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Protein

Cell division control protein 53

Gene

CDC53

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

Core component of multiple cullin-RING-based SCF (SKP1-CUL1-F-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. As a scaffold protein may contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The SCF complex associates with CDC34 as the E2 ubiquitin-conjugating enzyme. The functional specificity of the SCF complex depends on the type of F-box protein. SCF(CDC4) controls the G1-to-S phase transition; it directs ubiquitination of the phosphorylated CDK inhibitor SIC1 and of CDC6. SCF(CDC4) directs ubiquitination of GCN4. SCF(GRR1) directs ubiquitination of phosphorylated CLN1, CLN2 and GIC2. SCF(MET30) directs ubiquitination of MET4. SCF(DIA2) is specifically involved in the pheromone induced degradation of phosphorylated TEC1. SCF(MDM30) seems to direct ubiquitination of FZ01. Involved in the regulation of methionine biosynthesis genes.8 Publications

GO - Molecular functioni

  • DNA replication origin binding Source: SGD
  • protein binding, bridging Source: SGD
  • ubiquitin protein ligase binding Source: GO_Central

GO - Biological processi

  • cell division Source: UniProtKB-KW
  • G1/S transition of mitotic cell cycle Source: SGD
  • G2/M transition of mitotic cell cycle Source: SGD
  • protein ubiquitination involved in ubiquitin-dependent protein catabolic process Source: SGD
  • SCF-dependent proteasomal ubiquitin-dependent protein catabolic process Source: SGD
Complete GO annotation...

Keywords - Biological processi

Cell cycle, Cell division

Enzyme and pathway databases

BioCyciYEAST:G3O-29530-MONOMER.
ReactomeiR-SCE-110314. Recognition of DNA damage by PCNA-containing replication complex.
R-SCE-174113. SCF-beta-TrCP mediated degradation of Emi1.
R-SCE-5696394. DNA Damage Recognition in GG-NER.
R-SCE-5696395. Formation of Incision Complex in GG-NER.
R-SCE-5696400. Dual Incision in GG-NER.
R-SCE-6781823. Formation of TC-NER Pre-Incision Complex.
R-SCE-6782135. Dual incision in TC-NER.
R-SCE-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SCE-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Names & Taxonomyi

Protein namesi
Recommended name:
Cell division control protein 53
Alternative name(s):
Cullin-A
E3 ubiquitin ligase complex SCF subunit CDC53
Gene namesi
Name:CDC53
Ordered Locus Names:YDL132W
ORF Names:D2190
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL132W.
SGDiS000002290. CDC53.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nucleus Source: UniProtKB-SubCell
  • SCF ubiquitin ligase complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi488 – 4881R → C: Prevents CDC34/UBC3 interaction. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 815815Cell division control protein 53PRO_0000119805Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki760 – 760Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8)By similarity

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiQ12018.

PTM databases

iPTMnetiQ12018.

Interactioni

Subunit structurei

Component of multiple SCF (SKP1-CUL1-F-box) E3 ubiquitin-protein ligase complexes formed of CUL1, SKP1/HRT1, RBX1 and a variable F-box domain-containing protein as substrate-specific adapter. Component of the SCF(CDC4) complex containing CDC4. Component of the SCF(MET30) complex containing MET30. Component of the SCF(GRR1) complex containig GRR1. Component of the probable SCF(DIA2) complex containing DIA2. Component of the probable SCF(YDR131C) complex containing YDR131C. Component of the probable SCF(YDR306C) complex containing YDR306C. Component of the probable SCF(YLR224W) complex containing YLR224W. Component of the probable SCF(YJL149W) complex containing YJL149W. Component of the probable SCF(YNL311C) complex containing YNL311C. Component of the probable SCF(MDM30) complex containing MDM30. Component of the probable SCF(UFO1) complex containing UFO1. Component of the probable SCF(HRT3) complex containing HRT3. Component of the probable SCF(YBR280C) complex containing YBR280C. Component of the probable SCF(YBR352W) complex containing YBR352W. Interacts with DCN1, YBR280C, YLR224W and YLR352W. The unneddylated form interacts with LAG2/CAND1 and the interaction mediates the exchange of the F-box substrate-specific subunit.8 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CDC34P146823EBI-4321,EBI-19730
CDC4P078348EBI-4321,EBI-4434
DCN1Q123953EBI-4321,EBI-29871
GRR1P248148EBI-4321,EBI-7898
HRT1Q082738EBI-4321,EBI-31686
LAG2Q9232510EBI-4321,EBI-2045650
MET30P390149EBI-4321,EBI-11507
SAF1P383525EBI-4321,EBI-21172
SKP1P5228613EBI-4321,EBI-4090

