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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: Annotation score: 5 out of 5-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 nuclear division Source: UniProtKB-KW
  • negative regulation of exit from mitosis Source: SGD
  • positive regulation of meiosis I Source: SGD
  • positive regulation of protein kinase activity Source: SGD
  • premeiotic DNA replication Source: SGD
Complete GO annotation...

Keywords - Biological processi

Cell cycle, Cell division, Chromosome partition, DNA replication, Meiosis, Mitosis

Keywords - Ligandi

DNA-binding, Metal-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

GO - Cellular componenti

  • chromosome, centromeric region Source: SGD
  • Dbf4-dependent protein kinase complex Source: SGD
  • nucleus Source: GOC
Complete GO annotation...

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.
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

WithEntry#Exp.IntActNotes
CDC7P062438EBI-5575,EBI-4451

Protein-protein interaction databases

BioGridi32106. 130 interactors.
DIPiDIP-2290N.
IntActiP32325. 4 interactors.
MINTiMINT-364128.

Structurei

Secondary structure

1704
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi106 – 123Combined sources18
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[»]
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

Sequence similaritiesi

Contains 1 DBF4-type zinc finger.PROSITE-ProRule annotation

Zinc finger

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

Keywords - Domaini

Zinc-finger

Phylogenomic databases

HOGENOMiHOG000112168.
InParanoidiP32325.
KOiK02309.
OMAiNSGYCEN.
OrthoDBiEOG092C4W9O.

Family and domain databases

InterProiIPR013939. Regulatory_Dfp1/Him1.
IPR006572. Znf_DBF.
[Graphical view]
PfamiPF08630. Dfp1_Him1_M. 1 hit.
PF07535. zf-DBF. 1 hit.
[Graphical view]
SMARTiSM00586. ZnF_DBF. 1 hit.
[Graphical view]
PROSITEiPS51265. ZF_DBF4. 1 hit.
[Graphical view]

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.

Cross-referencesi

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.

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[»]
5T2SX-ray2.40A/C105-220[»]
ProteinModelPortaliP32325.
SMRiP32325.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32106. 130 interactors.
DIPiDIP-2290N.
IntActiP32325. 4 interactors.
MINTiMINT-364128.

PTM databases

iPTMnetiP32325.

Proteomic databases

MaxQBiP32325.
PRIDEiP32325.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDR052C; YDR052C; YDR052C.
GeneIDi851623.
KEGGisce:YDR052C.

Organism-specific databases

EuPathDBiFungiDB:YDR052C.
SGDiS000002459. DBF4.

Phylogenomic databases

HOGENOMiHOG000112168.
InParanoidiP32325.
KOiK02309.
OMAiNSGYCEN.
OrthoDBiEOG092C4W9O.

Enzyme and pathway databases

BioCyciYEAST:G3O-29662-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP32325.
PROiP32325.

Family and domain databases

InterProiIPR013939. Regulatory_Dfp1/Him1.
IPR006572. Znf_DBF.
[Graphical view]
PfamiPF08630. Dfp1_Him1_M. 1 hit.
PF07535. zf-DBF. 1 hit.
[Graphical view]
SMARTiSM00586. ZnF_DBF. 1 hit.
[Graphical view]
PROSITEiPS51265. ZF_DBF4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDBF4_YEAST
AccessioniPrimary (citable) accession number: P32325
Secondary accession number(s): D6VS39, P32355
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: February 1, 1996
Last modified: November 30, 2016
This is version 141 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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.