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(-) Description

Title :  THYMIDINE KINASE FROM B. ANTHRACIS IN COMPLEX WITH DT.
 
Authors :  U. Kosinska, C. Carnrot, M. P. B. Sandrini, A. R. Clausen, L. Wang, J. Pis S. Eriksson, H. Eklund
Date :  15 Nov 06  (Deposition) - 23 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Tk1, Dnk, Lasso, Kinase, Transferase, Atp-Binding, Deoxyribonucleoside Kinase, Dna Synthesis, Phosphate Acceptor, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Kosinska, C. Carnrot, M. P. B. Sandrini, A. R. Clausen, L. Wang, J. Piskur, S. Eriksson, H. Eklund
Structural Studies Of Thymidine Kinases From Bacillus Anthracis And Bacillus Cereus Provide Insights Into Quaternary Structure And Conformational Changes Upon Substrate Binding
Febs J. V. 274 727 2007
PubMed-ID: 17288553  |  Reference-DOI: 10.1111/J.1742-4658.2006.05617.X

(-) Compounds

Molecule 1 - THYMIDINE KINASE
    Chains: A
    EC Number: 2.7.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: PET-14B
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 260799
    Strain: STERNE
    Variant: 34F2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2THM1Ligand/IonTHYMIDINE
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
2THM4Ligand/IonTHYMIDINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:145 , CYS A:148 , CYS A:183 , CYS A:186BINDING SITE FOR RESIDUE ZN A1194
2AC2SOFTWARESER A:16 , PHE A:18 , SER A:19 , GLY A:20 , LYS A:21 , SER A:22 , HOH A:2001 , HOH A:2019BINDING SITE FOR RESIDUE PO4 A1196
3AC3SOFTWAREGLU A:89 , PHE A:92 , LEU A:116 , ASP A:119 , PHE A:120 , PHE A:125 , THR A:155 , ILE A:170 , ILE A:171 , LEU A:172 , VAL A:173 , GLY A:174 , TYR A:179BINDING SITE FOR RESIDUE THM A1195

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J9R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J9R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J9R)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TK_CELLULAR_TYPEPS00603 Thymidine kinase cellular-type signature.KITH_BACAN174-187  1A:174-187
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TK_CELLULAR_TYPEPS00603 Thymidine kinase cellular-type signature.KITH_BACAN174-187  4A:174-187

(-) Exons   (0, 0)

(no "Exon" information available for 2J9R)

(-) 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:178
 aligned with KITH_BACAN | Q81JX0 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:195
                              1                                                                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188     
           KITH_BACAN     - --MYLINQNGWIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSASKDIFKHITEEMDVIAIDEVQFFDGDIVEVVQVLANRGYRVIVAGLDQDFRGLPFGQVPQLMAIAEHVTKLQAVCSACGSPASRTQRLIDGEPAAFDDPIILVGASESYEPRCRHCHAVPTKQ 193
               SCOP domains d2j9ra1 A:-1-142 automated matches                                                                                                              d2j9ra2 A:143-193 automated matches                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee.....hhhhhhhhhhhhhhhh...eeeee..-----------------..eee..hhhhhhhhh.....eeee.hhhhh..hhhhhhhhhhhh..eeeeee...........hhhhhhhhh.eeee..eee...eeee.eeeeee..ee...............eeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j9r A  -1 SHMYLINQNGWIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPC-----------------VKAVPVSASKDIFKHITEEMDVIAIDEVQFFDGDIVEVVQVLANRGYRVIVAGLDQDFRGLPFGQVPQLMAIAEHVTKLQAVCSACGSPASRTQRLIDGEPAAFDDPIILVGASESYEPRCRHCHAVPTKQ 193
                                     8        18        28        38      |  -         -    |   68        78        88        98       108       118       128       138       148       158       168       178       188     
                                                                         45                63
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J9R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J9R)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (KITH_BACAN | Q81JX0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    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: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.

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  2j9r
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  2.7.1.21
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