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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN THYMIDYLATE KINASE WITH D4TMP + APPNHP
 
Authors :  N. Ostermann, D. Segura-Pena, C. Meier, T. Veit, M. Monnerjahn, M. Konr A. Lavie
Date :  12 Jan 03  (Deposition) - 18 Mar 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Thymidylate Kinase, P-Loop, D4Tmp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Ostermann, D. Segura-Pena, C. Meier, T. Veit, M. Monnerjahn, M. Konrad, A. Lavie
Structures Of Human Thymidylate Kinase In Complex With Prodrugs: Implications For The Structure-Based Design Of Novel Compounds
Biochemistry V. 42 2568 2003
PubMed-ID: 12614151  |  Reference-DOI: 10.1021/BI027302T

(-) Compounds

Molecule 1 - SIMILAR TO DEOXYTHYMIDYLATE KINASE (THYMIDYLATE KINASE)
    ChainsA
    EC Number2.7.4.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
12DT1Mod. Residue3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
12DT2Mod. Residue3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:20 , ANP A:303 , HOH A:504 , HOH A:505 , HOH A:506BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREHOH A:501 , HOH A:502 , HOH A:503BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWAREPHE A:42 , PRO A:43 , ARG A:45 , LEU A:57 , PHE A:72 , ARG A:76 , ARG A:97 , GLY A:102 , PHE A:105 , GLU A:149 , TYR A:151 , ANP A:303 , HOH A:505 , HOH A:509 , HOH A:518 , HOH A:530 , HOH A:545 , HOH A:556 , HOH A:639BINDING SITE FOR RESIDUE 2DT A 301
4AC4SOFTWAREASP A:15 , ARG A:16 , ALA A:17 , GLY A:18 , LYS A:19 , SER A:20 , THR A:21 , ARG A:97 , ARG A:143 , ALA A:180 , LYS A:182 , SER A:183 , ILE A:184 , ARG A:192 , 2DT A:301 , MG A:401 , HOH A:504 , HOH A:505 , HOH A:506 , HOH A:518 , HOH A:539 , HOH A:570 , HOH A:577 , HOH A:587 , HOH A:597 , HOH A:607 , HOH A:634 , HOH A:639 , HOH A:676 , HOH A:695 , HOH A:710 , HOH A:717BINDING SITE FOR RESIDUE ANP A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NN5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:42 -Pro A:43

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NN5)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_KINASEPS01331 Thymidylate kinase signature.KTHY_HUMAN94-106  1A:94-106
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_KINASEPS01331 Thymidylate kinase signature.KTHY_HUMAN94-106  2A:94-106

(-) Exons   (5, 5)

Asymmetric Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003057841aENSE00001856557chr2:242626406-242626069338KTHY_HUMAN1-44441A:4-4441
1.2bENST000003057842bENSE00001630292chr2:242625292-242625184109KTHY_HUMAN44-80371A:44-8037
1.7ENST000003057847ENSE00001748052chr2:242619734-24261964491KTHY_HUMAN80-110311A:80-11031
1.8ENST000003057848ENSE00001663158chr2:242618064-242617867198KTHY_HUMAN111-176661A:111-176 (gaps)66
1.9fENST000003057849fENSE00001645872chr2:242615652-242615157496KTHY_HUMAN177-212361A:177-21236

(-) 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:204
 aligned with KTHY_HUMAN | P23919 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:209
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203         
           KTHY_HUMAN     4 RRGALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLRFPERSTEIGKLLSSYLQKKSDVEDHSVHLLFSANRWEQVPLIKEKLSQGVTLVVDRYAFSGVAFTGAKENFSLDWCKQPDVGLPKPDLVLFLQLQLADAAKRGAFGHERYENGAFQERALRCFHQLMKDTTLNWKMVDASKSIEAVHEDIRVLSEDAIRTATEKPLGELWK 212
               SCOP domains d1nn5a_ A: Thymidylate kinase                                                                                                                                                                                     SCOP domains
               CATH domains 1nn5A00 A:4-212 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh....hhhhhhhhhh......eeeeee.hhhhhhhh-----....hhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------THYMIDYLATE_K---------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:4-44 UniProt: 1-44     -----------------------------------Exon 1.7  PDB: A:80-110        Exon 1.8  PDB: A:111-176 (gaps) UniProt: 111-176                  Exon 1.9f  PDB: A:177-212            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.2b  PDB: A:44-80              ------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1nn5 A   4 RRGALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLRFPERSTEIGKLLSSYLQKKSDVEDHSVHLLFSANRWEQVPLIKEKLSQGVTLVVDRYAFSGVAFTGAKENFSLDWCKQPDVGLPKPDLVLFLQLQLADAAKR-----ERYENGAFQERALRCFHQLMKDTTLNWKMVDASKSIEAVHEDIRVLSEDAIATATEKPLGELWK 212
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143     | 153       163       173       183       193       203         
                                                                                                                                                                     143   149                                                               

   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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NN5)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A   (KTHY_HUMAN | P23919)
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:0050145    nucleoside phosphate kinase activity    Catalysis of the reaction: ATP + nucleoside phosphate = ADP + nucleoside diphosphate.
    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: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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0071363    cellular response to growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus.
    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:0045445    myoblast differentiation    The process in which a relatively unspecialized cell acquires specialized features of a myoblast. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into striated muscle fibers.
    GO:0015949    nucleobase-containing small molecule interconversion    The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
    GO:0046940    nucleoside monophosphate phosphorylation    The process of introducing one or more phosphate groups into a nucleoside monophosphate to produce a polyphosphorylated nucleoside.
    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.
    GO:0046686    response to cadmium ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus.
    GO:0043627    response to estrogen    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
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:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    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_HUMAN | P239191e2d 1e2e 1e2f 1e2g 1e2q 1e98 1e99 1e9a 1e9b 1e9c 1e9d 1e9e 1e9f 1nmx 1nmy 1nmz 1nn0 1nn1 1nn3 2xx3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1NN5)