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Protein

Cell division control protein 48

Gene

CDC48

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 (PubMed:11733065, PubMed:11740563, PubMed:11813000, PubMed:11847109, PubMed:21070972, PubMed:21148305). Component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation. CDC48 may provide the mechanical force that dislodges the polyubiquitinated nascent peptides from the exit channel (PubMed:23178123, PubMed:24261871).8 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei358ATPBy similarity1
Binding sitei394ATPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi257 – 263ATPBy similarity7

GO - Molecular functioni

  • ATPase activity Source: SGD
  • ATP binding Source: UniProtKB-KW
  • protein phosphatase type 1 regulator activity Source: SGD
  • ubiquitin binding Source: SGD

GO - Biological processi

  • ATP metabolic process Source: ParkinsonsUK-UCL
  • cytoplasm-associated proteasomal ubiquitin-dependent protein catabolic process Source: SGD
  • endoplasmic reticulum membrane fusion Source: SGD
  • ER-associated misfolded protein catabolic process Source: SGD
  • ER-associated ubiquitin-dependent protein catabolic process Source: SGD
  • macroautophagy Source: SGD
  • mitochondria-associated ubiquitin-dependent protein catabolic process Source: SGD
  • mitotic spindle disassembly Source: SGD
  • negative regulation of telomerase activity Source: SGD
  • nonfunctional rRNA decay Source: SGD
  • nucleus-associated proteasomal ubiquitin-dependent protein catabolic process Source: SGD
  • piecemeal microautophagy of nucleus Source: SGD
  • positive regulation of histone H2B ubiquitination Source: SGD
  • positive regulation of protein localization to nucleus Source: SGD
  • proteasome-mediated ubiquitin-dependent protein catabolic process Source: SGD
  • retrograde protein transport, ER to cytosol Source: SGD
  • ribophagy Source: SGD
  • ribosome-associated ubiquitin-dependent protein catabolic process Source: SGD
  • SCF complex disassembly in response to cadmium stress Source: SGD
  • sister chromatid biorientation Source: SGD
Complete GO annotation...

Keywords - Biological processi

Cell cycle, Protein transport, Transport

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29525-MONOMER.
ReactomeiR-SCE-110320. Translesion Synthesis by POLH.
R-SCE-3371511. HSF1 activation.
R-SCE-5689896. Ovarian tumor domain proteases.
R-SCE-6798695. Neutrophil degranulation.

Protein family/group databases

TCDBi3.A.16.1.2. the endoplasmic reticular retrotranslocon (er-rt) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Cell division control protein 481 Publication
Alternative name(s):
Cell division cycle protein 481 Publication
Gene namesi
Name:CDC481 Publication
Ordered Locus Names:YDL126CImported
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL126C.
SGDiS000002284. CDC48.

Subcellular locationi

  • Microsome 1 Publication
  • Endoplasmic reticulum 1 Publication
  • Cytoplasm 1 Publication

  • Note: Bound loosely to components of the microsomal fraction.1 Publication

GO - Cellular componenti

  • Cdc48p-Npl4p-Vms1p AAA ATPase complex Source: SGD
  • cytosol Source: SGD
  • Doa10p ubiquitin ligase complex Source: SGD
  • endoplasmic reticulum membrane Source: SGD
  • Hrd1p ubiquitin ligase ERAD-L complex Source: SGD
  • nucleus Source: SGD
  • RQC complex Source: SGD
  • VCP-NPL4-UFD1 AAA ATPase complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endoplasmic reticulum, Microsome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000845871 – 835Cell division control protein 48Add BLAST835

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki305Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki322Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki346Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei472PhosphoserineCombined sources1
Modified residuei519PhosphoserineCombined sources1
Cross-linki522Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki539Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki594Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki673Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Modified residuei735PhosphothreonineCombined sources1
Modified residuei770PhosphoserineCombined sources1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP25694.
PRIDEiP25694.

PTM databases

iPTMnetiP25694.

