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(-) Description

Title :  PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH TMP AND ADP
 
Authors :  J. L. Whittingham, J. Carrero-Lerida, J. A. Brannigan, L. M. Ruiz-Perez, A. P. G. Silva, M. J. Fogg, A. J. Wilkinson, I. H. Gilbert, K. S. Wilson, D. Gonzalez-Pacanowska
Date :  23 Oct 09  (Deposition) - 21 Apr 10  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Transferase, Kinase, Malaria (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Whittingham, J. Carrero-Lerida, J. A. Brannigan, L. M. Ruiz-Perez, A. P. G. Silva, M. J. Fogg, A. J. Wilkinson, I. H. Gilbert, K. S. Wilson, D. Gonzalez-Pacanowska
Structural Basis For The Efficient Phosphorylation Of Aztmp And Dgmp By Plasmodium Falciparum Type I Thymidylate Kinase.
Biochem. J. V. 428 499 2010
PubMed-ID: 20353400  |  Reference-DOI: 10.1042/BJ20091880

(-) Compounds

Molecule 1 - THYMIDILATE KINASE, PUTATIVE
    Chains: A, B, C
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric Unit (4, 22)
No.NameCountTypeFull Name
1ADP3Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL9Ligand/IonGLYCEROL
3NA7Ligand/IonSODIUM ION
4TMP3Ligand/IonTHYMIDINE-5'-PHOSPHATE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL6Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4TMP2Ligand/IonTHYMIDINE-5'-PHOSPHATE
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL6Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4TMP2Ligand/IonTHYMIDINE-5'-PHOSPHATE

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:17 , PRO A:45 , ARG A:47 , LEU A:59 , PHE A:74 , ARG A:78 , ARG A:99 , SER A:103 , GLY A:104 , TYR A:107 , TYR A:153 , NA A:213 , HOH A:2029 , HOH A:2083 , HOH A:2119 , HOH A:2176 , HOH A:2177 , HOH A:2178 , HOH A:2179 , HOH A:2180 , HOH A:2181BINDING SITE FOR RESIDUE TMP A 211
02AC2SOFTWAREARG A:18 , SER A:19 , GLY A:20 , LYS A:21 , SER A:22 , THR A:23 , ARG A:145 , ARG A:182 , ILE A:184 , NA A:214 , HOH A:2115 , HOH A:2181 , HOH A:2182 , HOH A:2184 , HOH A:2185 , HOH A:2186 , HOH A:2187 , HOH A:2188 , HOH A:2189 , HOH A:2190 , ALA B:170 , HIS B:171BINDING SITE FOR RESIDUE ADP A 212
03AC3SOFTWAREASP A:17 , GLU A:154 , TMP A:211 , HOH A:2117 , HOH A:2179BINDING SITE FOR RESIDUE NA A 213
04AC4SOFTWARESER A:22 , ASP A:98 , ADP A:212 , HOH A:2083 , HOH A:2084 , HOH A:2177BINDING SITE FOR RESIDUE NA A 214
05AC5SOFTWAREGLU A:38 , THR A:49 , GLY A:50 , ILE A:51 , ASN A:63 , GLU A:80 , HOH A:2191 , HOH A:2192BINDING SITE FOR RESIDUE GOL A 215
06AC6SOFTWAREGLU A:68 , LEU A:114 , ASN A:115 , TRP A:118 , GLN A:124 , GLY A:125 , HOH A:2193 , HOH A:2194 , HOH A:2195 , HOH A:2196BINDING SITE FOR RESIDUE GOL A 216
07AC7SOFTWARELYS A:40 , GLU A:80 , HIS A:81 , GLU A:84 , LEU A:88 , LYS A:91 , HOH A:2074 , HOH A:2197 , HOH A:2198 , HOH A:2199BINDING SITE FOR RESIDUE GOL A 217
08AC8SOFTWARETRP A:175 , HOH A:2041 , HOH A:2141 , HOH A:2144 , HOH A:2146BINDING SITE FOR RESIDUE NA A 218
09AC9SOFTWAREASP B:17 , PHE B:44 , PRO B:45 , ARG B:47 , LEU B:59 , PHE B:74 , ARG B:78 , ARG B:99 , GLY B:104 , TYR B:107 , TYR B:153 , NA B:213 , HOH B:2022 , HOH B:2023 , HOH B:2091 , HOH B:2133 , HOH B:2134 , HOH B:2135 , HOH B:2136BINDING SITE FOR RESIDUE TMP B 211
10BC1SOFTWAREARG B:18 , SER B:19 , GLY B:20 , LYS B:21 , SER B:22 , THR B:23 , GLN B:143 , ARG B:145 , ARG B:182 , ILE B:184 , ILE B:187 , NA B:214 , HOH B:2137 , HOH B:2138 , HOH B:2139BINDING SITE FOR RESIDUE ADP B 212
11BC2SOFTWAREASP B:17 , GLU B:154 , TMP B:211 , HOH B:2090BINDING SITE FOR RESIDUE NA B 213
12BC3SOFTWARESER B:22 , ASP B:98 , ADP B:212 , HOH B:2068 , HOH B:2133 , HOH B:2134BINDING SITE FOR RESIDUE NA B 214
13BC4SOFTWAREGLU B:38 , ASN B:63 , HOH B:2038 , THR C:49 , GLY C:50 , ILE C:51 , GLU C:80BINDING SITE FOR RESIDUE GOL B 215
14BC5SOFTWARETHR B:49 , GLY B:50 , ILE B:51 , GLU B:80 , HOH B:2140 , GLU C:38 , ILE C:54 , ASN C:63 , HOH C:2042BINDING SITE FOR RESIDUE GOL B 216
15BC6SOFTWAREGLU B:68 , LEU B:114 , ASN B:115 , TRP B:118 , HOH B:2141 , HOH B:2142 , HOH B:2143 , HOH B:2144 , GLN C:124 , GLY C:125BINDING SITE FOR RESIDUE GOL B 217
16BC7SOFTWAREASN B:46 , GLU B:80 , HIS B:81 , GLU B:84 , HOH B:2145 , LYS C:40 , LYS C:91 , ILE C:93BINDING SITE FOR RESIDUE GOL B 218
17BC8SOFTWAREASP C:17 , PHE C:44 , PRO C:45 , ARG C:47 , LEU C:59 , PHE C:74 , ARG C:78 , ARG C:99 , SER C:103 , GLY C:104 , TYR C:107 , TYR C:153 , NA C:213 , HOH C:2024 , HOH C:2025 , HOH C:2067 , HOH C:2095 , HOH C:2097 , HOH C:2098 , HOH C:2135 , HOH C:2136 , HOH C:2137BINDING SITE FOR RESIDUE TMP C 211
18BC9SOFTWAREARG C:18 , SER C:19 , GLY C:20 , LYS C:21 , SER C:22 , THR C:23 , ARG C:145 , SER C:146 , ARG C:182 , ILE C:184 , ILE C:187 , NA C:214 , HOH C:2092 , HOH C:2138 , HOH C:2139 , HOH C:2140 , HOH C:2141 , HOH C:2142 , HOH C:2143BINDING SITE FOR RESIDUE ADP C 212
19CC1SOFTWAREASP C:17 , GLU C:154 , TMP C:211 , HOH C:2095 , HOH C:2136 , HOH C:2143BINDING SITE FOR RESIDUE NA C 213
20CC2SOFTWARESER C:22 , ASP C:98 , ADP C:212 , HOH C:2066 , HOH C:2067 , HOH C:2135BINDING SITE FOR RESIDUE NA C 214
21CC3SOFTWARETRP B:79 , GLN B:124 , GLY B:125 , HOH B:2083 , GLU C:68 , LEU C:114 , ASN C:115 , TRP C:118 , HOH C:2144 , HOH C:2145BINDING SITE FOR RESIDUE GOL C 215
22CC4SOFTWARELYS B:91 , ILE B:93 , ASN C:46 , GLU C:80 , HIS C:81 , GLU C:84 , HOH C:2055 , HOH C:2060BINDING SITE FOR RESIDUE GOL C 216

