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NPL4/YBR170C 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: 578081 to 576339 CDS: 578081 - 576339 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
NPL4	YBR170C	HRD4	ORF, Verified	S000000374
Description
Endoplasmic reticulum and nuclear membrane protein, forms a complex with Cdc48p and Ufd1p that recognizes ubiquitinated proteins in the endoplasmic reticulum and delivers them to the proteasome for degradation

GO Annotations [TOP] [NEXT]
Molecular Function Annotation(s) Reference(s) Evidence Assigned By molecular_function unknown SGD (2002) Use of the ND evidence code for Gene Ontology (GO) terms in SGD    ND : No Biological Data Available Assigned on 2003-10-10 SGD
Biological Process Annotation(s) Reference(s) Evidence Assigned By ER-associated protein catabolic process Bays NW, et al. (2001) HRD4/NPL4 is required for the proteasomal processing of ubiquitinated ER proteins. Mol Biol Cell 12(12):4114-28        IMP : Inferred from Mutant Phenotype Assigned on 2003-10-10 SGD mRNA transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0509 Assigned on 2008-06-16 UniProtKB 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 2008-06-16 UniProtKB proteolysis 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 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 2008-06-16 UniProtKB
Cellular Component Annotation(s) Reference(s) Evidence Assigned By Cdc48p-Npl4p-Ufd1p AAA ATPase complex Schuberth C and Buchberger A (2005) Membrane-bound Ubx2 recruits Cdc48 to ubiquitin ligases and their substrates to ensure efficient ER-associated protein degradation. Nat Cell Biol 7(10):999-1006        IDA : Inferred from Direct Assay Assigned on 2008-02-06 SGD Doa10p ubiquitin ligase 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 cytoplasm GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0963 Assigned on 2009-06-29 UniProtKB endoplasmic reticulum Ye Y, et al. (2001) The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol. Nature 414(6864):652-6        IDA : Inferred from Direct Assay Assigned on 2002-09-06 SGD GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0256 Assigned on 2008-06-16 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 2008-06-16 UniProtKB nuclear envelope-endoplasmic reticulum network Hitchcock AL, et al. (2001) The conserved npl4 protein complex mediates proteasome-dependent membrane-bound transcription factor activation. Mol Biol Cell 12(10):3226-41        IDA : Inferred from Direct Assay Assigned on 2003-10-10 SGD nucleus GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0539 Assigned on 2008-07-02 UniProtKB perinuclear region of cytoplasm 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-0198 Assigned on 2009-05-06 UniProtKB

Pathways [TOP] [NEXT]
No pathways available

Summary Paragraph [TOP] [NEXT]

SUMMARY PARAGRAPH for NPL4/YBR170C for NPL4 NPL4 encodes an essential nuclear pore protein (1, 2). Transport of macromolecules between the nucleus and the cytoplasm of eukaryotic cells occurs through the nuclear pore complex (NPC), a large macromolecular complex that spans the nuclear envelope (reviewed in 2, 3, 4, 5). The structure of the vertebrate NPC has been studied extensively; recent reviews include 6, 7, 8, and 9. The yeast NPC shares several features with the vertebrate NPC, despite being smaller and less elaborate (10, 11). Many yeast nuclear pore proteins, or nucleoporins, have been identified by a variety of genetic approaches (reviewed in 2, 3, 12, 13, 14). Mutations in NPL4 cause defects in nuclear protein import, nuclear poly(A) RNA export, and nuclear envelope morphology (1). Note that NPL4 corresponds to YBR170C, not YOR123C as stated in Fabre and Hurt (2). Last Updated: 1999-08-05

Basic References [TOP]

