B |RPS31 |UBA1 |UBA2 |UBC4 |UBI4 |UFD1
Cell Growth and Metabolism
Mutants/Phenotypes
Boer VM, et al. (2008) Influence of genotype and nutrition on survival and metabolism of starving yeast. Proc Natl Acad Sci U S A 105(19):6930-5
       |ACF4 |CPR3 |GCD1 |HAP1 |HRD1 |KEX1 |KOG1 |PPM1 |SCH9 |TOR1 |TPD3
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 |KAR2 |NPL4 |SHP1 |UBX2 |UBX7 |UFD1 |USA1 |YOS9
Genetic Interactions
Mutants/Phenotypes
Mazon MJ, et al. (2007) Efficient degradation of misfolded mutant Pma1 by endoplasmic reticulum-associated degradation requires Atg19 and the Cvt/autophagy pathway. Mol Microbiol 63(4):1069-1077
       |ATG19 |CUE1 |DER1 |HRD1 |NPL4 |PEP4 |PMA1 |PRE1 |PRE2 |UBC7
Reviews
Mittl PR and Schneider-Brachert W (2007) Sel1-like repeat proteins in signal transduction. Cell Signal 19(1):20-31
       |SHC1
Mutants/Phenotypes
Strains/Constructs
Substrates/Ligands/Cofactors
Apodaca J, et al. (2006) Cellular tolerance of prion protein PrP in yeast involves proteolysis and the unfolded protein response. Biochem Biophys Res Commun 347(1):319-26
       |CUE1 |DER1 |HRD1 |IRE1 |KAR2 |SSM4
Reviews
Boyce M and Yuan J (2006) Cellular response to endoplasmic reticulum stress: a matter of life or death. Cell Death Differ 13(3):363-73
       |CDC48 |CUE1 |DER1 |GCN2 |GCN4 |HAC1 |HRD1 |IRE1 |KAR2 |PDI1 |SEC61 |UBC1 |UBC6 |UBC7
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 |IRE1 |NPL4 |SSM4 |UBC7 |UBX2 |USA1 |YOS9
Mutants/Phenotypes
Protein Sequence Features
Protein-protein Interactions
Strains/Constructs
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 |KAR2 |UBX2 |YOS9
Cellular Location
Function/Process
Protein Sequence Features
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 |YOS9
Cellular Location
Function/Process
Protein-protein Interactions
Gauss R, et al. (2006) The Hrd1p ligase complex forms a linchpin between ER-lumenal substrate selection and Cdc48p recruitment. EMBO J 25(9):1827-35
       |CDC48 |DER1 |HRD1
Function/Process
Mutants/Phenotypes
Strains/Constructs
Liao M, et al. (2006) Endoplasmic reticulum-associated degradation of cytochrome P450 CYP3A4 in Saccharomyces cerevisiae: further characterization of cellular participants and structural determinants. Mol Pharmacol 69(6):1897-904
       |CDC48 |CUE1 |HRD1 |NPL4 |PEP4 |RPN1 |RSP5 |SSM4 |UBC6 |UBC7 |UFD1
Non-Fungal Related Genes/Proteins
Mueller B, et al. (2006) SEL1L, the homologue of yeast Hrd3p, is involved in protein dislocation from the mammalian ER. J Cell Biol 175(2):261-70

Non-Fungal Related Genes/Proteins
Lilley BN and Ploegh HL (2005) Multiprotein complexes that link dislocation, ubiquitination, and extraction of misfolded proteins from the endoplasmic reticulum membrane. Proc Natl Acad Sci U S A 102(40):14296-301
       |DER1 |HRD1
Mutants/Phenotypes
Sliwa P and Korona R (2005) Loss of dispensable genes is not adaptive in yeast. Proc Natl Acad Sci U S A 102(49):17670-4
         |AIM19 |CRZ1 |GVP36 |LCL2 |YGR035C |YIA6 |YIL001W |YIL077C |YJL150W |YJL215C |YLF2
Non-Fungal Related Genes/Proteins
Kaneko M and Nomura Y (2003) ER signaling in unfolded protein response. Life Sci 74(2-3):199-205
       |HRD1
Reviews
Kostova Z and Wolf DH (2003) For whom the bell tolls: protein quality control of the endoplasmic reticulum and the ubiquitin-proteasome connection. EMBO J 22(10):2309-17
           |CDC48 |IRE1 |KAR2 |MNL1 |MNS1 |SEC61 |UBC7
Function/Process
Strains/Constructs
Substrates/Ligands/Cofactors
Taxis C, et al. (2003) Use of modular substrates demonstrates mechanistic diversity and reveals differences in chaperone requirement of ERAD. J Biol Chem 278(38):35903-13
     |CDC48 |CWC23 |DER1 |HLJ1 |HRD1 |HSP104 |JID1 |KAR2 |NPL4 |SSA1 |SSA2 |SSA3 |SSA4 |UBC1 |MORE
Function/Process
Substrates/Ligands/Cofactors
Haynes CM, et al. (2002) An HRD/DER-independent ER quality control mechanism involves Rsp5p-dependent ubiquitination and ER-Golgi transport. J Cell Biol 158(1):91-101
       |DER1 |HRD1 |IRE1 |RSP5 |SEC61 |UBC7
Function/Process
