Q12018 (CDC53_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Cell division control protein 53

Alternative name(s):
Cullin-A
E3 ubiquitin ligase complex SCF subunit CDC53

Gene names

Name:	CDC53
Ordered Locus Names:	YDL132W
ORF Names:	D2190

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	815 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.12 Ref.17
Subunit structure	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. Ref.6 Ref.7 Ref.10 Ref.11 Ref.13
Subcellular location	Cytoplasm. Nucleus Ref.14.
Miscellaneous	Present with 377 molecules/cell in log phase SD medium. Ref.15
Sequence similarities	Belongs to the cullin family.

Ontologies

Keywords
Biological process	Cell cycle Cell division
Cellular component	Cytoplasm Nucleus
PTM	Isopeptide bond Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	G1/S transition of mitotic cell cycle Inferred from mutant phenotype Ref.1. Source: SGD G2/M transition of mitotic cell cycle Inferred from genetic interaction Ref.9. Source: SGD SCF-dependent proteasomal ubiquitin-dependent protein catabolic process Inferred from direct assay Ref.6Ref.7. Source: SGD cell division Inferred from electronic annotation. Source: UniProtKB-KW protein ubiquitination involved in ubiquitin-dependent protein catabolic process Inferred from direct assay Ref.6Ref.7. Source: SGD
Cellular component	SCF ubiquitin ligase complex Inferred from direct assay Ref.6Ref.7. Source: SGD cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	DNA replication origin binding Inferred from physical interaction Ref.17. Source: SGD protein binding, bridging Inferred from mutant phenotype Ref.10. Source: SGD ubiquitin protein ligase binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CDC34	P14682	3	EBI-4321,EBI-19730
CDC4	P07834	8	EBI-4321,EBI-4434
GRR1	P24814	8	EBI-4321,EBI-7898
HRT1	Q08273	7	EBI-4321,EBI-31686
MET30	P39014	12	EBI-4321,EBI-11507
SAF1	P38352	5	EBI-4321,EBI-21172
SKP1	P52286	13	EBI-4321,EBI-4090

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 815

815

Cell division control protein 53

PRO_0000119805

Regions

Region

9 – 280

272

Required for interaction with SKP1/CBF3D and F-box protein

Region

448 – 748

301

Required for interaction with CDC34/UBC3

Amino acid modifications

Cross-link

760

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8) By similarity

Experimental info

Mutagenesis

488

1

R → C: Prevents CDC34/UBC3 interaction. Ref.10

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

815

Helix Strand Turn

Details...

Helix

735 – 762

28

Beta strand

763 – 766

4

Helix

767 – 778

12

Turn

779 – 781

3

Helix

786 – 798

13

Beta strand

810 – 813

4

Sequences

	Sequence		Length	Mass (Da)
	Q12018 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: 22BC8B35034EDDEF	FASTA	815	93,944
	10 20 30 40 50 60 MSETLPRSDD LEATWNFIEP GINQILGNEK NQASTSKRVY KILSPTMYME VYTAIYNYCV 70 80 90 100 110 120 NKSRSSGHFS TDSRTGQSTI LVGSEIYEKL KNYLKNYILN FKQSNSETFL QFYVKRWKRF 130 140 150 160 170 180 TIGAIFLNHA FDYMNRYWVQ KERSDGKRHI FDVNTLCLMT WKEVMFDPSK DVLINELLDQ 190 200 210 220 230 240 VTLGREGQII QRSNISTAIK SLVALGIDPQ DLKKLNLNVY IQVFEKPFLK KTQEYYTQYT 250 260 270 280 290 300 NDYLEKHSVT EYIFEAHEII KREEKAMTIY WDDHTKKPLS MALNKVLITD HIEKLENEFV 310 320 330 340 350 360 VLLDARDIEK ITSLYALIRR DFTLIPRMAS VFENYVKKTG ENEISSLLAM HKHNIMKNEN 370 380 390 400 410 420 ANPKKLALMT AHSLSPKDYI KKLLEVHDIF SKIFNESFPD DIPLAKALDN ACGAFININE 430 440 450 460 470 480 FALPAGSPKS ATSKTSEMLA KYSDILLKKA TKPEVASDMS DEDIITIFKY LTDKDAFETH 490 500 510 520 530 540 YRRLFAKRLI HGTSTSAEDE ENIIQRLQAA NSMEYTGKIT KMFQDIRLSK ILEDDFAVAL 550 560 570 580 590 600 KNEPDYSKAK YPDLQPFVLA ENMWPFSYQE VEFKLPKELV PSHEKLKESY SQKHNGRILK 610 620 630 640 650 660 WLWPLCRGEL KADIGKPGRM PFNFTVTLFQ MAILLLYNDA DVLTLENIQE GTSLTIQHIA 670 680 690 700 710 720 AAMVPFIKFK LIQQVPPGLD ALVKPETQFK LSRPYKALKT NINFASGVKN DILQSLSGGG 730 740 750 760 770 780 HDNHGNKLGN KRLTEDERIE KELNTERQIF LEACIVRIMK AKRNLPHTTL VNECIAQSHQ 790 800 810 RFNAKVSMVK RAIDSLIQKG YLQRGDDGES YAYLA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cdc53p acts in concert with Cdc4p and Cdc34p to control the G1-to-S-phase transition and identifies a conserved family of proteins." Mathias N., Johnson S.L., Winey M., Adams A.E., Goetsch L., Pringle J.R., Byers B., Goebl M.G. Mol. Cell. Biol. 16:6634-6643(1996) [PubMed: 8943317] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Analysis of a 26,756 bp segment from the left arm of yeast chromosome IV." Woelfl S., Haneman V., Saluz H.P. Yeast 12:1549-1554(1996) [PubMed: 8972577] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[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 96604 / S288c / FY1679.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Regulated degradation of the transcription factor Gcn4." Kornitzer D., Raboy B., Kulka R.G., Fink G.R. EMBO J. 13:6021-6030(1994) [PubMed: 7813440] [Abstract] Cited for: FUNCTION.
[6]	"F-box proteins are receptors that recruit phosphorylated substrates to the SCF ubiquitin-ligase complex." Skowyra D., Craig K.L., Tyers M., Elledge S.J., Harper J.W. Cell 91:209-219(1997) [PubMed: 9346238] [Abstract] Cited for: FUNCTION, SUBUNIT.
[7]	"A complex of Cdc4p, Skp1p, and Cdc53p/cullin catalyzes ubiquitination of the phosphorylated CDK inhibitor Sic1p." Feldman R.M., Correll C.C., Kaplan K.B., Deshaies R.J. Cell 91:221-230(1997) [PubMed: 9346239] [Abstract] Cited for: FUNCTION, SUBUNIT.
[8]	"The Cdc4/34/53 pathway targets Cdc6p for proteolysis in budding yeast." Drury L.S., Perkins G., Diffley J.F. EMBO J. 16:5966-5976(1997) [PubMed: 9312054] [Abstract] Cited for: FUNCTION.
[9]	"The Cdc42p effector Gic2p is targeted for ubiquitin-dependent degradation by the SCFGrr1 complex." Jaquenoud M., Gulli M.P., Peter K., Peter M. EMBO J. 17:5360-5373(1998) [PubMed: 9736614] [Abstract] Cited for: FUNCTION.
[10]	"Cdc53 is a scaffold protein for multiple Cdc34/Skp1/F-box protein complexes that regulate cell division and methionine biosynthesis in yeast." Patton E.E., Willems A.R., Sa D., Kuras L., Thomas D., Craig K.L., Tyers M. Genes Dev. 12:692-705(1998) [PubMed: 9499404] [Abstract] Cited for: FUNCTION, SUBUNIT, MUTAGENESIS OF ARG-488.
[11]	"Cdc53/cullin and the essential Hrt1 RING-H2 subunit of SCF define a ubiquitin ligase module that activates the E2 enzyme Cdc34." Seol J.H., Feldman R.M.R., Zachariae W., Shevchenko A., Correll C.C., Lyapina S., Chi Y., Galova M., Claypool J., Sandmeyer S., Nasmyth K., Shevchenko A., Deshaies R.J. Genes Dev. 13:1614-1626(1999) [PubMed: 10385629] [Abstract] Cited for: INTERACTION WITH HRT1.
[12]	"Reconstitution of G1 cyclin ubiquitination with complexes containing SCFGrr1 and Rbx1." Skowyra D., Koepp D.M., Kamura T., Conrad M.N., Conaway R.C., Conaway J.W., Elledge S.J., Harper J.W. Science 284:662-665(1999) [PubMed: 10213692] [Abstract] Cited for: FUNCTION, RECONSTITUTION OF THE SKF(GRR1)COMPLEX.
[13]	"Skp1 forms multiple protein complexes, including RAVE, a regulator of V-ATPase assembly." Seol J.H., Shevchenko A., Shevchenko A., Deshaies R.J. Nat. Cell Biol. 3:384-391(2001) [PubMed: 11283612] [Abstract] Cited for: INTERACTION WITH DCN1; YBR280C; YLR224W AND YLR352W.
[14]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[15]	"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].
[16]	"Functional interaction of 13 yeast SCF complexes with a set of yeast E2 enzymes in vitro." Kus B.M., Caldon C.E., Andorn-Broza R., Edwards A.M. Proteins 54:455-467(2004) [PubMed: 14747994] [Abstract] Cited for: RECONSTITUTION OF THE SCF(DIA2) COMPLEX, RECONSTITUTION OF THE SCF(YDR131C) COMPLEX, RECONSTITUTION OF THE SCF(YDR306C) COMPLEX, RECONSTITUTION OF THE SCF(YLR224W) COMPLEX, RECONSTITUTION OF THE SCF(YJL149W) COMPLEX, RECONSTITUTION OF THE SCF(YNL311C) COMPLEX, RECONSTITUTION OF THE SCF(MDM30) COMPLEX, RECONSTITUTION OF THE SCF(CDC4) COMPLEX, RECONSTITUTION OF THE SCF(UFO1) COMPLEX, RECONSTITUTION OF THE SCF(GRR1) COMPLEX, RECONSTITUTION OF THE SCF(HRT3) COMPLEX.
[17]	"The F-box protein Dia2 regulates DNA replication." Koepp D.M., Kile A.C., Swaminathan S., Rodriguez-Rivera V. Mol. Biol. Cell 17:1540-1548(2006) [PubMed: 16421250] [Abstract] Cited for: IDENTIFICATION IN THE SCF(DIA2) COMPLEX, FUNCTION OF THE SCF(DIA2) COMPLEX.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U43564 Genomic DNA. Translation: AAB38821.1.
X96876 Genomic DNA. Translation: CAA65628.1.
Z74180 Genomic DNA. Translation: CAA98702.1.
BK006938 Genomic DNA. Translation: DAA11727.1.

