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(-) Description

Title :  YEAST THYMIDYLATE KINASE COMPLEXED WITH 3'-AZIDO-3'-DEOXYTHYMIDINE MONOPHOSPHATE (AZT-MP)
 
Authors :  A. Lavie, I. Schlichting
Date :  12 Jun 97  (Deposition) - 17 Jun 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase (Phosphotransferase), Kinase, Thymidine Activation Pathway, Enzyme, Azt (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Lavie, I. R. Vetter, M. Konrad, R. S. Goody, J. Reinstein, I. Schlichting
Structure Of Thymidylate Kinase Reveals The Cause Behind The Limiting Step In Azt Activation.
Nat. Struct. Biol. V. 4 601 1997
PubMed-ID: 9253404  |  Reference-DOI: 10.1038/NSB0897-601
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CDC8
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 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
1ATM2Ligand/Ion3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:13 , ASP A:14 , ARG A:15 , THR A:16 , GLY A:17 , LYS A:18 , THR A:19BINDING SITE FOR RESIDUE SO4 A 218
2AC2SOFTWARELEU B:13 , ASP B:14 , ARG B:15 , THR B:16 , GLY B:17 , LYS B:18 , THR B:19 , HOH B:1023 , HOH B:1105 , HOH B:1197 , HOH B:1204BINDING SITE FOR RESIDUE SO4 B 218
3AC3SOFTWAREASP A:14 , LYS A:37 , PHE A:38 , ARG A:41 , PHE A:69 , ARG A:73 , ARG A:94 , GLY A:99 , TYR A:102 , ARG A:150 , TYR A:151 , GLU A:152 , HOH A:1122 , HOH A:1123 , HOH A:1140 , HOH A:1143BINDING SITE FOR RESIDUE ATM A 217
4AC4SOFTWAREASP B:14 , LYS B:37 , PHE B:38 , PRO B:39 , ARG B:41 , LEU B:53 , PHE B:69 , ARG B:73 , ARG B:94 , GLY B:99 , TYR B:102 , GLU B:149 , TYR B:151 , GLU B:152 , GLN B:157 , HOH B:1016 , HOH B:1017 , HOH B:1024 , HOH B:1204BINDING SITE FOR RESIDUE ATM B 217

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:38 -Pro A:39
2Gln B:30 -Pro B:31
3Phe B:38 -Pro B:39

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_KINASEPS01331 Thymidylate kinase signature.KTHY_YEAST91-103
 		  2A:91-103
B:91-103

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YJR057W1YJR057W.1X:544054-544704651KTHY_YEAST1-2162162A:3-216 (gaps)
B:3-216 (gaps)		214
214

(-) 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:204
 aligned with KTHY_YEAST | P00572 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:214
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    
           KTHY_YEAST     3 GRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
               SCOP domains d2tmka_ A: Thymidylate kinase                                                                                                                                                                                          SCOP domains
               CATH domains 2tmkA00 A:3-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhh...eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhh...eeeee..hhhhhhhhhhh......hhhhhhhh.......eeeeee..----------........hhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------THYMIDYLATE_K----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-216 (gaps) UniProt: 1-216 [INCOMPLETE]                                                                                                                                                              Transcript 1
                 2tmk A   3 GRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQ----------FGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132  |      -   |   152       162       172       182       192       202       212    
                                                                                                                                                              135        146                                                                      


Chain B from PDB  Type:PROTEIN  Length:204
 aligned with KTHY_YEAST | P00572 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:214
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    
           KTHY_YEAST     3 GRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
               SCOP domains d2tmkb_ B: Thymidylate kinase                                                                                                                                                                                          SCOP domains
               CATH domains 2tmkB00 B:3-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                   CATH domains
           Pfam domains (1) -------Thymidylate_kin-2tmkB01 B:10-196                                                                                                                                                           -------------------- Pfam domains (1)
           Pfam domains (2) -------Thymidylate_kin-2tmkB02 B:10-196                                                                                                                                                           -------------------- Pfam domains (2)
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhh...eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhh...eeeee..hhhhhhhhhhh......hhhhhhhh.......eeeeee..----------........hhhhhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------THYMIDYLATE_K----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-216 (gaps) UniProt: 1-216 [INCOMPLETE]                                                                                                                                                              Transcript 1
                 2tmk B   3 GRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQ----------FGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132  |      -   |   152       162       172       182       192       202       212    
                                                                                                                                                              135        146
   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  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KTHY_YEAST | P00572)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004798    thymidylate kinase activity    Catalysis of the reaction: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.
    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:0009041    uridylate kinase activity    Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP.
biological process
    GO:0006233    dTDP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTDP, deoxyribosylthymine diphosphate (2'-deoxyribosylthymine5'-diphosphate).
    GO:0006235    dTTP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.
    GO:0006227    dUDP biosynthetic process    The chemical reactions and pathways resulting in the formation of dUDP, deoxyuridine diphosphate (2'-deoxy-5'-uridylyl phosphate).
    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: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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        KTHY_YEAST | P00572: 1tmk 3tmk

(-) Related Entries Specified in the PDB File

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