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(-) Description

Title :  STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK INHIBITOR BINDING TO DROSOPHILA MELANOGASTER MULTISUBSTRATE DEOXYRIBONUCLEOSIDE KINASE
 
Authors :  N. E. Mikkelsen, B. Munch-Petersen, H. Eklund
Date :  26 Feb 08  (Deposition) - 29 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Atp-Binding, Dna Synthesis, Phosphoprotein, Feedback Inhibition, Deoxyribonucleoside Kinase, Salvage Pathway, Nucleotide-Binding, Dttp, Kinase, Complex, Drosophila, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. E. Mikkelsen, B. Munch-Petersen, H. Eklund
Structural Studies Of Nucleoside Analog And Feedback Inhibitor Binding To Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase.
Febs J. V. 275 2151 2008
PubMed-ID: 18384378  |  Reference-DOI: 10.1111/J.1742-4658.2008.06369.X

(-) Compounds

Molecule 1 - DEOXYNUCLEOSIDE KINASE
    Chains: A, B, C, D
    EC Number: 2.7.1.145
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-2T
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: RESIDUES 1-230
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: DEOXYRIBONUCLEOSIDE KINASE, DM-DNK, MULTISPECIFIC DEOXYNUCLEOSIDE KINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1DCP4Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE D:29 , GLY D:30 , SER D:31 , GLY D:32 , LYS D:33 , THR D:34 , TRP D:57 , LEU D:66 , MET D:69 , TYR D:70 , PHE D:80 , GLN D:81 , VAL D:84 , GLU D:104 , ARG D:105 , ALA D:110 , PHE D:114 , MET D:118 , ARG D:167 , ARG D:169 , GLU D:172 , HOH D:2085 , HOH D:2103 , HOH D:2104 , HOH D:2105BINDING SITE FOR RESIDUE DCP D1211
2AC2SOFTWAREILE C:29 , GLY C:30 , SER C:31 , GLY C:32 , LYS C:33 , THR C:34 , TRP C:57 , LEU C:66 , MET C:69 , TYR C:70 , PHE C:80 , GLN C:81 , VAL C:84 , GLU C:104 , ARG C:105 , ALA C:110 , PHE C:114 , MET C:118 , ARG C:167 , ARG C:169 , GLU C:172 , HOH C:2089 , HOH C:2104 , HOH C:2105 , HOH C:2106BINDING SITE FOR RESIDUE DCP C1209
3AC3SOFTWAREILE B:29 , GLY B:30 , SER B:31 , GLY B:32 , LYS B:33 , THR B:34 , VAL B:54 , TRP B:57 , TYR B:70 , PHE B:80 , GLN B:81 , VAL B:84 , GLU B:104 , ARG B:105 , ALA B:110 , PHE B:114 , ARG B:167 , ARG B:169 , GLU B:172 , HOH B:2099 , HOH B:2119 , HOH B:2120 , HOH B:2121BINDING SITE FOR RESIDUE DCP B1210
4AC4SOFTWAREILE A:29 , GLY A:30 , SER A:31 , GLY A:32 , LYS A:33 , THR A:34 , TRP A:57 , LEU A:66 , MET A:69 , TYR A:70 , PHE A:80 , GLN A:81 , VAL A:84 , GLU A:104 , ARG A:105 , ALA A:110 , PHE A:114 , ARG A:167 , ARG A:169 , GLU A:172 , HOH A:2105 , HOH A:2125 , HOH A:2126 , HOH A:2127BINDING SITE FOR RESIDUE DCP A1210

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VP4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln C:198 -Ser C:199

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VP4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VP4)

(-) Exons   (0, 0)

(no "Exon" information available for 2VP4)

(-) Sequences/Alignments

Asymmetric/Biological 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:198
 aligned with DNK_DROME | Q9XZT6 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:198
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        
            DNK_DROME    12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDADL 209
               SCOP domains d2vp4a_ A: Deoxyribonucleoside kinase                                                                                                                                                                  SCOP domains
               CATH domains 2vp4A00 A:12-209 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeee.....hhhhhhhhhhhhh..eeee..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vp4 A  12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDADL 209
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        


