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(-) Description

Title :  S74E-DCK MUTANT IN COMPLEX WITH UDP
 
Authors :  S. Hazra, A. Lavie
Date :  20 Jan 11  (Deposition) - 16 Mar 11  (Release) - 08 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta, Phosphoryl Transfer, Atp Binding, Phosphorylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Hazra, A. Szewczak, S. Ort, M. Konrad, A. Lavie
Post-Translational Phosphorylation Of Serine 74 Of Human Deoxycytidine Kinase Favors The Enzyme Adopting The Open Conformation Making It Competent For Nucleoside Binding And Release.
Biochemistry V. 50 2870 2011
PubMed-ID: 21351740  |  Reference-DOI: 10.1021/BI2001032

(-) Compounds

Molecule 1 - DEOXYCYTIDINE KINASE
    ChainsA, B
    EC Number2.7.1.74
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneDCK
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDCK

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:31 , ALA A:32 , GLY A:33 , LYS A:34 , SER A:35 , THR A:36 , ARG A:188 , ARG A:192 , ASP A:241 , PHE A:242 , LYS A:243 , HOH A:296BINDING SITE FOR RESIDUE UDP A 401
2AC2SOFTWAREASN B:29 , ALA B:31 , ALA B:32 , GLY B:33 , LYS B:34 , SER B:35 , THR B:36 , ARG B:188 , ARG B:192 , ASP B:241 , PHE B:242 , LYS B:243 , HOH B:281 , HOH B:286 , HOH B:295BINDING SITE FOR RESIDUE UDP B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (7, 14)

Asymmetric/Biological Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3aENST000002866483aENSE00002041408chr4:71859156-71859643488DCK_HUMAN1-31312A:19-31
B:19-31
13
13
1.4ENST000002866484ENSE00001024728chr4:71863784-71863899116DCK_HUMAN31-69392A:31-61
B:31-62
31
32
1.5ENST000002866485ENSE00001024734chr4:71888084-71888277194DCK_HUMAN70-134652A:70-134
B:71-134
65
64
1.6ENST000002866486ENSE00001024731chr4:71889276-71889423148DCK_HUMAN134-183502A:134-183
B:134-183
50
50
1.7aENST000002866487aENSE00001024724chr4:71891533-71891648116DCK_HUMAN184-222392A:184-222
B:184-222
39
39
1.8aENST000002866488aENSE00001076634chr4:71892382-7189247291DCK_HUMAN222-252312A:222-252
B:222-252
31
31
1.10ENST0000028664810ENSE00001235483chr4:71895069-718966311563DCK_HUMAN253-26082A:253-260
B:253-260
8
8

(-) 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:234
 aligned with DCK_HUMAN | P27707 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:242
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  
            DCK_HUMAN    19 TRIKKISIEGNIAAGKSTFVNILKQLCEDWEVVPEPVARWCNVQSTQDEFEELTMSQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESECMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
               SCOP domains d3qeja_ A: Deoxycytidine kinase                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhh..eeee.hhhhhhhh.--------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhh..eeeee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a    --------------------------------------Exon 1.5  PDB: A:70-134 UniProt: 70-134                          -------------------------------------------------Exon 1.7a  PDB: A:184-222              ------------------------------1.10     Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.4  PDB: A:31-61 UniProt: 31-69  ----------------------------------------------------------------Exon 1.6  PDB: A:134-183 UniProt: 134-183         --------------------------------------Exon 1.8a  PDB: A:222-252      -------- Transcript 1 (2)
                 3qej A  19 TRIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNV--------ELTMEQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
                                    28        38        48        58  |      - |      78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  
                                                                     61       70                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:234
 aligned with DCK_HUMAN | P27707 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:242
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  
            DCK_HUMAN    19 TRIKKISIEGNIAAGKSTFVNILKQLCEDWEVVPEPVARWCNVQSTQDEFEELTMSQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESECMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
               SCOP domains d3qejb_ B: Deoxycytidine kinase                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------dNK-3qejB01 B:96-253                                                                                                                                          ------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------dNK-3qejB02 B:96-253                                                                                                                                          ------- Pfam domains (2)
         Sec.struct. author ...eeeeee.....hhhhhhhhhhh....eeee.hhhhhhh...--------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhh..eeeee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a    --------------------------------------Exon 1.5  PDB: B:71-134 UniProt: 70-134 [INCOMPLETE]             -------------------------------------------------Exon 1.7a  PDB: B:184-222              ------------------------------1.10     Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.4  PDB: B:31-62 UniProt: 31-69  ----------------------------------------------------------------Exon 1.6  PDB: B:134-183 UniProt: 134-183         --------------------------------------Exon 1.8a  PDB: B:222-252      -------- Transcript 1 (2)
                 3qej B  19 TRIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNVQ--------LTMEQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
                                    28        38        48        58   |     -  |     78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  
                                                                      62       71                                                                                                                                                                                             

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Family: dNK (33)
1adNK-3qejB01B:96-253
1bdNK-3qejB02B:96-253

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,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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  2.7.1.74
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 Related Entries

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

UniProtKB/Swiss-Prot
        DCK_HUMAN | P277071p5z 1p60 1p61 1p62 2a2z 2a30 2a7q 2no0 2no1 2no6 2no7 2no9 2noa 2qrn 2qro 2zi3 2zi4 2zi5 2zi6 2zi7 2zi9 2zia 3hp1 3ipx 3ipy 3kfx 3mjr 3qen 3qeo 4jlj 4jlk 4jlm 4jln 4kcg 4l5b 4q18 4q19 4q1a 4q1b 4q1c 4q1d 4q1e 4q1f

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3QEJ)