BASIC INFORMATION REFERENCES forNPL4/YBR170C for NPL4 1) DeHoratius C and Silver PA (1996) Nuclear transport defects and nuclear envelope alterations are associated with mutation of the Saccharomyces cerevisiae NPL4 gene. Mol Biol Cell 7(11):1835-55      2) Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313      3) Wente SR, et al. (1997) "The nucleus and nucleocytoplasmic transport in Saccharomyces cerevisiae." Pp. 471-546 in The Molecular and Cellular Biology of the Yeast Saccharomyces: Cell Cycle and Cell Biology, edited by Pringle JR, Broach JR and Jones EW. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press    4) Pemberton LF, et al. (1998) Transport routes through the nuclear pore complex. Curr Opin Cell Biol 10(3):392-9      5) Izaurralde E and Adam S (1998) Transport of macromolecules between the nucleus and the cytoplasm. RNA 4(4):351-64      6) Hinshaw JE (1994) Architecture of the nuclear pore complex and its involvement in nucleocytoplasmic transport. Biochem Pharmacol 47(1):15-20      7) Pante N and Aebi U (1996) Molecular dissection of the nuclear pore complex. Crit Rev Biochem Mol Biol 31(2):153-99      8) Davis LI (1995) The nuclear pore complex. Annu Rev Biochem 64:865-96      9) Pante N and Aebi U (1994) Toward the molecular details of the nuclear pore complex. J Struct Biol 113(3):179-89      10) Rout MP and Blobel G (1993) Isolation of the yeast nuclear pore complex. J Cell Biol 123(4):771-83      11) Yang Q, et al. (1998) Three-dimensional architecture of the isolated yeast nuclear pore complex: functional and evolutionary implications. Mol Cell 1(2):223-34        12) Doye V and Hurt E (1997) From nucleoporins to nuclear pore complexes. Curr Opin Cell Biol 9(3):401-11      13) Doye V and Hurt EC (1995) Genetic approaches to nuclear pore structure and function. Trends Genet 11(6):235-41        14) Newmeyer DD (1993) The nuclear pore complex and nucleocytoplasmic transport. Curr Opin Cell Biol 5(3):395-407      15) Hitchcock AL, et al. (2001) The conserved npl4 protein complex mediates proteasome-dependent membrane-bound transcription factor activation. Mol Biol Cell 12(10):3226-41        16) Bays NW, et al. (2001) HRD4/NPL4 is required for the proteasomal processing of ubiquitinated ER proteins. Mol Biol Cell 12(12):4114-28        17) Bays NW and Hampton RY (2002) Cdc48-Ufd1-Npl4: stuck in the middle with Ub. Curr Biol 12(10):R366-71          18) Bossie MA, et al. (1992) A mutant nuclear protein with similarity to RNA binding proteins interferes with nuclear import in yeast. Mol Biol Cell 3(8):875-93

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for NPL4/YBR170C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for NPL4/YBR170C

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 MLIRFRS C-term MILQESG Length(aa) 580 MW(Da) 65,782 pI 5.57 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias 0.041   Codon Adaptation Index 0.129   Frequency of Optimal Codons 0.438   Hydropathicity of Protein -0.500   Aromaticity Score 0.093

10 20 30 40 50 | | | | | MLIRFRSKNGTHRVSCQENDLFGTVIEKLVGNLDPNADVDTFTVCEKPGQ GIHAVSELADRTVMDLGLKHGDMLILNYSDKPANEKDGVNVEIGSVGIDS KGIRQHRYGPLRIKELAVDEELEKEDGLIPRQKSKLCKHGDRGMCEYCSP LPPWDKEYHEKNKIKHISFHSYLKKLNENANKKENGSSYISPLSEPDFRI NKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHVEFQKSEIINEFIQ AWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMDV EQVKNEMLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGSVFCKRHKDSFFL SSLEVIMAARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQ VSTEAEALVTADMISGSTFPSMAYINDTTDERYVPEIFYMKSNEYGITVK ENAKPAFPVDYLLVTLTHGFPNTDTETNSKFVSSTGFPWSNRQAMGQSQD YQELKKYLFNVASSGDFNLLHEKISNFHLLLYINSLQILSPDEWKLLIES AVKNEWEESLLKLVSSAGWQTLVMILQESG*

Protein Structures from PDB: proteins of known structure with sequence similarity to NPL4/YBR170C, 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
NPL4	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 BLASTP BLASTN Design Primers FASTA aa FASTA nt Restriction Fragment Map Restriction Fragment Sizes Six-Frame Translation

