P25694 (CDC48_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Cell division control protein 48

Gene names

Name:	CDC48
Ordered Locus Names:	YDL126C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	835 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Involved in spindle disassembly, degradation of ubiquitinated proteins and protein export from the endoplasmic reticulum to the cytoplasm. Acts as a chaperone that collects ubiquitinated substrates. Has a role in the endoplasmic reticulum-associated degradation (ERAD) pathway. Required for the proteasome-dependent processing/activation of MGA2 and SPT23 transcription factors leading to the subsequent expression of OLE1. Has an additional role in the turnover of OLE1 where it targets ubiquitinated OLE1 and other proteins to the ERAD. Ref.5 Ref.7 Ref.8 Ref.9 Ref.19 Ref.20
Subunit structure	Interacts with OTU1 and DOA1/UFD3, leading to prevent multiubiquitination of substrates. Interacts with UFD2, leading to add further ubiquitin moities; the interaction with UFD2 is prevented by DOA1/UFD3. Component of the heterotrimeric Ufd1-Npl4-Cdc48/p97 (UNC) complex. Interacts with NPL4 and VMS1. Ref.5 Ref.6 Ref.12 Ref.14 Ref.19 Ref.20
Subcellular location	Microsome. Endoplasmic reticulum. Note: Bound loosely to components of the microsomal fraction. Ref.5 Ref.20
Miscellaneous	Present with 78400 molecules/cell in log phase SD medium. Ref.10
Sequence similarities	Belongs to the AAA ATPase family.

Ontologies

Keywords
Biological process	Cell cycle Protein transport Transport
Cellular component	Endoplasmic reticulum Microsome
Domain	Repeat
Ligand	ATP-binding Nucleotide-binding
PTM	Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	ER-associated protein catabolic process Inferred from mutant phenotype. Source: SGD cytoplasm-associated proteasomal ubiquitin-dependent protein catabolic process Inferred from mutant phenotype. Source: SGD macroautophagy Inferred from mutant phenotype. Source: SGD mitochondria-associated protein catabolic process Inferred from mutant phenotype Ref.19. Source: SGD piecemeal microautophagy of nucleus Inferred from mutant phenotype. Source: SGD protein transport Inferred from direct assay Ref.8. Source: SGD sister chromatid biorientation Inferred from mutant phenotype. Source: SGD vesicle fusion Inferred from direct assay. Source: SGD
Cellular component	Cdc48p-Npl4p-Ufd1p AAA ATPase complex Inferred from direct assay. Source: SGD Doa10p ubiquitin ligase complex Inferred from direct assay. Source: SGD cytosol Inferred from direct assay Ref.8. Source: SGD mating projection tip Inferred from direct assay. Source: SGD microsome Inferred from direct assay Ref.1. Source: SGD nucleus Inferred from direct assay. Source: SGD
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATPase activity Inferred from direct assay. Source: SGD protein binding Inferred from physical interaction Ref.12. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
NPL4	P33755	7	EBI-4308,EBI-12193
SHP1	P34223	9	EBI-4308,EBI-17093
SSM4	P40318	4	EBI-4308,EBI-18208
UBX2	Q04228	11	EBI-4308,EBI-27730
UBX3	Q12229	3	EBI-4308,EBI-35335
UBX4	P54730	5	EBI-4308,EBI-28127
UBX5	Q06682	3	EBI-4308,EBI-32041
UBX6	P47049	3	EBI-4308,EBI-25866
UBX7	P38349	4	EBI-4308,EBI-21157

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 835	835	Cell division control protein 48		PRO_0000084587
Regions
	Nucleotide binding	255 – 262	8	ATP Potential
	Nucleotide binding	528 – 535	8	ATP Potential
Amino acid modifications
	Modified residue	292	1	Phosphoserine Ref.18
	Modified residue	318	1	Phosphoserine Ref.18
	Modified residue	423	1	Phosphoserine Ref.18
	Modified residue	472	1	Phosphoserine Ref.18
	Modified residue	519	1	Phosphoserine Ref.13 Ref.15 Ref.17 Ref.18
	Modified residue	599	1	Phosphoserine Ref.18
	Modified residue	683	1	Phosphothreonine Ref.11
	Modified residue	735	1	Phosphothreonine Ref.17 Ref.18
	Modified residue	770	1	Phosphoserine Ref.15 Ref.16 Ref.17 Ref.18
	Cross-link	594		Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.11
	Cross-link	673		Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.11

