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Protein

DDK kinase regulatory subunit DBF4

Gene

DBF4

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

Functioni

Regulatory subunit of the CDC7-DBF4 kinase, also called DBF4-dependent kinase (DDK), which is involved in cell cycle regulation of premitotic and premeiotic chromosome replication and in chromosome segregation. DDK plays an essential role in initiating DNA replication at replication origins by phosphorylating the MCM2 and MCM4 subunits of the MCM2-7 helicase complex. DBF4 recruits the catalytic subunit CDC7 to MCM2 and to origins of replication. DDK has also postreplicative functions in meiosis. DDK phosphorylates the meiosis-specific double-strand break protein MER2 for initiation of meiotic recombination. Interacts with CDC5 during meiosis to promote double-strand breaks and monopolar spindle orientation. Inhibits CDC5 activity during mitosis through direct binding to its PBD.12 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri654 – 703DBF4-typePROSITE-ProRule annotationAdd BLAST50

GO - Molecular functioni

  • DNA replication origin binding Source: SGD
  • protein serine/threonine kinase activator activity Source: SGD
  • zinc ion binding Source: InterPro

GO - Biological processi

  • cell division Source: UniProtKB-KW
  • chromosome segregation Source: UniProtKB-KW
  • DNA replication initiation Source: SGD
  • mitotic DNA replication checkpoint Source: SGD
  • negative regulation of exit from mitosis Source: SGD
  • positive regulation of DNA replication initiation Source: SGD
  • positive regulation of meiosis I Source: SGD
  • positive regulation of protein kinase activity Source: SGD
  • positive regulation of protein serine/threonine kinase activity Source: SGD
  • premeiotic DNA replication Source: SGD

Keywordsi

Molecular functionDNA-binding
Biological processCell cycle, Cell division, Chromosome partition, DNA replication, Meiosis, Mitosis
LigandMetal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-29662-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
DDK kinase regulatory subunit DBF4
Alternative name(s):
Dumbbell forming protein 4
Gene namesi
Name:DBF4
Synonyms:DNA52
Ordered Locus Names:YDR052C
ORF Names:D4205, YD9609.07C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDR052C
SGDiS000002459 DBF4

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi83R → A or E: Defective for interaction with CDC5. 1 Publication1
Mutagenesisi84S → A: No effect. 1 Publication1
Mutagenesisi85I → A: Defective for interaction with CDC5. 1 Publication1
Mutagenesisi86E → K: No effect. 1 Publication1
Mutagenesisi87G → A: Defective for interaction with CDC5. 1 Publication1
Mutagenesisi88A → V: Defective for interaction with CDC5. 1 Publication1
Mutagenesisi661C → A in DBF4-AAHH; weakens interaction with ARS1 origin DNA and MCM2, but not other known ligands; when associated with A-664. 1 Publication1
Mutagenesisi664C → A in DBF4-AAHH; weakens interaction with ARS1 origin DNA and MCM2, but not other known ligands; when associated with A-661. 1 Publication1
Mutagenesisi674H → A in DBF4-CCAA; weakens interaction with ARS1 origin DNA and MCM2, but not other known ligands; when associated with A-680. 1 Publication1
Mutagenesisi680H → A: Weakens interaction with ARS1 origin DNA and MCM2, but not other known ligands. In DBF4-CCAA; weakens interaction with ARS1 origin DNA and MCM2, but not other known ligands; when associated with A-674. 1 Publication1
Mutagenesisi680H → C: Weakens interaction with ARS1 origin DNA and MCM2, but not other known ligands. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000797911 – 704DDK kinase regulatory subunit DBF4Add BLAST704

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei59PhosphoserineCombined sources1
Modified residuei84PhosphoserineCombined sources1
Modified residuei235PhosphoserineCombined sources1
Modified residuei623PhosphoserineCombined sources1

Post-translational modificationi

Phosphorylated by CDC7 and by CDC5.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP32325
PaxDbiP32325
PRIDEiP32325

PTM databases

iPTMnetiP32325

Expressioni

Inductioni

Cell cycle-regulated. Protein levels increase as cells begin S phase and remain high through late mitosis.2 Publications

Interactioni

Subunit structurei

Heterodimer with CDC7 to form the DBF4-dependent kinase (DDK) complex. Interacts (via PBD-binding motif) with CDC5 (via POLO box domains). Interacts (via N-terminus) with ORC2, ORC3 and RAD53. Binds to ARS1 origin DNA.6 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi32106783 interactors.
DIPiDIP-2290N
IntActiP32325 13 interactors.
MINTiP32325
STRINGi4932.YDR052C

Structurei

Secondary structure

1704
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi106 – 122Combined sources17
Beta strandi125 – 128Combined sources4
Helixi138 – 157Combined sources20
Beta strandi161 – 165Combined sources5
Beta strandi172 – 177Combined sources6
Helixi179 – 184Combined sources6
Helixi190 – 196Combined sources7
Beta strandi200 – 203Combined sources4
Helixi204 – 213Combined sources10
Helixi218 – 221Combined sources4
Helixi233 – 241Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3OQ0X-ray2.70A/B/C/D/E/F/G/H/I/J120-250[»]
3OQ4X-ray2.40A/B/C/D/E120-250[»]
3QBZX-ray2.69A66-221[»]
5T2FX-ray2.66A/B/C/D105-220[»]
5T2SX-ray2.40A/C105-220[»]
ProteinModelPortaliP32325
SMRiP32325
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP32325