PIR

S67675.

RefSeq

NP_010150.1. NM_001180191.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3O2P	X-ray	2.23	E	730-815	[»]
3O6B	X-ray	3.10	B/D/F/H/J	742-815	[»]

ProteinModelPortal

Q12018.

SMR

Q12018. Positions 11-815.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1234N.

IntAct

Q12018. 52 interactions.

MINT

MINT-384023.

STRING

Q12018.

Proteomic databases

PeptideAtlas

Q12018.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDL132W; YDL132W; YDL132W.

GeneID

851424.

KEGG

sce:YDL132W.

NMPDR

fig|4932.3.peg.887.

Organism-specific databases

CYGD

YDL132w.

SGD

S000002290. CDC53.

Phylogenomic databases

eggNOG

fuNOG04882.

GeneTree

EFGT00050000002854.

HOGENOM

HBG622322.

OMA

CVNKSRS.

OrthoDB

EOG4W3WW4.

Gene expression databases

ArrayExpress

Q12018.

Genevestigator

Q12018.

GermOnline

YDL132W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR016157. Cullin_CS.
IPR016158. Cullin_homology.
IPR001373. Cullin_N.
IPR019559. Cullin_neddylation_domain.
IPR016159. Cullin_repeat-like_dom.
IPR011991. WHTH_trsnscrt_rep_DNA-bd.
[Graphical view]

Gene3D

G3DSA:1.10.10.10. Wing_hlx_DNA_bd. 2 hits.

KO

K03347.

Pfam

PF00888. Cullin. 1 hit.
PF10557. Cullin_Nedd8. 1 hit.
[Graphical view]

SMART

SM00182. CULLIN. 1 hit.
SM00884. Cullin_Nedd8. 1 hit.
[Graphical view]

SUPFAM

SSF75632. Cullin_homology. 1 hit.
SSF74788. Cullin_repeat-like. 1 hit.

PROSITE

PS01256. CULLIN_1. 1 hit.
PS50069. CULLIN_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

968633.

Entry information

Entry name

CDC53_YEAST

Accession

Primary (citable) accession number: Q12018
Secondary accession number(s): D6VRL7

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	December 14, 2011
This is version 93 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program