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(-) Description

Title :  CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH PENCICLOVIR
 
Authors :  J. N. Champness, M. S. Bennett, F. Wien, R. Visse, R. L. Jarvest, W. C. Summers, M. R. Sanderson
Date :  15 May 98  (Deposition) - 18 May 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphotransferase, Thymidine Kinase, Viridae, Ds-Dna Enveloped Viruses, Herpesviridae, Alphaherpesvirinae, Antiviral Drug Penciclovir (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. N. Champness, M. S. Bennett, F. Wien, R. Visse, W. C. Summers, P. Herdewijn, E. De Clerq, T. Ostrowski, R. L. Jarvest, M. R. Sanderson
Exploring The Active Site Of Herpes Simplex Virus Type-1 Thymidine Kinase By X-Ray Crystallography Of Complexes With Aciclovir And Other Ligands.
Proteins V. 32 350 1998 (for further references see the PDB file header)

(-) Compounds

Molecule 1 - THYMIDINE KINASE
    Chains: A, B
    EC Number: 2.7.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: TK
    Expression System Plasmid: PT7:HSVTK
    Expression System Strain: SY211
    Expression System Taxid: 562
    Gene: TK
    Organism Scientific: HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17)
    Organism Taxid: 10299
    Strain: 17
    Synonym: TK

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1PE22Ligand/Ion9-(4-HYDROXY-3-(HYDROXYMETHYL)BUT-1-YL)GUANINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:58 , GLY A:59 , MET A:60 , GLY A:61 , LYS A:62 , THR A:63 , GLN A:221 , ARG A:222BINDING SITE FOR RESIDUE SO4 A 3
2AC2SOFTWAREGLY B:59 , MET B:60 , GLY B:61 , LYS B:62 , THR B:63 , GLN B:221 , HOH B:510BINDING SITE FOR RESIDUE SO4 B 4
3AC3SOFTWAREHIS A:58 , GLU A:83 , ILE A:97 , ILE A:100 , TYR A:101 , GLN A:125 , MET A:128 , ARG A:163 , TYR A:172 , ARG A:176 , ARG A:222 , GLU A:225BINDING SITE FOR RESIDUE PE2 A 1
4AC4SOFTWAREHIS B:58 , GLU B:83 , TRP B:88 , ILE B:100 , TYR B:101 , MET B:121 , GLN B:125 , MET B:128 , TYR B:172 , ARG B:176 , GLU B:225 , HOH B:527BINDING SITE FOR RESIDUE PE2 B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KI3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:153 -Pro A:154
2Pro B:153 -Pro B:154

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_KITH_HHV11_005 *C251GKITH_HHV11  ---  ---A/BC251G
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KI3)

(-) Exons   (0, 0)

(no "Exon" information available for 1KI3)

(-) 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:309
 aligned with KITH_HHV11 | P03176 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:329
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365         
           KITH_HHV11    46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
               SCOP domains d1ki3a_ A: Thymidine kinase                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1ki3A00 A:46-374 P-loop con    taining nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......hhhhhhhhh..----.eeee...hhhhh......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........-.....eeeee...hhhhh.hhhhhhhhh....hhhhhhhhhh........eeeeee..hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh...hhhh......---------------....hhh...hhh..hhh........hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G--------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ki3 A  46 MPTLLRVYIDGPHGMGKTTTTQLLVAL----DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSS-APPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSG---------------PRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
                                    55        65      |  - |      85        95       105       115       125       135       145    | |155       165       175       185       195       205       215       225       235       245       255        |-         -    |  285       295       305       315       325       335       345       355       365         
                                                     72   77                                                                      150 |                                                                                                             264             280                                                                                              
                                                                                                                                    152                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:311
 aligned with KITH_HHV11 | P03176 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:329
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365         
           KITH_HHV11    46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
               SCOP domains d1ki3b_ B: Thymidine kinase                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1ki3B00 B:46-374 P-loop cont   aining nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) ----------Herpes_TK-1ki3B01    B:56-330                                                                                                                                                                                                                                                      -------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------Herpes_TK-1ki3B02    B:56-330                                                                                                                                                                                                                                                      -------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeee.......hhhhhhhhh...---.eeee...hhhhh......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhh........-.....eeeeee..hhhhh.hhhhhhhh.....hhhhhhhh..........eeeeee..hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..--------------......hhh..hhhh.............hhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G--------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ki3 B  46 MPTLLRVYIDGPHGMGKTTTTQLLVALG---DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSS-APPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLS--------------AGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
                                    55        65       | - |      85        95       105       115       125       135       145    | |155       165       175       185       195       205       215       225       235       245       255       | -         -  |    285       295       305       315       325       335       345       355       365         
                                                      73  77                                                                      150 |                                                                                                            263            278                                                                                                
                                                                                                                                    152
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KITH_HHV11 | P03176)
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: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: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.

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  1ki3
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 Related Entries

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

UniProtKB/Swiss-Prot
        KITH_HHV11 | P03176: 1e2h 1e2i 1e2j 1e2k 1e2l 1e2m 1e2n 1e2p 1ki2 1ki4 1ki6 1ki7 1ki8 1kim 1of1 1p7c 1qhi 1vtk 2ki5 2vtk 3f0t 3rdp 3vtk 4ivp 4ivq 4ivr 4jbx 4jby 4oql 4oqm 4oqn 4oqx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1KI3)