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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD-TYPE PFDHFR-TS COMPLEXED WITH NADPH, DUMP AND PYRIMETHAMINE
 
Authors :  P. Chitnumsub, Y. Yuthavong
Date :  24 Jan 11  (Deposition) - 29 Jun 11  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Malarial Dhfr-Ts Antifolate Complex, Rossmann Fold, Reductase, Dihydrofolate Binding, Dump Binding, Nadph Binding, Oxidoreductase, Transferase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Vanichtanankul, S. Taweechai, J. Yuvaniyama, T. Vilaivan, P. Chitnumsub, S. Kamchonwongpaisan, Y. Yuthavong
Trypanosomal Dihydrofolate Reductase Reveals Natural Antifolate Resistance
Acs Chem. Biol. V. 6 905 2011
PubMed-ID: 21650210  |  Reference-DOI: 10.1021/CB200124R

(-) Compounds

Molecule 1 - BIFUNCTIONAL DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE
    Chains: A, B
    EC Number: 1.5.1.3, 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DHFR-TS
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
    Strain: TM4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CP62Ligand/Ion5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:14 , CYS A:15 , ASP A:54 , PHE A:58 , SER A:108 , SER A:111 , ILE A:112 , ILE A:164 , TYR A:170 , THR A:185 , NDP A:610 , HOH A:1103BINDING SITE FOR RESIDUE CP6 A 609
2AC2SOFTWARECYS A:15 , ALA A:16 , LEU A:40 , GLY A:41 , GLY A:44 , VAL A:45 , LEU A:46 , GLY A:105 , ARG A:106 , THR A:107 , SER A:108 , LEU A:127 , SER A:128 , ARG A:129 , THR A:130 , ASN A:144 , ILE A:164 , GLY A:165 , GLY A:166 , SER A:167 , VAL A:168 , VAL A:169 , TYR A:170 , GLU A:172 , CP6 A:609 , HOH A:1105 , HOH A:1131 , HOH A:1133 , HOH A:1277BINDING SITE FOR RESIDUE NDP A 610
3AC3SOFTWARECYS A:490 , HIS A:491 , GLN A:509 , ARG A:510 , SER A:511 , ASP A:513 , GLY A:517 , ASN A:521 , HIS A:551 , TYR A:553 , HOH A:1303 , ARG B:470 , ARG B:471BINDING SITE FOR RESIDUE UMP A 611
4AC4SOFTWAREILE B:14 , CYS B:15 , ALA B:16 , ASP B:54 , PHE B:58 , SER B:108 , SER B:111 , ILE B:112 , ILE B:164 , TYR B:170 , THR B:185 , NDP B:610BINDING SITE FOR RESIDUE CP6 B 609
5AC5SOFTWARECYS B:15 , ALA B:16 , LEU B:40 , GLY B:44 , VAL B:45 , TRP B:48 , ARG B:106 , THR B:107 , SER B:108 , LYS B:115 , LEU B:127 , SER B:128 , ARG B:129 , THR B:130 , ASN B:144 , LYS B:145 , ILE B:164 , GLY B:165 , GLY B:166 , SER B:167 , VAL B:168 , VAL B:169 , TYR B:170 , GLU B:172 , CP6 B:609 , HOH B:1096BINDING SITE FOR RESIDUE NDP B 610
6AC6SOFTWAREARG A:470 , ARG A:471 , CYS B:490 , HIS B:491 , GLN B:509 , ARG B:510 , SER B:511 , ASP B:513 , GLY B:517 , ASN B:521 , HIS B:551 , TYR B:553 , HOH B:1216BINDING SITE FOR RESIDUE UMP B 611

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:117 -Pro A:118
2Lys B:117 -Pro B:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QGT)

(-) 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:547
 aligned with A7UD81_PLAFA | A7UD81 from UniProtKB/TrEMBL  Length:608