Sequence from other databases
Sequence ID	Source
YBR170C	SGD Systematic Sequence
852468	NCBI: Gene ID
NP_009729.1	NCBI: RefSeq protein version ID
NP_009729.1	NCBI: RefSeq protein version ID
6319647	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
57 curated references; 0 references not yet curated
Function/Process Regulatory Role Strains/Constructs	Bhattacharya S, et al. (2009) Identification of lysines within membrane-anchored Mga2p120 that are targets of Rsp5p ubiquitination and mediate mobilization of tethered Mga2p90. J Mol Biol 385(3):718-25	|CDC48 |MGA2 |OLE1 |RSP5 |SPT23 |UFD1
Genetic Interactions Mutants/Phenotypes Strains/Constructs	Bosis E, et al. (2009) Ssz1 Restores ERAD in Cells Expressing Defective Cdc48-Ufd1-Npl4 Complex by Upregulating Cdc48. Genetics	|CDC48 |HMG2 |HRD1 |PDR1 |RPN4 |RPT1 |SSZ1 |UFD1
RNA Levels and Processing Transcription	Ghazal G, et al. (2009) Yeast RNase III triggers polyadenylation-independent transcription termination. Mol Cell 36(1):99-109	|CDC19 |CSR1 |FTR1 |GIC2 |GPI17 |KEM1 |LGE1 |LYP1 |MED7 |MIC17 |MRH1 |NAB2 |NAM7 |NCB2 |MORE
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 |HRD3 |RPL40A |RPL40B |RPS31 |UBA1 |UBA2 |UBC4 |UBI4 |UFD1
Function/Process Mutants/Phenotypes Strains/Constructs	Wang Y, et al. (2009) Abnormal proteins can form aggresome in yeast: aggresome-targeting signals and components of the machinery. FASEB J 23(2):451-63	|ADH1 |ATP2 |BMH1 |CDC48 |DSK2 |ENO2 |FBA1 |HSP42 |HSP60 |HSP82 |ILV5 |IPP1 |MDR1 |NOG2 |MORE
Cellular Location Genetic Interactions Mutants/Phenotypes Non-Fungal Related Genes/Proteins Strains/Constructs	Duennwald ML and Lindquist S (2008) Impaired ERAD and ER stress are early and specific events in polyglutamine toxicity. Genes Dev 22(23):3308-3319	|CDC48 |CUE1 |HAC1 |IRE1 |OLE1 |PMR1 |PRC1 |PRE1 |PRE2 |PRE9 |RAD6 |RPN2 |SEC22 |SEC61 |MORE
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 |SHP1 |UBX2 |UBX7 |UFD1 |USA1 |YOS9
Mutants/Phenotypes Strains/Constructs	Medicherla B and Goldberg AL (2008) Heat shock and oxygen radicals stimulate ubiquitin-dependent degradation mainly of newly synthesized proteins. J Cell Biol 182(4):663-73	|CDC48 |RPN10 |SOD1 |SOD2 |UBC4 |UBC5 |UBC7 |UFD1 |UFD4
Function/Process Mutants/Phenotypes Substrates/Ligands/Cofactors	Metzger MB, et al. (2008) Degradation of a Cytosolic Protein Requires Endoplasmic Reticulum-associated Degradation Machinery. J Biol Chem 283(47):32302-16	|CDC48 |CUE1 |HLJ1 |SSA1 |SSM4 |UBC4 |UBC5 |UBC6 |UBC7 |UFD1 |URA3 |YDJ1
RNA Levels and Processing	Trott A, et al. (2008) Activation of Heat Shock and Antioxidant Responses by the Natural Product Celastrol: Transcriptional Signatures of a Thiol-targeted Molecule. Mol Biol Cell 19(3):1104-12	|AAD14 |AAD15 |AAD16 |AAD3 |AAD4 |AAD6 |ADH5 |ADH6 |AHP1 |ALD3 |ALD4 |ALD6 |ARI1 |ATR1 |MORE
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 |HRD3 |PEP4 |PMA1 |PRE1 |PRE2 |UBC7
Genetic Interactions Strains/Constructs	Mulder KW, et al. (2007) Modulation of Ubc4p/Ubc5p-Mediated Stress Responses by the RING-Finger-Dependent Ubiquitin-Protein Ligase Not4p in Saccharomyces cerevisiae. Genetics 176(1):181-92	|ARF1 |BRO1 |BUD19 |BUL1 |BUR2 |CAF120 |CAF40 |CBF1 |CCR4 |DOA1 |DOA4 |ECM4 |EST1 |GAL11 |MORE