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni10 – 19D box 110
Regioni62 – 70D box 29

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi83 – 88POLO box domain (PBD)-binding6

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri654 – 703DBF4-typePROSITE-ProRule annotationAdd BLAST50

Keywords - Domaini

Zinc-finger

Phylogenomic databases

HOGENOMiHOG000112168
InParanoidiP32325
KOiK02309
OMAiYCENCQD
OrthoDBiEOG092C4W9O

Family and domain databases

Gene3Di3.30.160.6801 hit
3.40.50.101901 hit
InterProiView protein in InterPro
IPR036420 BRCT_dom_sf
IPR013939 Regulatory_Dfp1/Him1
IPR006572 Znf_DBF
IPR038545 Znf_DBF_sf
PfamiView protein in Pfam
PF08630 Dfp1_Him1_M, 1 hit
PF07535 zf-DBF, 1 hit
SMARTiView protein in SMART
SM00586 ZnF_DBF, 1 hit
PROSITEiView protein in PROSITE
PS51265 ZF_DBF4, 1 hit

Sequencei

Sequence statusi: Complete.

P32325-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVSPTKMIIR SPLKETDTNL KHNNGIAAST TAAGHLNVFS NDNNCNNNNT
60 70 80 90 100
TESFPKKRSL ERLELQQQQH LHEKKRARIE RARSIEGAVQ VSKGTGLKNV
110 120 130 140 150
EPRVTPKELL EWQTNWKKIM KRDSRIYFDI TDDVEMNTYN KSKMDKRRDL
160 170 180 190 200
LKRGFLTLGA QITQFFDTTV TIVITRRSVE NIYLLKDTDI LSRAKKNYMK
210 220 230 240 250
VWSYEKAARF LKNLDVDLDH LSKTKSASLA APTLSNLLHN EKLYGPTDRD
260 270 280 290 300
PRTKRDDIHY FKYPHVYLYD LWQTWAPIIT LEWKPQELTN LDELPYPILK
310 320 330 340 350
IGSFGRCPFI GDRNYDESSY KRVVKRYSRD KANKKYALQL RALFQYHADT
360 370 380 390 400
LLNTSSVNDQ TKNLIFIPHT CNDSTKSFKK WMQEKAKNFE KTELKKTDDS
410 420 430 440 450
AVQDVRNEHA DQTDEKNSIL LNETETKEPP LKEEKENKQS IAEESNKYPQ
460 470 480 490 500
RKELAATPKL NHPVLATFAR QETEEVPDDL CTLKTKSRQA FEIKASGAHQ
510 520 530 540 550
SNDVATSFGN GLGPTRASVM SKNMKSLSRL MVDRKLGVKQ TNGNNKNYTA
560 570 580 590 600
TIATTAETSK ENRHRLDFNA LKKDEAPSKE TGKDSAVHLE TNRKPQNFPK
610 620 630 640 650
VATKSVSADS KVHNDIKITT TESPTASKKS TSTNVTLHFN AQTAQTAQPV
660 670 680 690 700
KKETVKNSGY CENCRVKYES LEQHIVSEKH LSFAENDLNF EAIDSLIENL

RFQI
Length:704
Mass (Da):80,690
Last modified:February 1, 1996 - v2
Checksum:iBDB93E72EF2ABC0B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti159 – 160GA → NT in CAA42819 (PubMed:1592236).Curated2
Sequence conflicti177R → RR in CAA42819 (PubMed:1592236).Curated1
Sequence conflicti197N → K in CAA42819 (PubMed:1592236).Curated1
Sequence conflicti256D → G in CAA42819 (PubMed:1592236).Curated1
Sequence conflicti416 – 425Missing in CAA42819 (PubMed:1592236).Curated10
Sequence conflicti439Q → R in CAA42819 (PubMed:1592236).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X60279 Genomic DNA Translation: CAA42819.1
M83539 Genomic DNA Translation: AAA34573.1
X84162 Genomic DNA Translation: CAA58969.1
Z49209 Genomic DNA Translation: CAA89082.1
Z74348 Genomic DNA Translation: CAA98869.1
BK006938 Genomic DNA Translation: DAA11899.1
PIRiS25371
RefSeqiNP_010337.3, NM_001180360.3

Genome annotation databases

EnsemblFungiiYDR052C; YDR052C; YDR052C
GeneIDi851623
KEGGisce:YDR052C

Similar proteinsi

Entry informationi

Entry nameiDBF4_YEAST
AccessioniPrimary (citable) accession number: P32325
Secondary accession number(s): D6VS39, P32355
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: February 1, 1996
Last modified: March 28, 2018
This is version 155 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome