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(-) Description

Title :  PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH AP5DT
 
Authors :  J. L. Whittingham, J. Carrero-Lerida, J. A. Brannigan, L. M. Ruiz-Pere 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) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  B,C  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Transferase, 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 (1x):  BC
Biological Unit 2 (2x): A  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1NA5Ligand/IonSODIUM ION
2T5A3Ligand/IonP1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2T5A2Ligand/IonP1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2T5A2Ligand/IonP1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:17 , ARG A:18 , SER A:19 , GLY A:20 , LYS A:21 , SER A:22 , THR A:23 , PHE A:44 , ARG A:47 , LEU A:59 , PHE A:74 , ARG A:78 , ARG A:99 , GLY A:104 , TYR A:107 , ARG A:145 , TYR A:153 , ARG A:182 , ILE A:184 , NA A:212 , NA A:213 , HOH A:2037 , HOH A:2061 , HOH A:2062 , HOH A:2063 , ALA B:170 , HIS B:171BINDING SITE FOR RESIDUE T5A A 211
2AC2SOFTWAREASP B:17 , ARG B:18 , SER B:19 , GLY B:20 , LYS B:21 , SER B:22 , THR B:23 , PHE B:44 , ARG B:47 , LEU B:59 , PHE B:74 , ARG B:78 , ARG B:99 , GLY B:104 , TYR B:107 , ARG B:145 , TYR B:153 , GLU B:154 , ARG B:182 , ILE B:184 , ILE B:187 , NA B:212 , HOH B:2001BINDING SITE FOR RESIDUE T5A B 211
3AC3SOFTWAREASP C:17 , ARG C:18 , SER C:19 , GLY C:20 , LYS C:21 , SER C:22 , THR C:23 , 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 , ARG C:145 , ARG C:182 , ILE C:184 , ILE C:187 , NA C:212 , NA C:213 , HOH C:2002BINDING SITE FOR RESIDUE T5A C 211
4AC4SOFTWAREASP A:17 , GLU A:151 , GLU A:154 , T5A A:211BINDING SITE FOR RESIDUE NA A 212
5AC5SOFTWARESER A:22 , ASP A:98 , T5A A:211 , HOH A:2037 , HOH A:2061BINDING SITE FOR RESIDUE NA A 213
6AC6SOFTWARESER B:22 , ASP B:98 , T5A B:211BINDING SITE FOR RESIDUE NA B 212
7AC7SOFTWARESER C:22 , ASP C:98 , T5A C:211BINDING SITE FOR RESIDUE NA C 212
8AC8SOFTWAREASP C:17 , GLU C:154 , T5A C:211 , HOH C:2012BINDING SITE FOR RESIDUE NA C 213

(-) SS Bonds  (0, 0)

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

(-) 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 2WWH)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WWH)

(-) 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 d2wwha_ A: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains 2wwhA00 A:-1-210 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee....hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh..hhhhhhhhhh......eeeeee..................hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wwh 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:210
 aligned with Q8I4S1_PLAF7 | Q8I4S1 from UniProtKB/TrEMBL  Length:210

    Alignment length:210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
         Q8I4S1_PLAF7     1 MTDDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
               SCOP domains d2wwhb_ B: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains 2wwhB00 B:1-210 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeee....hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh..hhhhhhhhhh......eeeeee.hhhhhh...........hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wwh B   1 MTDDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210


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

    Alignment length:210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
         Q8I4S1_PLAF7     1 MTDDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
               SCOP domains d2wwhc_ C: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains 2wwhC00 C:1-210 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                               CATH domains
           Pfam domains (1) ------------Thymidylate_kin-2wwhC01 C:13-191                                                                                                                                                   ------------------- Pfam domains (1)
           Pfam domains (2) ------------Thymidylate_kin-2wwhC02 C:13-191                                                                                                                                                   ------------------- Pfam domains (2)
           Pfam domains (3) ------------Thymidylate_kin-2wwhC03 C:13-191                                                                                                                                                   ------------------- Pfam domains (3)
         Sec.struct. author .........eeeee.....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh..hhhhhhhhhh......eeeeee..................hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wwh C   1 MTDDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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, 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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  2wwh
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 Related Entries

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

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        Q8I4S1_PLAF7 | Q8I4S1: 2wwf 2wwg 2wwi 2yof 2yog 2yoh

(-) Related Entries Specified in the PDB File

2wwf PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH TMP AND ADP
2wwg PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH DGMP AND ADP
2wwi PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH AZTMP AND ADP