Protein-protein Interactions Regulation of Strains/Constructs	Shcherbik N and Haines DS (2007) Cdc48p(Npl4p/Ufd1p) binds and segregates membrane-anchored/tethered complexes via a polyubiquitin signal present on the anchors. Mol Cell 25(3):385-97	|CDC48 |MGA2 |RSP5 |SPT23 |UFD1
Genetic Interactions Mutants/Phenotypes Other Features Regulation of Strains/Constructs Transcription	Auld KL, et al. (2006) The Conserved ATPase Get3/Arr4 Modulates the Activity of Membrane-Associated Proteins in Saccharomyces cerevisiae. Genetics 174(1):215-27	|CDC48 |GET1 |GET2 |GET3 |UFD1
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 |SSM4 |UBC7 |UBX2 |USA1 |YOS9
Evolution Fungal Related Genes/Proteins	De Hertogh B, et al. (2006) Emergence of species-specific transporters during evolution of the hemiascomycete phylum. Genetics 172(2):771-81	|AAC1 |AAC3 |ACS2 |ADP1 |ADY2 |AGC1 |AGP1 |AGP2 |AGP3 |ALP1 |ALR1 |ALR2 |ANT1 |AQR1 |MORE
Mutants/Phenotypes	Heiligenstein S, et al. (2006) Retrotranslocation of a viral A/B toxin from the yeast endoplasmic reticulum is independent of ubiquitination and ERAD. EMBO J 25(20):4717-27	|CDC48 |DSK2 |HRD1 |JEM1 |KAR2 |PDI1 |PMR1 |RAD23 |RSP5 |SCJ1 |SPF1 |UBC1 |UBC4 |UBC6 |MORE
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 |HRD3 |PEP4 |RPN1 |RSP5 |SSM4 |UBC6 |UBC7 |UFD1
Reviews	Pety de Thozee C and Ghislain M (2006) ER-associated degradation of membrane proteins in yeast. ScientificWorldJournal 6:967-83	|CDC48 |SAR1 |UFD1
Mutants/Phenotypes	Ravid T, et al. (2006) Membrane and soluble substrates of the Doa10 ubiquitin ligase are degraded by distinct pathways. EMBO J 25(3):533-43	|CBF2 |CDC48 |CUE1 |MATALPHA2 |MPS2 |QRI1 |SSM4 |UBC6 |UFD1
Non-Fungal Related Genes/Proteins Reviews	Romisch K (2006) Cdc48p is UBX-linked to ER ubiquitin ligases. Trends Biochem Sci 31(1):24-5	|CDC48 |DER1 |HRD1 |UBX2 |UFD1
Protein-protein Interactions	Rumpf S and Jentsch S (2006) Functional division of substrate processing cofactors of the ubiquitin-selective Cdc48 chaperone. Mol Cell 21(2):261-9	|CDC48 |DOA1 |OTU1 |OTU2 |SHP1 |SPT23 |UBP6 |UFD2
Genetic Interactions Strains/Constructs	Sato BK and Hampton RY (2006) Yeast Derlin Dfm1 interacts with Cdc48 and functions in ER homeostasis. Yeast 23(14-15):1053-64	|CDC48 |DER1 |DFM1 |SEC61 |UFE1
Protein-protein Interactions	Wilson JD, et al. (2006) Sel1p/Ubx2p participates in a distinct Cdc48p-dependent endoplasmic reticulum-associated degradation pathway. Traffic 7(9):1213-23	|CDC48 |SHP1 |UBX2
Reviews	Bazirgan OA and Hampton RY (2005) Cdc48-Ufd2-Rad23: the road less ubiquitinated? Nat Cell Biol 7(3):207-9	|CDC48 |DSK2 |RAD23 |UFD1 |UFD2
Genetic Interactions Mutants/Phenotypes Strains/Constructs	Davierwala AP, et al. (2005) The synthetic genetic interaction spectrum of essential genes. Nat Genet 37(10):1147-52	|ABD1 |ACT1 |ALG13 |ALG14 |ALG7 |APC11 |ARL3 |ARP2 |ARP7 |ASK1 |AVO1 |BET3 |BET5 |BIM1 |MORE
Reviews	Lord JM, et al. (2005) Quality control: another player joins the ERAD cast. Curr Biol 15(23):R963-4	|CDC48 |DER1 |HRD1 |SSM4 |UBX2 |UFD1
Function/Process Mutants/Phenotypes Protein Sequence Features Protein-protein Interactions Strains/Constructs	Richly H, et al. (2005) A series of ubiquitin binding factors connects CDC48/p97 to substrate multiubiquitylation and proteasomal targeting. Cell 120(1):73-84	|CDC48 |DSK2 |RAD23 |RPN10 |SPT23 |UFD1 |UFD2