Chain B from PDB  Type:PROTEIN  Length:198
 aligned with DNK_DROME | Q9XZT6 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:198
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        
            DNK_DROME    12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDADL 209
               SCOP domains d2vp4b_ B: Deoxyribonucleoside kinase                                                                                                                                                                  SCOP domains
               CATH domains 2vp4B00 B:12-209 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeee.....hhhhhhhhhhhhh..eeee..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vp4 B  12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDADL 209
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        


Chain C from PDB  Type:PROTEIN  Length:197
 aligned with DNK_DROME | Q9XZT6 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:197
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       
            DNK_DROME    12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDAD 208
               SCOP domains d2vp4c_ C: Deoxyribonucleoside kinase                                                                                                                                                                 SCOP domains
               CATH domains 2vp4C00 C:12-208 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee.....hhhhhhhhhhhhh..eeee..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vp4 C  12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDAD 208
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       


Chain D from PDB  Type:PROTEIN  Length:199
 aligned with DNK_DROME | Q9XZT6 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:199
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201         
            DNK_DROME    12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDADLN 210
               SCOP domains d2vp4d_ D: Deoxyribonucleoside kinase                                                                                                                                                                   SCOP domains
               CATH domains 2vp4D00 D:12-210 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                   CATH domains
           Pfam domains (1) --------------------------------------------------------------------dNK-2vp4D01 D:80-210                                                                                                                Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------dNK-2vp4D02 D:80-210                                                                                                                Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------dNK-2vp4D03 D:80-210                                                                                                                Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------dNK-2vp4D04 D:80-210                                                                                                                Pfam domains (4)
         Sec.struct. author .........eeeeee.....hhhhhhhhhhhhh..eeee..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vp4 D  12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDADLN 210
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: dNK (33)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (DNK_DROME | Q9XZT6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019136    deoxynucleoside kinase activity    Catalysis of the reaction: ATP + 2'-deoxynucleoside = ADP + 2'-deoxynucleoside 5'-phosphate.
    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:0004797    thymidine kinase activity    Catalysis of the reaction: ATP + thymidine = ADP + thymidine 5'-phosphate.
    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:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006230    TMP biosynthetic process    The chemical reactions and pathways resulting in the formation of TMP, ribosylthymine monophosphate.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0006165    nucleoside diphosphate phosphorylation    The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
    GO:0046939    nucleotide phosphorylation    The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DNK_DROME | Q9XZT6: 1j90 1oe0 1ot3 1zm7 1zmx 2jcs 2jj8 2vp0 2vp2 2vp5 2vp6 2vp9 2vpp 2vqs

(-) Related Entries Specified in the PDB File

1j90 CRYSTAL STRUCTURE OF DROSOPHILA DEOXYRIBONUCLEOSIDE KINASE
1oe0 CRYSTAL STRUCTURE OF DROSOPHILA DEOXYRIBONUCLEOSIDE KINASE IN COMPLEX WITH DTTP
1ot3 CRYSTAL STRUCTURE OF DROSOPHILA DEOXYRIBONUCLEOTIDE KINASECOMPLEXED WITH THE SUBSTRATE DEOXYTHYMIDINE
1zm7 CRYSTAL STRUCTURE OF D. MELANOGASTER DEOXYRIBONUCLEOSIDEKINASE MUTANT N64D IN COMPLEX WITH DTTP
1zmx CRYSTAL STRUCTURE OF D. MELANOGASTER DEOXYRIBONUCLEOSIDEKINASE N64D MUTANT IN COMPLEX WITH THYMIDINE
2jcs ACTIVE SITE MUTANT OF DNK FROM D. MELANOGASTER WITH DTTP BOUND
2vp0 STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK INHIBITOR BINDING TO DROSOPHILA MELANOGASTER MULTISUBSTRATE DEOXYRIBONUCLEOSIDE KINASE
2vp2 STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK INHIBITOR BINDING TO DROSOPHILA MELANOGASTER MULTISUBSTRATE DEOXYRIBONUCLEOSIDE KINASE