Sequences

	Sequence		Length	Mass (Da)
	P25694 [UniParc]. Last modified October 1, 1996. Version 3. Checksum: 02ADDB9A227614D8	FASTA	835	91,996
	10 20 30 40 50 60 MGEEHKPLLD ASGVDPREED KTATAILRRK KKDNMLLVDD AINDDNSVIA INSNTMDKLE 70 80 90 100 110 120 LFRGDTVLVK GKKRKDTVLI VLIDDELEDG ACRINRVVRN NLRIRLGDLV TIHPCPDIKY 130 140 150 160 170 180 ATRISVLPIA DTIEGITGNL FDVFLKPYFV EAYRPVRKGD HFVVRGGMRQ VEFKVVDVEP 190 200 210 220 230 240 EEYAVVAQDT IIHWEGEPIN REDEENNMNE VGYDDIGGCR KQMAQIREMV ELPLRHPQLF 250 260 270 280 290 300 KAIGIKPPRG VLMYGPPGTG KTLMARAVAN ETGAFFFLIN GPEVMSKMAG ESESNLRKAF 310 320 330 340 350 360 EEAEKNAPAI IFIDEIDSIA PKRDKTNGEV ERRVVSQLLT LMDGMKARSN VVVIAATNRP 370 380 390 400 410 420 NSIDPALRRF GRFDREVDIG IPDATGRLEV LRIHTKNMKL ADDVDLEALA AETHGYVGAD 430 440 450 460 470 480 IASLCSEAAM QQIREKMDLI DLDEDEIDAE VLDSLGVTMD NFRFALGNSN PSALRETVVE 490 500 510 520 530 540 SVNVTWDDVG GLDEIKEELK ETVEYPVLHP DQYTKFGLSP SKGVLFYGPP GTGKTLLAKA 550 560 570 580 590 600 VATEVSANFI SVKGPELLSM WYGESESNIR DIFDKARAAA PTVVFLDELD SIAKARGGSL 610 620 630 640 650 660 GDAGGASDRV VNQLLTEMDG MNAKKNVFVI GATNRPDQID PAILRPGRLD QLIYVPLPDE 670 680 690 700 710 720 NARLSILNAQ LRKTPLEPGL ELTAIAKATQ GFSGADLLYI VQRAAKYAIK DSIEAHRQHE 730 740 750 760 770 780 AEKEVKVEGE DVEMTDEGAK AEQEPEVDPV PYITKEHFAE AMKTAKRSVS DAELRRYEAY 790 800 810 820 830 SQQMKASRGQ FSNFNFNDAP LGTTATDNAN SNNSAPSGAG AAFGSNAEED DDLYS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Yeast cell cycle protein CDC48p shows full-length homology to the mammalian protein VCP and is a member of a protein family involved in secretion, peroxisome formation, and gene expression." Froehlich K.-U., Fries H.W., Ruediger M., Erdmann R., Botstein D., Mecke D. J. Cell Biol. 114:443-453(1991) [PubMed: 1860879] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	Froehlich K.-U. Submitted (JUL-1996) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed: 9169867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Mobilization of processed, membrane-tethered SPT23 transcription factor by CDC48(UFD1/NPL4), a ubiquitin-selective chaperone." Rape M., Hoppe T., Gorr I., Kalocay M., Richly H., Jentsch S. Cell 107:667-677(2001) [PubMed: 11733065] [Abstract] Cited for: FUNCTION, INTERACTION WITH NPL4, SUBCELLULAR LOCATION.
[6]	"The conserved npl4 protein complex mediates proteasome-dependent membrane-bound transcription factor activation." Hitchcock A.L., Krebber H., Frietze S., Lin A., Latterich M., Silver P.A. Mol. Biol. Cell 12:3226-3241(2001) [PubMed: 11598205] [Abstract] Cited for: INTERACTION WITH NPL4.
[7]	"Protein dislocation from the ER requires polyubiquitination and the AAA-ATPase Cdc48." Jarosch E., Taxis C., Volkwein C., Bordallo J., Finley D., Wolf D.H., Sommer T. Nat. Cell Biol. 4:134-139(2002) [PubMed: 11813000] [Abstract] Cited for: FUNCTION.
[8]	"The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol." Ye Y., Meyer H.H., Rapoport T.A. Nature 414:652-656(2001) [PubMed: 11740563] [Abstract] Cited for: FUNCTION.
[9]	"Role of the ubiquitin-selective CDC48(UFD1/NPL4) chaperone (segregase) in ERAD of OLE1 and other substrates." Braun S., Matuschewski K., Rape M., Thoms S., Jentsch S. EMBO J. 21:615-621(2002) [PubMed: 11847109] [Abstract] Cited for: FUNCTION.
[10]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[11]	"A proteomics approach to understanding protein ubiquitination." Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P. Nat. Biotechnol. 21:921-926(2003) [PubMed: 12872131] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-683, UBIQUITINATION AT LYS-594 AND LYS-673, MASS SPECTROMETRY. Strain: SUB592.
[12]	"Shp1 and Ubx2 are adaptors of Cdc48 involved in ubiquitin-dependent protein degradation." Schuberth C., Richly H., Rumpf S., Buchberger A. EMBO Rep. 5:818-824(2004) [PubMed: 15258615] [Abstract] Cited for: INTERACTION WITH UBX PROTEINS.