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Taxis C, et al. (2002) ER-golgi traffic is a prerequisite for efficient ER degradation. Mol Biol Cell 13(6):1806-18
       |DER1 |HRD1 |KAR2 |SEC12 |SEC18 |SEC23 |SED5 |UFE1
Function/Process
Mutants/Phenotypes
Protein-protein Interactions
Regulatory Role
Strains/Constructs
Gardner RG, et al. (2001) In vivo action of the HRD ubiquitin ligase complex: mechanisms of endoplasmic reticulum quality control and sterol regulation. Mol Cell Biol 21(13):4276-91
       |CUE1 |HMG1 |HMG2 |HRD1 |RPN1 |UBC7
Cellular Location
Mutants/Phenotypes
Strains/Constructs
Substrates/Ligands/Cofactors
Murray BP and Correia MA (2001) Ubiquitin-dependent 26S proteasomal pathway: a role in the degradation of native human liver CYP3A4 expressed in Saccharomyces cerevisiae? Arch Biochem Biophys 393(1):106-16
       |HMG2 |HRD1 |PEP4 |RPN1 |SEC61 |SEC63 |UBC6 |UBC7
Function/Process
Mutants/Phenotypes
Regulatory Role
Strains/Constructs
Walter J, et al. (2001) Sec61p-independent degradation of the tail-anchored ER membrane protein Ubc6p. EMBO J 20(12):3124-31
               |CUE1 |DER1 |HRD1 |SEC61 |UBC1 |UBC6 |UBC7
Reviews
van Laar T, et al. (2001) Mif1: a missing link between the unfolded protein response pathway and ER-associated protein degradation? Curr Protein Pept Sci 2(2):169-90
       |HAC1 |HRD1 |IRE1 |KAR2 |MAS1 |UBC6
Cellular Location
Function/Process
Protein-protein Interactions
Gardner RG, et al. (2000) Endoplasmic reticulum degradation requires lumen to cytosol signaling. Transmembrane control of Hrd1p by Hrd3p. J Cell Biol 151(1):69-82
       |HRD1
Function/Process
Other Features
Hill K and Cooper AA (2000) Degradation of unassembled Vph1p reveals novel aspects of the yeast ER quality control system. EMBO J 19(4):550-61
       |DER1 |HRD1 |UBC4 |UBC5 |VMA22 |VPH1
Protein Sequence Features
Ponting CP (2000) Proteins of the endoplasmic-reticulum-associated degradation pathway: domain detection and function prediction. Biochem J 351 Pt 2():527-35
         |BRR2 |CUE1 |IRE1 |SEC63 |SEC72 |VPS9
Function/Process
Mutants/Phenotypes
Strains/Constructs
Wilhovsky S, et al. (2000) HRD gene dependence of endoplasmic reticulum-associated degradation. Mol Biol Cell 11(5):1697-708
         |HRD1 |UBC6 |UBC7
Function/Process
Mutants/Phenotypes
Strains/Constructs
Bordallo J and Wolf DH (1999) A RING-H2 finger motif is essential for the function of Der3/Hrd1 in endoplasmic reticulum associated protein degradation in the yeast Saccharomyces cerevisiae. FEBS Lett 448(2-3):244-8
     |HRD1 |SEC61
Cellular Location
Function/Process
Plemper RK and Wolf DH (1999) Endoplasmic reticulum degradation. Reverse protein transport and its end in the proteasome. Mol Biol Rep 26(1-2):125-30
     |DER1 |HRD1 |KAR2 |PDR5 |PRC1 |SEC61 |UBC6 |UBC7
Cellular Location
Function/Process
Mutants/Phenotypes
Protein-Nucleic Acid Interactions
Strains/Constructs
Plemper RK, et al. (1999) Genetic interactions of Hrd3p and Der3p/Hrd1p with Sec61p suggest a retro-translocation complex mediating protein transport for ER degradation. J Cell Sci 112 ( Pt 22)():4123-34
       |HRD1 |SEC61
Cellular Location
Function/Process
Genetic Interactions
Mutants/Phenotypes
Protein Sequence Features
Strains/Constructs
Saito Y, et al. (1999) Identification of SEC12, SED4, truncated SEC16, and EKS1/HRD3 as multicopy suppressors of ts mutants of Sar1 GTPase. J Biochem 125(1):130-7
       |HMG2 |KAR2 |SAR1 |SEC12 |SEC16 |SED4
Reviews
Sommer T and Wolf DH (1997) Endoplasmic reticulum degradation: reverse protein flow of no return. FASEB J 11(14):1227-33
     |CUE1 |DER1 |HRD1 |KAR2 |SEC61 |SEC63 |UBC6 |UBC7
DNA/RNA Sequence Features
Function/Process
Fungal Related Genes/Proteins
Mutants/Phenotypes
Non-Fungal Related Genes/Proteins
Protein Sequence Features
Strains/Constructs
Hampton RY, et al. (1996) Role of 26S proteasome and HRD genes in the degradation of 3-hydroxy-3-methylglutaryl-CoA reductase, an integral endoplasmic reticulum membrane protein. Mol Biol Cell 7(12):2029-44
     |HMG2 |HRD1 |RPN1

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