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:44 -Pro A:45
2Leu A:208 -Trp A:209
3Phe B:44 -Pro B:45
4Leu B:208 -Trp B:209
5Phe C:44 -Pro C:45
6Leu C:208 -Trp C:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WWF)

(-) Exons   (0, 0)

(no "Exon" information available for 2WWF)

(-) 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:211
 aligned with Q8I4S1_PLAF7 | Q8I4S1 from UniProtKB/TrEMBL  Length:210

    Alignment length:211
                             1                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209 
         Q8I4S1_PLAF7     - -MTDDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
               SCOP domains d2wwfa_ A: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains 2wwfA00 A:-1-210 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh..hhhhhhhhhh......eeeeee...hhhhhh.........hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wwf A  -1 HMTDDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
                            ||       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209 
                            ||                                                                                                                                                                                                                 
                           -1|                                                                                                                                                                                                                 
                             1                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:208
 aligned with Q8I4S1_PLAF7 | Q8I4S1 from UniProtKB/TrEMBL  Length:210

    Alignment length:208
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202        
         Q8I4S1_PLAF7     3 DDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
               SCOP domains d2wwfb_ B: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2wwfB00 B:3-210 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh..hhhhhhhhhh......eeeeee....hhhhh.........hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wwf B   3 DDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202        


Chain C from PDB  Type:PROTEIN  Length:212
 aligned with Q8I4S1_PLAF7 | Q8I4S1 from UniProtKB/TrEMBL  Length:210

    Alignment length:212
                              1                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208  
         Q8I4S1_PLAF7     - --MTDDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
               SCOP domains d2wwfc_ C: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains 2wwfC00 C:-2-210 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                CATH domains
           Pfam domains (1) --------------Thymidylate_kin-2wwfC01 C:13-191                                                                                                                                                   ------------------- Pfam domains (1)
           Pfam domains (2) --------------Thymidylate_kin-2wwfC02 C:13-191                                                                                                                                                   ------------------- Pfam domains (2)
           Pfam domains (3) --------------Thymidylate_kin-2wwfC03 C:13-191                                                                                                                                                   ------------------- Pfam domains (3)
         Sec.struct. author hhhhh......eeeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh..hhhhhhhhhh......eeeeee..................hhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wwf C  -2 SHMTDDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208  
                            -1|                                                                                                                                                                                                                 
                              1
   Legend:   → Mismatch (orange background)
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  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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q8I4S1_PLAF7 | Q8I4S1)
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:0004798    thymidylate kinase activity    Catalysis of the reaction: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.
    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: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: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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  2wwf
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    Protein Cavities: castP
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    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q8I4S1_PLAF7 | Q8I4S1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8I4S1_PLAF7 | Q8I4S1: 2wwg 2wwh 2wwi 2yof 2yog 2yoh

(-) Related Entries Specified in the PDB File

2wwg PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH DGMP AND ADP
2wwh PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH AP5DT
2wwi PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH AZTMP AND ADP