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(-) Description

Title :  KINETICS AND CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS TYPE 1 THYMIDINE KINASE INTERACTING WITH (SOUTH)-METHANOCARBA-THYMIDINE
 
Authors :  M. T. Claus, P. Schelling, G. Folkers, V. E. Marquez, L. Scapozza, G. E. Schulz
Date :  03 Apr 03  (Deposition) - 03 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Thymidine Kinase, Antiviral Drug, Enzyme- Prodrug Gene, Kinase, Dna Synthesis, Atp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Schelling, M. T. Claus, R. Johner, V. E. Marquez, G. E. Schulz, L. Scapozza
Biochemical And Structural Characterization Of (South)-Methanocarbathymidine That Specifically Inhibits Growth Of Herpes Simplex Virus Type 1 Thymidine Kinase-Transduced Osteosarcoma Cells
J. Biol. Chem. V. 279 32832 2004
PubMed-ID: 15163659  |  Reference-DOI: 10.1074/JBC.M313343200
(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 Taxid: 562
    Organism Scientific: HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17)
    Organism Taxid: 10299
    Strain: 17

 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
1SCT2Ligand/Ion(SOUTH)-METHANOCARBA-THYMIDINE
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 , ARG A:220 , ARG A:222 , HOH A:2063 , HOH A:2162 , HOH A:2164BINDING SITE FOR RESIDUE SO4 A 600
2AC2SOFTWAREHIS B:58 , GLY B:59 , MET B:60 , GLY B:61 , LYS B:62 , THR B:63 , HOH B:2069BINDING SITE FOR RESIDUE SO4 B 700
3AC3SOFTWAREHIS A:58 , GLU A:83 , ILE A:97 , TYR A:101 , GLN A:125 , MET A:128 , TYR A:132 , ARG A:163 , ALA A:168 , TYR A:172 , ARG A:222 , GLU A:225 , HOH A:2068 , HOH A:2162 , HOH A:2163BINDING SITE FOR RESIDUE SCT A 400
4AC4SOFTWAREHIS B:58 , GLU B:83 , TYR B:101 , GLN B:125 , MET B:128 , ARG B:163 , ALA B:168 , TYR B:172 , GLU B:225 , HOH B:2175 , HOH B:2176BINDING SITE FOR RESIDUE SCT B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OF1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OF1)

 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 1OF1)

(-) Exons   (0, 0)

(no "Exon" information available for 1OF1)

(-) 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:308
 aligned with KITH_HHV11 | P03176 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:330
                                    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       375
           KITH_HHV11    46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEA 375
               SCOP domains d1of1a_ A: Thymidine kinas    e                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1of1A00 A:46-375 P-loop co    ntaining nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhh----..eeee..hhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.-----....eeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhh........eeeeee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..-------------....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1of1 A  46 MPTLLRVYIDGPHGMGKTTTTQLLVA----DDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEA-----PPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGT-------------GPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEA 375
                                    55        65     |   -|       85        95       105       115       125       135       145 |     155       165       175       185       195       205       215       225       235       245       255       265         -   |   285       295       305       315       325       335       345       355       365       375
                                                    71   76                                                                    147   153                                                                                                             265           279                                                                                                


Chain B from PDB  Type:PROTEIN  Length:314
 aligned with KITH_HHV11 | P03176 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:330
                                    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       375
           KITH_HHV11    46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEA 375
               SCOP domains d1of1b_ B: Thymidine kinase                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1of1B00 B:46-375 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) ----------Herpes_TK-1of1B01 B:56-330                                                                                                                                                                                                                                                         --------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------Herpes_TK-1of1B02 B:56-330                                                                                                                                                                                                                                                         --------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhh......eeee..hhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.-----....eeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhh........eeeeee.hhhhhhhhhh..---....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...--------.........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhh....eee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1of1 B  46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEA-----PPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKR---GERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGT--------PQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEA 375
                                    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       375
                                                                                                                               147   153                                                                220 224                                      265      274
   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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 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 1ki3 1ki4 1ki6 1ki7 1ki8 1kim 1p7c 1qhi 1vtk 2ki5 2vtk 3f0t 3rdp 3vtk 4ivp 4ivq 4ivr 4jbx 4jby 4oql 4oqm 4oqn 4oqx

(-) Related Entries Specified in the PDB File

1e2h THE NUCLEOSIDE BINDING SITE OF HERPES SIMPLEX TYPE 1 THYMIDINE KINASE ANALYZED BY X-RAY CRYSTALLOGRAPHY
1e2i THE NUCLEOSIDE BINDING SITE OF HERPES SIMPLEX TYPE 1 THYMIDINE KINASE ANALYZED BY X-RAY CRYSTALLOGRAPHY
1e2j THE NUCLEOSIDE BINDING SITE OF HERPES SIMPLEX TYPE 1 THYMIDINE KINASE ANALYZED BY X-RAY CRYSTALLOGRAPHY
1e2k KINETICS AND CRYSTAL STRUCTURE OF THE WILD- TYPE AND THE ENGINEERED Y101F MUTANT OF HERPES SIMPLEX VIRUS TYPE 1 THYMIDINE KINASE INTERACTING WITH (NORTH)-METHANOCARBA- THYMIDINE
1e2l KINETICS AND CRYSTAL STRUCTURE OF THE WILD- TYPE AND THEENGINEERED Y101F MUTANT OF HERPES SIMPLEX VIRUS TYPE 1THYMIDINE KINASE INTERACTING WITH(NORTH)-METHANOCARBA-THYMIDINE
1e2m HPT + HMTT
1e2n HPT + HMTT
1e2p DHBT
1ki2 CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH GANCICLOVIR
1ki3 CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH PENCICLOVIR
1ki4 CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH 5-BROMOTHIENYLDEOXYURIDINE
1ki6 CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH A 5-IODOURACIL ANHYDROHEXITOL NUCLEOSIDE
1ki7 CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH 5-IODODEOXYURIDINE
1ki8 CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH 5-BROMOVINYLDEOXYURIDINE
1qhi HERPES SIMPLEX VIRUS TYPE-I THYMIDINE KINASE COMPLEXED WITH A NOVEL NON-SUBSTRATE INHIBITOR, 9-(4-HYDROXYBUTYL)-N2- PHENYLGUANINE
1vtk THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ADP AND DEOXYTHYMIDINE-MONOPHOSPHATE
2ki5 HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION
3vtk THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ADP AND 5-IODO- DEOXYURIDINE-MONOPHOSPHATE