Interactioni

Subunit structurei

Component of the HRD1 complex which contains HRD1, HRD3, USA1, DER1, YOS9, CDC48, NPL4, UFD1 AND UBX2/SEL1. The complex is composed of the core membrane complex, consisting of the E3 ligase HRD1 and its cofactors HRD3, DER1 and USA1, the substrate recruiting factor YOS9, and the heterotrimeric UFD1-NPL4-CDC48/p97 (UNC) ATPase complex recruited by UBX2/SEL1. Interacts with HRD1, HRD3, YOS9, UBX2, DER1, USA1 and UFD1. Interacts with OTU1 and DOA1/UFD3, to prevent multiubiquitination of substrates. Interacts with UFD2, to add further ubiquitin moieties; the interaction with UFD2 is prevented by DOA1/UFD3. Interacts with NPL4 and VMS1. Component of the ribosome quality control complex (RQC), composed of the E3 ubiquitin ligase RKR1/LTN1, RQC1 and RQC2, as well as CDC48 and its ubiquitin-binding cofactors. RQC forms a stable complex with 60S ribosomal subunits (PubMed:23178123, PubMed:23479637).9 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-4308,EBI-4308
BRE5P537414EBI-4308,EBI-28528
DER1P383075EBI-4308,EBI-5761
DOA1P360375EBI-4308,EBI-6017
HRD1Q081098EBI-4308,EBI-37613
HRD3Q057876EBI-4308,EBI-31647
NPL4P3375511EBI-4308,EBI-12193
SHP1P342239EBI-4308,EBI-17093
SSM4P403184EBI-4308,EBI-18208
UBP3Q014774EBI-4308,EBI-19834
UBX2Q0422815EBI-4308,EBI-27730
UBX3Q122293EBI-4308,EBI-35335
UBX4P547305EBI-4308,EBI-28127
UBX5Q066823EBI-4308,EBI-32041
UBX6P470493EBI-4308,EBI-25866
UBX7P383494EBI-4308,EBI-21157
VMS1Q043115EBI-4308,EBI-784329

GO - Molecular functioni

  • ubiquitin binding Source: SGD

Protein-protein interaction databases

BioGridi31937. 286 interactors.
DIPiDIP-2704N.
IntActiP25694. 81 interactors.
MINTiMINT-547129.

Structurei

3D structure databases

ProteinModelPortaliP25694.
SMRiP25694.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the AAA ATPase family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00860000133780.
HOGENOMiHOG000223224.
InParanoidiP25694.
KOiK13525.
OMAiREVAEYP.
OrthoDBiEOG092C0QVL.

Family and domain databases

Gene3Di3.10.330.10. 1 hit.
3.40.50.300. 2 hits.
InterProiIPR003593. AAA+_ATPase.
IPR005938. AAA_ATPase_CDC48.
IPR009010. Asp_de-COase-like_dom.
IPR003959. ATPase_AAA_core.
IPR003960. ATPase_AAA_CS.
IPR004201. Cdc48_dom2.
IPR029067. CDC48_domain_2-like.
IPR003338. CDC4_N-term_subdom.
IPR027417. P-loop_NTPase.
IPR015415. Vps4_C.
[Graphical view]
PfamiPF00004. AAA. 2 hits.
PF02933. CDC48_2. 1 hit.
PF02359. CDC48_N. 1 hit.
PF09336. Vps4_C. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 2 hits.
SM01072. CDC48_2. 1 hit.
SM01073. CDC48_N. 1 hit.
[Graphical view]
SUPFAMiSSF50692. SSF50692. 1 hit.
SSF52540. SSF52540. 2 hits.
SSF54585. SSF54585. 1 hit.
TIGRFAMsiTIGR01243. CDC48. 1 hit.
PROSITEiPS00674. AAA. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P25694-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGEEHKPLLD ASGVDPREED KTATAILRRK KKDNMLLVDD AINDDNSVIA
60 70 80 90 100
INSNTMDKLE LFRGDTVLVK GKKRKDTVLI VLIDDELEDG ACRINRVVRN
110 120 130 140 150
NLRIRLGDLV TIHPCPDIKY ATRISVLPIA DTIEGITGNL FDVFLKPYFV
160 170 180 190 200
EAYRPVRKGD HFVVRGGMRQ VEFKVVDVEP EEYAVVAQDT IIHWEGEPIN
210 220 230 240 250
REDEENNMNE VGYDDIGGCR KQMAQIREMV ELPLRHPQLF KAIGIKPPRG
260 270 280 290 300
VLMYGPPGTG KTLMARAVAN ETGAFFFLIN GPEVMSKMAG ESESNLRKAF
310 320 330 340 350
EEAEKNAPAI IFIDEIDSIA PKRDKTNGEV ERRVVSQLLT LMDGMKARSN
360 370 380 390 400
VVVIAATNRP NSIDPALRRF GRFDREVDIG IPDATGRLEV LRIHTKNMKL
410 420 430 440 450
ADDVDLEALA AETHGYVGAD IASLCSEAAM QQIREKMDLI DLDEDEIDAE
460 470 480 490 500
VLDSLGVTMD NFRFALGNSN PSALRETVVE SVNVTWDDVG GLDEIKEELK
510 520 530 540 550
ETVEYPVLHP DQYTKFGLSP SKGVLFYGPP GTGKTLLAKA VATEVSANFI
560 570 580 590 600
SVKGPELLSM WYGESESNIR DIFDKARAAA PTVVFLDELD SIAKARGGSL
610 620 630 640 650
GDAGGASDRV VNQLLTEMDG MNAKKNVFVI GATNRPDQID PAILRPGRLD
660 670 680 690 700
QLIYVPLPDE NARLSILNAQ LRKTPLEPGL ELTAIAKATQ GFSGADLLYI
710 720 730 740 750
VQRAAKYAIK DSIEAHRQHE AEKEVKVEGE DVEMTDEGAK AEQEPEVDPV
760 770 780 790 800
PYITKEHFAE AMKTAKRSVS DAELRRYEAY SQQMKASRGQ FSNFNFNDAP
810 820 830
LGTTATDNAN SNNSAPSGAG AAFGSNAEED DDLYS
Length:835
Mass (Da):91,996
Last modified:October 1, 1996 - v3
Checksum:i02ADDB9A227614D8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56956 Genomic DNA. Translation: CAA40276.1.
Z74174 Genomic DNA. Translation: CAA98694.1.
BK006938 Genomic DNA. Translation: DAA11734.1.
PIRiS67669.
RefSeqiNP_010157.1. NM_001180185.1.

