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(-) Description

Title :  STRUCTURE OF HUMAN DCK COMPLEXED WITH 2'-DEOXYCYTIDINE AND ADP, P 43 21 2 SPACE GROUP
 
Authors :  E. Sabini, S. Ort, C. Monnerjahn, M. Konrad, A. Lavie
Date :  28 Apr 03  (Deposition) - 01 Jul 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym. Unit :  B
Biol. Unit 1:  B  (2x)
Keywords :  Nucleoside Kinase, P-Loop, Deoxycytidine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Sabini, S. Ort, C. Monnerjahn, M. Konrad, A. Lavie
Structure Of Human Dck Suggests Strategies To Improve Anticancer And Antiviral Therapy
Nat. Struct. Biol. V. 10 513 2003
PubMed-ID: 12808445  |  Reference-DOI: 10.1038/NSB942

(-) Compounds

Molecule 1 - DEOXYCYTIDINE KINASE
    ChainsB
    EC Number2.7.1.74
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET14B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneDCK
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDCK

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit B
Biological Unit 1 (2x)B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2DCZ1Ligand/Ion2'-DEOXYCYTIDINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2DCZ2Ligand/Ion2'-DEOXYCYTIDINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:31 , ALA B:32 , GLY B:33 , LYS B:34 , SER B:35 , THR B:36 , ARG B:188 , ARG B:192 , TYR B:210 , GLU B:213 , HIS B:218 , VAL B:238 , GLU B:240 , ASP B:241 , PHE B:242 , HOH B:310 , HOH B:311 , HOH B:325 , HOH B:326 , HOH B:341 , HOH B:346BINDING SITE FOR RESIDUE ADP B 301
2AC2SOFTWAREILE B:30 , GLU B:53 , VAL B:55 , TRP B:58 , LEU B:82 , MET B:85 , TYR B:86 , PHE B:96 , GLN B:97 , ARG B:128 , ASP B:133 , PHE B:137 , GLU B:197 , HOH B:303 , HOH B:323BINDING SITE FOR RESIDUE DCZ B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P61)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P61)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P61)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P61)

(-) Exons   (7, 7)

Asymmetric Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3aENST000002866483aENSE00002041408chr4:71859156-71859643488DCK_HUMAN1-31311B:20-3112
1.4ENST000002866484ENSE00001024728chr4:71863784-71863899116DCK_HUMAN31-69391B:31-6434
1.5ENST000002866485ENSE00001024734chr4:71888084-71888277194DCK_HUMAN70-134651B:77-13458
1.6ENST000002866486ENSE00001024731chr4:71889276-71889423148DCK_HUMAN134-183501B:134-18350
1.7aENST000002866487aENSE00001024724chr4:71891533-71891648116DCK_HUMAN184-222391B:184-22239
1.8aENST000002866488aENSE00001076634chr4:71892382-7189247291DCK_HUMAN222-252311B:222-25231
1.10ENST0000028664810ENSE00001235483chr4:71895069-718966311563DCK_HUMAN253-26081B:253-2608

(-) 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 B from PDB  Type:PROTEIN  Length:229
 aligned with DCK_HUMAN | P27707 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:241
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259 
            DCK_HUMAN    20 RIKKISIEGNIAAGKSTFVNILKQLCEDWEVVPEPVARWCNVQSTQDEFEELTMSQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESECMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
               SCOP domains d1p61b_ B: Deoxycytidine kinase                                                                                                                                                                                                                   SCOP domains
               CATH domains 1p61B00 B:20-260 P-loop containing nucleotide             triphosphate hydrolases                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------dNK-1p61B01 B:96-253                                                                                                                                          ------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhh..eeee..hhhhhhh....------------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhh..eeeee...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a   --------------------------------------Exon 1.5  PDB: B:77-134 UniProt: 70-134 [INCOMPLETE]             -------------------------------------------------Exon 1.7a  PDB: B:184-222              ------------------------------1.10     Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.4  PDB: B:31-64 UniProt: 31-69  ----------------------------------------------------------------Exon 1.6  PDB: B:134-183 UniProt: 134-183         --------------------------------------Exon 1.8a  PDB: B:222-252      -------- Transcript 1 (2)
                 1p61 B  20 RIKKISIEGNIAAGKSTFVNILKQLCEDWEVVPEPVARWCNVQST------------NGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESECMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
                                    29        39        49        59    |    -       |79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259 
                                                                       64           77                                                                                                                                                                                       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain B   (DCK_HUMAN | P27707)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004137    deoxycytidine kinase activity    Catalysis of the reaction: NTP + deoxycytidine = NDP + CMP.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0019206    nucleoside kinase activity    Catalysis of the reaction: ATP + nucleoside = ADP + nucleoside monophosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009157    deoxyribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0043101    purine-containing compound salvage    Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis.
    GO:0043097    pyrimidine nucleoside salvage    Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
    GO:0006220    pyrimidine nucleotide metabolic process    The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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
        DCK_HUMAN | P277071p5z 1p60 1p62 2a2z 2a30 2a7q 2no0 2no1 2no6 2no7 2no9 2noa 2qrn 2qro 2zi3 2zi4 2zi5 2zi6 2zi7 2zi9 2zia 3hp1 3ipx 3ipy 3kfx 3mjr 3qej 3qen 3qeo 4jlj 4jlk 4jlm 4jln 4kcg 4l5b 4q18 4q19 4q1a 4q1b 4q1c 4q1d 4q1e 4q1f

(-) Related Entries Specified in the PDB File

1p5z COMPLEXED WITH CYTARABINE
1p60 COMPLEXED WITH 2'-DEOXYCYTIDINE AND ADP
1p62 COMPLEXED WITH GEMCITABINE