GO - Molecular functioni

  • protein binding, bridging Source: SGD
  • ubiquitin protein ligase binding Source: GO_Central

Protein-protein interaction databases

BioGridi31930. 80 interactions.
DIPiDIP-1234N.
IntActiQ12018. 48 interactions.
MINTiMINT-384023.

Structurei

Secondary structure

1
815
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi735 – 76228Combined sources
Beta strandi763 – 7664Combined sources
Helixi767 – 77812Combined sources
Turni779 – 7813Combined sources
Helixi786 – 79813Combined sources
Beta strandi801 – 8044Combined sources
Beta strandi808 – 8136Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3O2PX-ray2.23E730-815[»]
3O6BX-ray3.10B/D/F/H/J742-815[»]
ProteinModelPortaliQ12018.
SMRiQ12018. Positions 11-815.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ12018.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni9 – 280272Required for interaction with SKP1/CBF3D and F-box proteinAdd
BLAST
Regioni448 – 748301Required for interaction with CDC34/UBC3Add
BLAST

Sequence similaritiesi

Belongs to the cullin family.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00760000119212.
HOGENOMiHOG000176713.
InParanoidiQ12018.
KOiK03347.
OMAiCVNKSRS.
OrthoDBiEOG092C1L4K.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
InterProiIPR016157. Cullin_CS.
IPR016158. Cullin_homology.
IPR001373. Cullin_N.
IPR019559. Cullin_neddylation_domain.
IPR016159. Cullin_repeat-like_dom.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00888. Cullin. 1 hit.
PF10557. Cullin_Nedd8. 1 hit.
[Graphical view]
SMARTiSM00182. CULLIN. 1 hit.
SM00884. Cullin_Nedd8. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
SSF74788. SSF74788. 1 hit.
SSF75632. SSF75632. 1 hit.
PROSITEiPS01256. CULLIN_1. 1 hit.
PS50069. CULLIN_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q12018-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSETLPRSDD LEATWNFIEP GINQILGNEK NQASTSKRVY KILSPTMYME
60 70 80 90 100
VYTAIYNYCV NKSRSSGHFS TDSRTGQSTI LVGSEIYEKL KNYLKNYILN
110 120 130 140 150
FKQSNSETFL QFYVKRWKRF TIGAIFLNHA FDYMNRYWVQ KERSDGKRHI
160 170 180 190 200
FDVNTLCLMT WKEVMFDPSK DVLINELLDQ VTLGREGQII QRSNISTAIK
210 220 230 240 250
SLVALGIDPQ DLKKLNLNVY IQVFEKPFLK KTQEYYTQYT NDYLEKHSVT
260 270 280 290 300
EYIFEAHEII KREEKAMTIY WDDHTKKPLS MALNKVLITD HIEKLENEFV
310 320 330 340 350
VLLDARDIEK ITSLYALIRR DFTLIPRMAS VFENYVKKTG ENEISSLLAM
360 370 380 390 400
HKHNIMKNEN ANPKKLALMT AHSLSPKDYI KKLLEVHDIF SKIFNESFPD
410 420 430 440 450
DIPLAKALDN ACGAFININE FALPAGSPKS ATSKTSEMLA KYSDILLKKA
460 470 480 490 500
TKPEVASDMS DEDIITIFKY LTDKDAFETH YRRLFAKRLI HGTSTSAEDE
510 520 530 540 550
ENIIQRLQAA NSMEYTGKIT KMFQDIRLSK ILEDDFAVAL KNEPDYSKAK
560 570 580 590 600
YPDLQPFVLA ENMWPFSYQE VEFKLPKELV PSHEKLKESY SQKHNGRILK
610 620 630 640 650
WLWPLCRGEL KADIGKPGRM PFNFTVTLFQ MAILLLYNDA DVLTLENIQE
660 670 680 690 700
GTSLTIQHIA AAMVPFIKFK LIQQVPPGLD ALVKPETQFK LSRPYKALKT
710 720 730 740 750
NINFASGVKN DILQSLSGGG HDNHGNKLGN KRLTEDERIE KELNTERQIF
760 770 780 790 800
LEACIVRIMK AKRNLPHTTL VNECIAQSHQ RFNAKVSMVK RAIDSLIQKG
810
YLQRGDDGES YAYLA
Length:815
Mass (Da):93,944
Last modified:November 1, 1997 - v1
Checksum:i22BC8B35034EDDEF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U43564 Genomic DNA. Translation: AAB38821.1.
X96876 Genomic DNA. Translation: CAA65628.1.
Z74180 Genomic DNA. Translation: CAA98702.1.
BK006938 Genomic DNA. Translation: DAA11727.1.
PIRiS67675.
RefSeqiNP_010150.1. NM_001180191.1.