Protein-protein Interactions	Archambault V, et al. (2004) Targeted proteomic study of the cyclin-Cdk module. Mol Cell 14(6):699-711	|ACE2 |ACM1 |BEM3 |BIK1 |BMH2 |BUD3 |CBK1 |CDC25 |CDC28 |CDC4 |CDC48 |CDC53 |CDC6 |CDH1 |MORE
Reviews	Cao K and Zheng Y (2004) The Cdc48/p97-Ufd1-Npl4 complex: its potential role in coordinating cellular morphogenesis during the M-G1 transition. Cell Cycle 3(4):422-4	|CDC48 |UFD1
Reviews	Cheeseman IM and Desai A (2004) Cell division: AAAtacking the mitotic spindle. Curr Biol 14(2):R70-2	|ASE1 |CDC48 |UFD1
Function/Process	Gnann A, et al. (2004) Cystic fibrosis transmembrane conductance regulator degradation depends on the lectins Htm1p/EDEM and the Cdc48 protein complex in yeast. Mol Biol Cell 15(9):4125-35	|CDC48 |HRD1 |MNL1 |SSM4 |UFD1
Function/Process Protein-protein Interactions	Medicherla B, et al. (2004) A genomic screen identifies Dsk2p and Rad23p as essential components of ER-associated degradation. EMBO Rep 5(7):692-7	|CDC48 |DSK2 |RAD23 |UFD1
Regulation of Transcription	Schade B, et al. (2004) Cold adaptation in budding yeast. Mol Biol Cell 15(12):5492-502	|DBP2 |DED1 |GLC3 |GLK1 |GPD1 |GPH1 |GPX1 |GTT2 |HAP5 |HRP1 |HSP10 |HSP104 |HSP12 |HSP26 |MORE
Protein-protein Interactions Substrates/Ligands/Cofactors	Schuberth C, et al. (2004) Shp1 and Ubx2 are adaptors of Cdc48 involved in ubiquitin-dependent protein degradation. EMBO Rep 5(8):818-24	|CDC48 |RPN10 |SHP1 |UBX2 |UBX3 |UBX4 |UBX5 |UBX6 |UBX7 |UFD1
Non-Fungal Related Genes/Proteins	Cao K, et al. (2003) The AAA-ATPase Cdc48/p97 regulates spindle disassembly at the end of mitosis. Cell 115(3):355-67	|ASE1 |CDC48 |CDC5 |CLB2 |UFD1
Mutants/Phenotypes Strains/Constructs	Hitchcock AL, et al. (2003) A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery. Proc Natl Acad Sci U S A 100(22):12735-40	|UBC7
Reviews	Schnell JD and Hicke L (2003) Non-traditional functions of ubiquitin and ubiquitin-binding proteins. J Biol Chem 278(38):35857-60	|CDC48 |CUE1 |MMS2 |RPN10 |RSP5 |STP2 |UBI4 |UFD1
Function/Process Mutants/Phenotypes Strains/Constructs	Shcherbik N, et al. (2003) Rsp5p is required for ER bound Mga2p120 polyubiquitination and release of the processed/tethered transactivator Mga2p90. Curr Biol 13(14):1227-33	|MGA2 |OLE1 |RSP5 |SPT23
Function/Process Mutants/Phenotypes 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 |HRD3 |HSP104 |JID1 |KAR2 |SSA1 |SSA2 |SSA3 |SSA4 |UBC1 |MORE
Non-Fungal Related Genes/Proteins Reviews	Woodman PG (2003) p97, a protein coping with multiple identities. J Cell Sci 116(Pt 21):4283-90	|CDC48 |UFD1 |VPS4
Function/Process Protein-protein Interactions	Ye Y, et al. (2003) Function of the p97-Ufd1-Npl4 complex in retrotranslocation from the ER to the cytosol: dual recognition of nonubiquitinated polypeptide segments and polyubiquitin chains. J Cell Biol 162(1):71-84	|CDC48 |UFD1
Function/Process Protein-protein Interactions Reviews Substrates/Ligands/Cofactors	Bays NW and Hampton RY (2002) Cdc48-Ufd1-Npl4: stuck in the middle with Ub. Curr Biol 12(10):R366-71	|CDC48 |UFD1
Function/Process Protein-protein Interactions Substrates/Ligands/Cofactors	Braun S, et al. (2002) Role of the ubiquitin-selective CDC48(UFD1/NPL4 )chaperone (segregase) in ERAD of OLE1 and other substrates. EMBO J 21(4):615-21	|CDC48 |OLE1 |UFD1
