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(-) Description

Title :  5'-DIPHENYL NUCLEOSIDE INHIBITORS OF PLASMODIUM FALCIPARUM DUTPASE
 
Authors :  S. E. Hampton, B. Baragana, A. Schipani, C. Bosch-Navarrete, A. Musso- E. Recio, M. Kaiser, J. L. Whittingham, S. M. Roberts, M. Shevtsov, J. A. Brannigan, P. Kahnberg, R. Brun, K. S. Wilson, D. Gonzalez-Pacan N. G. Johansson, I. H. Gilbert
Date :  29 Jul 11  (Deposition) - 29 Aug 12  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,F
Keywords :  Dutp Binding, Nucleus, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. E. Hampton, B. Baragana, A. Schipani, C. Bosch-Navarrete, J. A. Musso-Buendia, E. Recio, M. Kaiser, J. L. Whittingham, S. M. Roberts, M. Shevtsov, J. A. Brannigan, P. Kahnberg, R. Brun, K. S. Wilson, D. Gonzalez-Pacanowska, N. G. Johansson, I. H. Gilbert
Design, Synthesis, And Evaluation Of 5'-Diphenyl Nucleoside Analogues As Inhibitors Of The Plasmodium Falciparum Dutpase.
Chemmedchem V. 6 1816 2011
PubMed-ID: 22049550

(-) Compounds

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE, PUTATIVE
    Chains: A, B, C
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PF11_0282
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7
 
Molecule 2 - PEPTIDE GLY-HIS-GLY
    Chains: F
    Engineered: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1DU43Ligand/Ion2',5'-DIDEOXY-5'-[(DIPHENYLMETHYL)(METHYL)AMINO]URIDINE
2SO46Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:46 , LEU A:88 , ASN A:103 , GLY A:106 , ILE A:108 , TYR A:112 , ILE A:117 , ALA A:119 , HOH A:237 , HOH A:395 , SER B:92 , SER B:95 , LYS B:96 , HOH B:253BINDING SITE FOR RESIDUE DU4 A 400
2AC2SOFTWAREARG A:91 , SER A:92 , GLN A:138 , HOH A:227 , HOH A:294 , DU4 C:400 , HOH C:402 , HOH C:506 , HOH C:544BINDING SITE FOR RESIDUE SO4 A 182
3AC3SOFTWAREPHE B:46 , LEU B:88 , ASN B:103 , GLY B:106 , LEU B:107 , ILE B:108 , TYR B:112 , ILE B:116 , ILE B:117 , ALA B:119 , HOH B:236 , SER C:92 , SO4 C:182 , HOH C:222BINDING SITE FOR RESIDUE DU4 B 400
4AC4SOFTWAREHOH A:382 , ARG B:91 , SER B:92 , GLN B:138 , HOH B:193 , HOH B:194 , HOH B:253 , HOH B:377BINDING SITE FOR RESIDUE SO4 B 182
5AC5SOFTWAREASN A:61 , HOH A:245 , GLN B:126 , GLU B:127 , HOH B:204 , HOH B:428BINDING SITE FOR RESIDUE SO4 B 183
6AC6SOFTWARELYS B:132 , ASN B:133BINDING SITE FOR RESIDUE SO4 B 184
7AC7SOFTWARESER A:92 , SO4 A:182 , LEU C:88 , ASN C:103 , GLY C:106 , LEU C:107 , TYR C:112 , ILE C:116 , ILE C:117 , ALA C:119 , HOH C:278 , HOH C:402 , HOH C:530 , HOH C:545BINDING SITE FOR RESIDUE DU4 C 400
8AC8SOFTWAREHOH B:359 , DU4 B:400 , ARG C:91 , SER C:92 , GLN C:138 , HOH C:222 , HOH C:268 , HOH C:512 , HOH C:514BINDING SITE FOR RESIDUE SO4 C 182
9AC9SOFTWAREGLY C:111 , TYR C:112 , ARG C:113 , ARG C:160BINDING SITE FOR RESIDUE SO4 C 183

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T70)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly C:166 -Ser C:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T70)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T70)

(-) Exons   (0, 0)

(no "Exon" information available for 3T70)

(-) 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:149
 aligned with Q8II92_PLAF7 | Q8II92 from UniProtKB/TrEMBL  Length:173

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
         Q8II92_PLAF7     1 MHLKIVCLSDEVREMYKNHKTHHEGDSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQYKSNYYYKCEKSENKKKDDDKSNIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEELDETSRGEGGFGS 167
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 3t70 A   1 MHLKIVCLSDEVREMYKNHK----GDSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQYKSNYYYK--------------NIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEELDETSRGEGGFGS 167
                                    10        20    |   30        40        50        60    |    -        80        90       100       110       120       130       140       150       160       
                                              20   25                                      65             80                                                                                       


Chain B from PDB  Type:PROTEIN  Length:137
 aligned with Q8II92_PLAF7 | Q8II92 from UniProtKB/TrEMBL  Length:173

    Alignment length:156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      
         Q8II92_PLAF7     1 MHLKIVCLSDEVREMYKNHKTHHEGDSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQYKSNYYYKCEKSENKKKDDDKSNIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEELD 156
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ 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
                 3t70 B   1 MHLKIVCLSDEVREMYKNH------DSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQYKSNYYYKC-------------NIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEELD 156
                                    10        |-     |  30        40        50        60     |   -        80        90       100       110       120       130       140       150      
                                             19     26                                      66            80                                                                            


Chain C from PDB  Type:PROTEIN  Length:148
 aligned with Q8II92_PLAF7 | Q8II92 from UniProtKB/TrEMBL  Length:173

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
         Q8II92_PLAF7     1 MHLKIVCLSDEVREMYKNHKTHHEGDSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQYKSNYYYKCEKSENKKKDDDKSNIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEELDETSRGEGGFGS 167
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         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
                 3t70 C   1 MHLKIVCLSDEVREMYKNH-----GDSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQYKSNYYYK--------------NIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEELDETSRGEGGFGS 167
                                    10        |-    |   30        40        50        60    |    -        80        90       100       110       120       130       140       150       160       
                                             19    25                                      65             80                                                                                       


Chain F from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 3t70 F   1 GHG   3
   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  (0, 0)

(no "SCOP Domain" information available for 3T70)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T70)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T70)

(-) 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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 Related Entries

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UniProtKB/TrEMBL
        Q8II92_PLAF7 | Q8II92: 1vyq 2y8c 3t60 3t64 3t6y

(-) Related Entries Specified in the PDB File

3t6y