Genome annotation databases

EnsemblFungiiYDL132W; YDL132W; YDL132W.
GeneIDi851424.
KEGGisce:YDL132W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U43564 Genomic DNA. Translation: AAB38821.1.
X96876 Genomic DNA. Translation: CAA65628.1.
Z74180 Genomic DNA. Translation: CAA98702.1.
BK006938 Genomic DNA. Translation: DAA11727.1.
PIRiS67675.
RefSeqiNP_010150.1. NM_001180191.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3O2PX-ray2.23E730-815[»]
3O6BX-ray3.10B/D/F/H/J742-815[»]
ProteinModelPortaliQ12018.
SMRiQ12018. Positions 11-815.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31930. 80 interactions.
DIPiDIP-1234N.
IntActiQ12018. 48 interactions.
MINTiMINT-384023.

PTM databases

iPTMnetiQ12018.

Proteomic databases

MaxQBiQ12018.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL132W; YDL132W; YDL132W.
GeneIDi851424.
KEGGisce:YDL132W.

Organism-specific databases

EuPathDBiFungiDB:YDL132W.
SGDiS000002290. CDC53.

Phylogenomic databases

GeneTreeiENSGT00760000119212.
HOGENOMiHOG000176713.
InParanoidiQ12018.
KOiK03347.
OMAiCVNKSRS.
OrthoDBiEOG092C1L4K.

Enzyme and pathway databases

BioCyciYEAST:G3O-29530-MONOMER.
ReactomeiR-SCE-110314. Recognition of DNA damage by PCNA-containing replication complex.
R-SCE-174113. SCF-beta-TrCP mediated degradation of Emi1.
R-SCE-5696394. DNA Damage Recognition in GG-NER.
R-SCE-5696395. Formation of Incision Complex in GG-NER.
R-SCE-5696400. Dual Incision in GG-NER.
R-SCE-6781823. Formation of TC-NER Pre-Incision Complex.
R-SCE-6782135. Dual incision in TC-NER.
R-SCE-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SCE-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Miscellaneous databases

EvolutionaryTraceiQ12018.
PROiQ12018.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
InterProiIPR016157. Cullin_CS.
IPR016158. Cullin_homology.
IPR001373. Cullin_N.
IPR019559. Cullin_neddylation_domain.
IPR016159. Cullin_repeat-like_dom.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00888. Cullin. 1 hit.
PF10557. Cullin_Nedd8. 1 hit.
[Graphical view]
SMARTiSM00182. CULLIN. 1 hit.
SM00884. Cullin_Nedd8. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
SSF74788. SSF74788. 1 hit.
SSF75632. SSF75632. 1 hit.
PROSITEiPS01256. CULLIN_1. 1 hit.
PS50069. CULLIN_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCDC53_YEAST
AccessioniPrimary (citable) accession number: Q12018
Secondary accession number(s): D6VRL7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: September 7, 2016
This is version 134 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 377 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. 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.