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(-) Description

Title :  CRYSTAL STRUCTURE OF MOTIF N OF SACCHAROMYCES CEREVISIAE DBF4
 
Authors :  L. A. Matthews, D. R. Jones, A. A. Prasad, B. P. Duncker, A. Guarne
Date :  02 Sep 10  (Deposition) - 07 Sep 11  (Release) - 07 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Keywords :  Ddk, Brct, Rad53, Replication Checkpoint, Fha Domain, Regulatory Subunit Of Ddk, Cdc7, Phosphorylation, Nuclear, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. A. Matthews, D. R. Jones, A. A. Prasad, B. P. Duncker, A. Guarne
Crystal Structure Of Saccharomyces Cerevisiae Dbf4-Motif N
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DBF4
    ChainsA, B, C, D, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)STARPRAREPLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 120-250
    GeneD4205, DBF4, DNA52, YD9609.07C, YDR052C
    Organism CommonBREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymPROTEIN DNA52

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (1x)A    
Biological Unit 2 (1x) B   
Biological Unit 3 (1x)  C  
Biological Unit 4 (1x)   D 
Biological Unit 5 (1x)    E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3OQ4)

(-) Sites  (0, 0)

(no "Site" information available for 3OQ4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OQ4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OQ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OQ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OQ4)

(-) Exons   (0, 0)

(no "Exon" information available for 3OQ4)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:124
 aligned with DBF4_YEAST | P32325 from UniProtKB/Swiss-Prot  Length:704

    Alignment length:124
                                   128       138       148       158       168       178       188       198       208       218       228       238    
           DBF4_YEAST   119 IMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVDLDHLSKTKSASLAAPTLSNLLHNEK 242
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee........hhhhhhhhhhhhhhhhhhhhhh..eee........eeee..hhhhhhhh...hhhhhhhhh..eeeehhhhhhhhhhh..hhhhhh.........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oq4 A 119 HMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVDLDHLSKTKSASLAAPTLSNLLHNEK 242
                                   128       138       148       158       168       178       188       198       208       218       228       238    

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with DBF4_YEAST | P32325 from UniProtKB/Swiss-Prot  Length:704

    Alignment length:102
                                   131       141       151       161       171       181       191       201       211       221  
           DBF4_YEAST   122 RDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVDLDHLSK 223
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee.....ee.hhhhhhhhhhhhhhhhhhhhh...eee........eeee..hhhhhhhh...hhhhhhhhh..eeeehhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 3oq4 B 122 RDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVDLDHLSK 223
                                   131       141       151       161       171       181       191       201       211       221  

Chain C from PDB  Type:PROTEIN  Length:99
 aligned with DBF4_YEAST | P32325 from UniProtKB/Swiss-Prot  Length:704

    Alignment length:99
                                   132       142       152       162       172       182       192       202       212         
           DBF4_YEAST   123 DSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVDLDHL 221
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....ee.hhhhhhhhhhhhhhhhhhhhhhh.eee........eeee..hhhhhhhh...hhhhhhhhh..eeeehhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3oq4 C 123 DSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVDLDHL 221
                                   132       142       152       162       172       182       192       202       212         

Chain D from PDB  Type:PROTEIN  Length:99
 aligned with DBF4_YEAST | P32325 from UniProtKB/Swiss-Prot  Length:704

    Alignment length:99
                                   128       138       148       158       168       178       188       198       208         
           DBF4_YEAST   119 IMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVD 217
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.....ee.hhhhhhhhhhhhhhhhhhhhhh..eee........eeee..hhhhhhhh...hhhhhhhhh..eeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3oq4 D 119 HMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVD 217
                                   128       138       148       158       168       178       188       198       208         

Chain E from PDB  Type:PROTEIN  Length:96
 aligned with DBF4_YEAST | P32325 from UniProtKB/Swiss-Prot  Length:704

    Alignment length:96
                                   130       140       150       160       170       180       190       200       210      
           DBF4_YEAST   121 KRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDV 216
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.....ee.hhhhhhhhhhhhhhhhhhhhhh..ee.........eeee.....hhhhh...hhhhhhhhh..eeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 3oq4 E 121 KRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDV 216
                                   130       140       150       160       170       180       190       200       210      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3OQ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OQ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3OQ4)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (DBF4_YEAST | P32325)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003688    DNA replication origin binding    Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043539    protein serine/threonine kinase activator activity    Binds to and increases the activity of a protein serine/threonine kinase.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006270    DNA replication initiation    The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0051321    meiotic cell cycle    Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
    GO:0001100    negative regulation of exit from mitosis    Any process involved in the inhibition of progression from anaphase/telophase (high mitotic CDK activity) to G1 (low mitotic CDK activity).
    GO:0060903    positive regulation of meiosis I    Any process that increases the rate, frequency, or extent of meiosis I, a cell cycle process comprising the steps by which a cell progresses through the first phase of meiosis, in which cells divide and homologous chromosomes are paired and segregated from each other, producing two daughter cells.
    GO:0045860    positive regulation of protein kinase activity    Any process that activates or increases the frequency, rate or extent of protein kinase activity.
    GO:0071902    positive regulation of protein serine/threonine kinase activity    Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity.
    GO:0006279    premeiotic DNA replication    The replication of DNA that precedes meiotic cell division.
cellular component
    GO:0031431    Dbf4-dependent protein kinase complex    A heterodimeric protein complex required for the activation of DNA replication origins; comprises a catalytic subunit and a regulatory subunit (in Saccharomyces, Cdc7p and Dbf4p, respectively); complexes identified in other species generally contain proteins related to the Saccharomyces proteins.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DBF4_YEAST | P323253oq0 3qbz 5t2f 5t2s

(-) Related Entries Specified in the PDB File

3oq0 (6XHIS)DBF4-N