Genome annotation databases

EnsemblFungiiYDL126C; YDL126C; YDL126C.
GeneIDi851431.
KEGGisce:YDL126C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56956 Genomic DNA. Translation: CAA40276.1.
Z74174 Genomic DNA. Translation: CAA98694.1.
BK006938 Genomic DNA. Translation: DAA11734.1.
PIRiS67669.
RefSeqiNP_010157.1. NM_001180185.1.

3D structure databases

ProteinModelPortaliP25694.
SMRiP25694.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31937. 286 interactors.
DIPiDIP-2704N.
IntActiP25694. 81 interactors.
MINTiMINT-547129.

Protein family/group databases

TCDBi3.A.16.1.2. the endoplasmic reticular retrotranslocon (er-rt) family.

PTM databases

iPTMnetiP25694.

Proteomic databases

MaxQBiP25694.
PRIDEiP25694.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL126C; YDL126C; YDL126C.
GeneIDi851431.
KEGGisce:YDL126C.

Organism-specific databases

EuPathDBiFungiDB:YDL126C.
SGDiS000002284. CDC48.

Phylogenomic databases

GeneTreeiENSGT00860000133780.
HOGENOMiHOG000223224.
InParanoidiP25694.
KOiK13525.
OMAiREVAEYP.
OrthoDBiEOG092C0QVL.

Enzyme and pathway databases

BioCyciYEAST:G3O-29525-MONOMER.
ReactomeiR-SCE-110320. Translesion Synthesis by POLH.
R-SCE-3371511. HSF1 activation.
R-SCE-5689896. Ovarian tumor domain proteases.
R-SCE-6798695. Neutrophil degranulation.

Miscellaneous databases

PROiP25694.

Family and domain databases

Gene3Di3.10.330.10. 1 hit.
3.40.50.300. 2 hits.
InterProiIPR003593. AAA+_ATPase.
IPR005938. AAA_ATPase_CDC48.
IPR009010. Asp_de-COase-like_dom.
IPR003959. ATPase_AAA_core.
IPR003960. ATPase_AAA_CS.
IPR004201. Cdc48_dom2.
IPR029067. CDC48_domain_2-like.
IPR003338. CDC4_N-term_subdom.
IPR027417. P-loop_NTPase.
IPR015415. Vps4_C.
[Graphical view]
PfamiPF00004. AAA. 2 hits.
PF02933. CDC48_2. 1 hit.
PF02359. CDC48_N. 1 hit.
PF09336. Vps4_C. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 2 hits.
SM01072. CDC48_2. 1 hit.
SM01073. CDC48_N. 1 hit.
[Graphical view]
SUPFAMiSSF50692. SSF50692. 1 hit.
SSF52540. SSF52540. 2 hits.
SSF54585. SSF54585. 1 hit.
TIGRFAMsiTIGR01243. CDC48. 1 hit.
PROSITEiPS00674. AAA. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCDC48_YEAST
AccessioniPrimary (citable) accession number: P25694
Secondary accession number(s): D6VRM4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: October 1, 1996
Last modified: November 30, 2016
This is version 169 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 78400 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.