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(-) Description

Title :  NOVEL INHIBITORS OF PLASMODIUM FALCIPARUM DUTPASE PROVIDE A PLATFORM FOR ANTI-MALARIAL DRUG DESIGN
 
Authors :  J. L. Whittingham, I. Leal, G. Kasinathan, C. Nguyen, E. Bell, A. F. Jones, C. Berry, A. Benito, J. P. Turkenburg, E. J. Dodson, L. M. Ruiz Perez, A. J. Wilkinson, N. G. Johansson, R. Brun, I. H. Gilbert, D. Gonzalez Pacanowska, K. S. Wilson
Date :  05 May 04  (Deposition) - 26 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Drug Design, Plasmodium Falciparum, Dutpase, Deoxyuridine Nucleotidohydrolase, Malaria, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Whittingham, I. Leal, C. Nguyen, G. Kasinathan, E. Bell, A. F. Jones, C. Berry, A. Benito, J. P. Turkenburg, E. J. Dodson, L. M. Ruiz Perez, A. J. Wilkinson, N. G. Johansson, R. Brun, I. H. Gilbert, D. Gonzalez Pacanowska, K. S. Wilson
Dutpase As A Platform For Antimalarial Drug Design: Structural Basis For The Selectivity Of A Class Of Nucleoside Inhibitors.
Structure V. 13 329 2005
PubMed-ID: 15698576  |  Reference-DOI: 10.1016/J.STR.2004.11.015

(-) Compounds

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
    Chains: A, B, C
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11PFDUT
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Other Details: INHIBITOR COMPLEX
    Strain: 3D7
    Synonym: DUTP PYROPHOSPHATASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1DUX3Ligand/Ion2,3-DEOXY-3-FLUORO-5-O-TRITYLURIDINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:46 , LEU A:88 , ASN A:103 , GLY A:106 , TYR A:112 , ILE A:117 , HOH A:2051 , SER B:92 , SER B:93 , LYS C:48 , HOH C:2017BINDING SITE FOR RESIDUE DUX A1160
2AC2SOFTWAREASN B:103 , GLY B:106 , TYR B:112 , ILE B:117 , ALA B:119 , HOH B:2025 , SER C:92 , SER C:95 , LYS C:96BINDING SITE FOR RESIDUE DUX B1160
3AC3SOFTWAREVAL A:6 , LYS A:52 , SER A:92 , SER A:95 , GLU A:153 , PHE C:46 , ASN C:103 , GLY C:106 , TYR C:112 , ILE C:116 , ILE C:117 , ALA C:119 , HOH C:2042BINDING SITE FOR RESIDUE DUX C1160

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VYQ)

(-) Exons   (0, 0)

(no "Exon" information available for 1VYQ)

(-) 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:142
 aligned with Q8II92_PLAF7 | Q8II92 from UniProtKB/TrEMBL  Length:173

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
         Q8II92_PLAF7     1 MHLKIVCLSDEVREMYKNHKTHHEGDSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQYKSNYYYKCEKSENKKKDDDKSNIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEELDETS 159
               SCOP domains d1vyqa1 A:1-159 Deoxyuri dine 5'-triphosphate nucleotidohydrola                se (dUTPase)                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhh......-..eeee.....eee...eeeeeeeeeeeeeeee.....----------------.eee..eeeee.hhhhhh.eee....eee......eeeeeeee.....eee......eeee.......eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vyq A   1 MHLKIVCLSDEVREMYKNHKTHHE-DSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQYKSNYY----------------NIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEELDETS 159
                                    10        20   | |  30        40        50        60  |      -        80        90       100       110       120       130       140       150         
                                                  24 |                                   63               80                                                                               
                                                    26                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:140
 aligned with Q8II92_PLAF7 | Q8II92 from UniProtKB/TrEMBL  Length:173

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
         Q8II92_PLAF7     1 MHLKIVCLSDEVREMYKNHKTHHEGDSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQYKSNYYYKCEKSENKKKDDDKSNIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEE 154
               SCOP domains d1vyqb_ B: automated matches                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhh.........eeeee....eee...eeeeee..eeeeeeee.......--------------.eeee.eeeee.hhhhhh.eee....eee........eeeeee.....eee....eeeeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vyq B   1 MHLKIVCLSDEVREMYKNHKTHHEGDSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQYKSNYYYK--------------NIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEE 154
                                    10        20        30        40        50        60    |    -        80        90       100       110       120       130       140       150    
                                                                                           65             80                                                                          


Chain C from PDB  Type:PROTEIN  Length:141
 aligned with Q8II92_PLAF7 | Q8II92 from UniProtKB/TrEMBL  Length:173

    Alignment length:155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     
         Q8II92_PLAF7     1 MHLKIVCLSDEVREMYKNHKTHHEGDSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQYKSNYYYKCEKSENKKKDDDKSNIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEEL 155
               SCOP domains d1vyqc_ C: automated ma  tches                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------dUTPase-1vyqC01 C:80-155                                                     Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------dUTPase-1vyqC02 C:80-155                                                     Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------dUTPase-1vyqC03 C:80-155                                                     Pfam domains (3)
         Sec.struct. author .eeeeee.hhhhhhhhhh.....--..eeee.....eee...eeeeee..eeeeeeee.......------------...eeee.eeeee.hhhhhh.eee....eee........eeeeee.....eee......eeee.......eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vyq C   1 MHLKIVCLSDEVREMYKNHKTHH--DSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQYKSNYYYK------------KSNIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEEL 155
                                    10        20  |  |  30        40        50        60    |    -       |80        90       100       110       120       130       140       150     
                                                 23 26                                     65           78
   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  (2, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VYQ)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: dUTPase (38)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q8II92_PLAF7 | Q8II92)
molecular function
    GO:0004170    dUTP diphosphatase activity    Catalysis of the reaction: dUTP + H2O = dUMP + diphosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006226    dUMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
    GO:0046081    dUTP catabolic process    The chemical reactions and pathways resulting in the breakdown of dUTP, deoxyuridine (5'-)triphosphate.
    GO:0046080    dUTP metabolic process    The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.
    GO:0006399    tRNA metabolic process    The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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        Q8II92_PLAF7 | Q8II92: 2y8c 3t60 3t64 3t6y 3t70

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