Alias Cellular Location Function/Process Mutants/Phenotypes Protein-protein Interactions Strains/Constructs Substrates/Ligands/Cofactors	Bays NW, et al. (2001) HRD4/NPL4 is required for the proteasomal processing of ubiquitinated ER proteins. Mol Biol Cell 12(12):4114-28	|CDC48 |UFD1
Function/Process Non-Fungal Related Genes/Proteins Protein Sequence Features	Botta A, et al. (2001) Cloning and characterization of the gene encoding human NPL4, a protein interacting with the ubiquitin fusion-degradation protein (UFD1L). Gene 275(1):39-46	|UFD1
Cellular Location Function/Process Protein-protein Interactions	Hetzer M, et al. (2001) Distinct AAA-ATPase p97 complexes function in discrete steps of nuclear assembly. Nat Cell Biol 3(12):1086-91	|UFD1
Cellular Location Function/Process Mutants/Phenotypes Protein-protein Interactions Regulatory Role Strains/Constructs Substrates/Ligands/Cofactors	Hitchcock AL, et al. (2001) The conserved npl4 protein complex mediates proteasome-dependent membrane-bound transcription factor activation. Mol Biol Cell 12(10):3226-41	|CDC48 |MGA2 |OLE1 |SPT23 |UFD1
Cellular Location Function/Process Protein-protein Interactions Strains/Constructs Substrates/Ligands/Cofactors	Rape M, et al. (2001) Mobilization of processed, membrane-tethered SPT23 transcription factor by CDC48(UFD1/NPL4), a ubiquitin-selective chaperone. Cell 107(5):667-77	|CDC48 |OLE1 |SPT23 |UFD1
Cellular Location Function/Process Protein-protein Interactions Substrates/Ligands/Cofactors	Ye Y, et al. (2001) The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol. Nature 414(6864):652-6	|CDC48 |UFD1
Function/Process	Hoppe T, et al. (2000) Activation of a membrane-bound transcription factor by regulated ubiquitin/proteasome-dependent processing. Cell 102(5):577-86	|CDC48 |MGA2 |OLE1 |RSP5 |SPT23 |UFD1
Function/Process Mutants/Phenotypes Strains/Constructs Substrates/Ligands/Cofactors	Stage-Zimmermann T, et al. (2000) Factors affecting nuclear export of the 60S ribosomal subunit in vivo. Mol Biol Cell 11(11):3777-89	|CRM1 |CSE1 |DBP5 |FAL1 |GLE1 |GLE2 |KAP104 |KAP120 |KAP123 |KAP95 |MEX67 |MSN5 |MTR10 |MTR2 |MORE
Mutants/Phenotypes Strains/Constructs	Entian KD, et al. (1999) Functional analysis of 150 deletion mutants in Saccharomyces cerevisiae by a systematic approach. Mol Gen Genet 262(4-5):683-702	|ABM1 |AIM3 |ALT1 |AMN1 |APD1 |APL2 |AVT3 |BIO3 |BIO4 |BIO5 |BNA3 |BUD4 |CFD1 |CHA4 |MORE
RNA Levels and Processing Regulation of	Jelinsky SA and Samson LD (1999) Global response of Saccharomyces cerevisiae to an alkylating agent. Proc Natl Acad Sci U S A 96(4):1486-91	|AAD14 |AAD16 |AAD4 |AAD6 |ABF1 |ADP1 |AGX1 |AMD2 |ARG1 |ARG3 |ARG4 |ARG5,6 |ARG7 |ARO1 |MORE
Reviews	Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313	|ACC1 |ASM4 |CBC2 |GLE1 |GLE2 |GSP1 |HRP1 |KAP104 |KAP123 |KAP95 |LOS1 |MEX67 |MTR2 |MTR3 |MORE
Cellular Location Function/Process Mutants/Phenotypes Protein Physical Properties Strains/Constructs	DeHoratius C and Silver PA (1996) Nuclear transport defects and nuclear envelope alterations are associated with mutation of the Saccharomyces cerevisiae NPL4 gene. Mol Biol Cell 7(11):1835-55
DNA/RNA Sequence Features	Schaaff-Gerstenschlager I, et al. (1993) Sequence and function analysis of a 4.3 kb fragment of Saccharomyces cerevisiae chromosome II including three open reading frames. Yeast 9(8):915-21	|MYO2 |SEC66 |SMY2

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