[13]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N. Mol. Cell. Proteomics 4:310-327(2005) [PubMed: 15665377] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-519, MASS SPECTROMETRY. Strain: YAL6B.
[14]	"Functional division of substrate processing cofactors of the ubiquitin-selective Cdc48 chaperone." Rumpf S., Jentsch S. Mol. Cell 21:261-269(2006) [PubMed: 16427015] [Abstract] Cited for: INTERACTION WITH OTU1; UFD2 AND DOA1.
[15]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed: 17330950] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-519 AND SER-770, MASS SPECTROMETRY. Strain: ADR376.
[16]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed: 17287358] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-770, MASS SPECTROMETRY.
[17]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-519; THR-735 AND SER-770, MASS SPECTROMETRY.
[18]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-292; SER-318; SER-423; SER-472; SER-519; SER-599; THR-735 AND SER-770, MASS SPECTROMETRY.
[19]	"A stress-responsive system for mitochondrial protein degradation." Heo J.M., Livnat-Levanon N., Taylor E.B., Jones K.T., Dephoure N., Ring J., Xie J., Brodsky J.L., Madeo F., Gygi S.P., Ashrafi K., Glickman M.H., Rutter J. Mol. Cell 40:465-480(2010) [PubMed: 21070972] [Abstract] Cited for: FUNCTION, INTERACTION WITH VMS1.
[20]	"A Cdc48p-associated factor modulates endoplasmic reticulum-associated degradation, cell stress, and ubiquitinated protein homeostasis." Tran J.R., Tomsic L.R., Brodsky J.L. J. Biol. Chem. 286:5744-5755(2011) [PubMed: 21148305] [Abstract] Cited for: SUBCELLULAR LOCATION, FUNCTION, INTERACTION WITH CDC48.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X56956 Genomic DNA. Translation: CAA40276.1. Z74174 Genomic DNA. Translation: CAA98694.1. BK006938 Genomic DNA. Translation: DAA11734.1.
PIR	S67669.
RefSeq	NP_010157.1. NM_001180185.1.
3D structure databases
ProteinModelPortal	P25694.
SMR	P25694. Positions 27-785.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2704N.
IntAct	P25694. 73 interactions.
MINT	MINT-547129.
STRING	P25694.
Protein family/group databases
TCDB	3.A.16.1.2. endoplasmic reticular retrotranslocon (ER-RT) family.
Proteomic databases
PeptideAtlas	P25694.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YDL126C; YDL126C; YDL126C.
GeneID	851431.
KEGG	sce:YDL126C.
NMPDR	fig|4932.3.peg.894.
Organism-specific databases
CYGD	YDL126c.
SGD	S000002284. CDC48.
Phylogenomic databases
eggNOG	fuNOG04884.
GeneTree	EFGT00050000000010.
HOGENOM	HBG597299.
OMA	DAINDDN.
OrthoDB	EOG47H8Z3.
Gene expression databases
ArrayExpress	P25694.
Genevestigator	P25694.
GermOnline	YDL126C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR009010. Asp_de-COase-like_fold. IPR003593. ATPase_AAA+_core. IPR005938. ATPase_AAA_CDC48. IPR003959. ATPase_AAA_core. IPR003960. ATPase_AAA_CS. IPR004201. Cdc48_dom2. IPR003338. CDC4_N-term_subdom. [Graphical view]
Gene3D	G3DSA:2.40.40.20. Asp_decarboxylase-like_fold. 1 hit.
KO	K13525.
PANTHER	PTHR23077:SF18. PTHR23077:SF18. 1 hit.
Pfam	PF00004. AAA. 2 hits. PF02933. CDC48_2. 1 hit. PF02359. CDC48_N. 1 hit. [Graphical view]
SMART	SM00382. AAA. 2 hits. SM01072. CDC48_2. 1 hit. SM01073. CDC48_N. 1 hit. [Graphical view]
SUPFAM	SSF50692. Asp_decarb_fold. 1 hit.
TIGRFAMs	TIGR01243. CDC48. 1 hit.
PROSITE	PS00674. AAA. 2 hits. [Graphical view]
ProtoNet	Search...
Other
NextBio	968654.

Entry information

Entry name

CDC48_YEAST

Accession

Primary (citable) accession number: P25694
Secondary accession number(s): D6VRM4

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1992
Last sequence update:	October 1, 1996
Last modified:	January 25, 2012
This is version 118 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program