    Alignment length:608
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600        
         A7UD81_PLAFA     1 MMEQVCDVFDIYAICACCKVESKNEGKKNEVFNNYTFRGLGNKGVLPWKCNSLDMKYFCAVTTYVNESKYEKLKYKRCKYLNKETVDNVNDMPNSKKLQNVVVMGRTSWESIPKKFKPLSNRINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFIIGGSVVYQEFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSNNTTLDFIIYKKTNNKMLNEQNCIKGEEKNNDMPLKNDDKDTCHMKKLTEFYKNVDKYKINYENDDDDEEEDDFVYFNFNKEKEEKNKNSIHPNDFQIYNSLKYKYHPEYQYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTKKLFLRGIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHREVNDLGPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRILLCAWNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNIASYSIFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFPTLKLNPDIKNIEDFTISDFTIQNYVHHEKISMDMAA 608
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.eeeeeeeeee............hhh.eeeee.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....----------....eeeeeehhhhhhhhhhhh....eeeeee....hhhhh....eee.hhhhhhhhhh......eeeeehhhhhhhhhhh....eeeeeeeeeee...ee........eeeeeeeeeee....eeeeeeeee...---------------------------------------------------....hhhhhhhh........hhhhhhhhhhhhhhhh.ee..hhhhhhhhhhhhhhhheee.......eeeeeeeeeeee..............hhhhhhhhhhhhh...hhhhhhhh.....hhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qgt A   1 MMEQVCDVFDIYAICACCKVESKNEGKKNEVFNNYTFRGLGNKGVLPWKCNSLDMKYFCAVTTYVNESKYEKLKYKRCKYLNKET----------KKLQNVVVMGRTSWESIPKKFKPLSNRINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFIIGGSVVYQEFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSNNTTLDFIIYKKTNN---------------------------------------------------DDEEEDDFVYFNFNKEKEEKNKNSIHPNDFQIYNSLKYKYHPEYQYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTKKLFLRGIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHREVNDLGPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRILLCAWNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNIASYSIFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFPTLKLNPDIKNIEDFTISDFTIQNYVHHEKISMDMAA 608
                                    10        20        30        40        50        60        70        80    |    -     | 100       110       120       130       140       150       160       170       180       190       200       210       220       230|        -         -         -         -         -  |    290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600        
                                                                                                               85         96                                                                                                                                    231                                                 283                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:542
 aligned with A7UD81_PLAFA | A7UD81 from UniProtKB/TrEMBL  Length:608

    Alignment length:608
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600        
         A7UD81_PLAFA     1 MMEQVCDVFDIYAICACCKVESKNEGKKNEVFNNYTFRGLGNKGVLPWKCNSLDMKYFCAVTTYVNESKYEKLKYKRCKYLNKETVDNVNDMPNSKKLQNVVVMGRTSWESIPKKFKPLSNRINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFIIGGSVVYQEFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSNNTTLDFIIYKKTNNKMLNEQNCIKGEEKNNDMPLKNDDKDTCHMKKLTEFYKNVDKYKINYENDDDDEEEDDFVYFNFNKEKEEKNKNSIHPNDFQIYNSLKYKYHPEYQYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTKKLFLRGIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHREVNDLGPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRILLCAWNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNIASYSIFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFPTLKLNPDIKNIEDFTISDFTIQNYVHHEKISMDMAA 608
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------DHFR_1-3qgtB01 B:97-228                                                                                                             ------------------------------------------------------------------------------------------------Thymidylat_synt-3qgtB03 B:325-608                                                                                                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------DHFR_1-3qgtB02 B:97-228                                                                                                             ------------------------------------------------------------------------------------------------Thymidylat_synt-3qgtB04 B:325-608                                                                                                                                                                                                                                                            Pfam domains (2)
         Sec.struct. author ...hhhhhh.eeeeeeeeee............hhh.eeeee.........hhhhhhhhhhhhhh.....hhhhhhhhhh..---------------..eeeeeeehhhhhhh.........eeeeee.................hhhhhhhhhh...eeeeeeeehhhhhhhhhhh....eeeeeeeeeee...ee........eeeeee...eee..eeeeeeeeee...---------------------------------------------------.hhhhhhhhhh.........hhhhhh...hhhhhhh.ee..hhhhhhhhhhhhhhhheeee.....eeeeeeeeeeeee..............hhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee..........hhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qgt B   1 MMEQVCDVFDIYAICACCKVESKNEGKKNEVFNNYTFRGLGNKGVLPWKCNSLDMKYFCAVTTYVNESKYEKLKYKRCKYL---------------KLQNVVVMGRTSWESIPKKFKPLSNRINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFIIGGSVVYQEFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSNNTTLDFIIYKKTNN---------------------------------------------------DDEEEDDFVYFNFNKEKEEKNKNSIHPNDFQIYNSLKYKYHPEYQYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTKKLFLRGIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHREVNDLGPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRILLCAWNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNIASYSIFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFPTLKLNPDIKNIEDFTISDFTIQNYVHHEKISMDMAA 608
                                    10        20        30        40        50        60        70        80|        -      |100       110       120       130       140       150       160       170       180       190       200       210       220       230|        -         -         -         -         -  |    290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600        
                                                                                                           81              97                                                                                                                                   231                                                 283
   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 3QGT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: DHFred (95)
(-)
Clan: no clan defined [family: Thymidylat_synt] (68)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A7UD81_PLAFA | A7UD81)
molecular function
    GO:0004146    dihydrofolate reductase activity    Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor 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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004799    thymidylate synthase activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dUMP = 7,8-dihydrofolate + thymidylate.
    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.
biological process
    GO:0006231    dTMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate).
    GO:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    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:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0046654    tetrahydrofolate biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.

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 Related Entries

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

UniProtKB/TrEMBL
        A7UD81_PLAFA | A7UD81: 3um5 3um6 3um8 4dpd

(-) Related Entries Specified in the PDB File

1j3i WILD-TYPE PFDHFR-TS COMPLEXED WITH WR99210, NADPH, AND DUMP
1j3j DOUBLE MUTANT PFDHFR-TS (C59R+S108N) COMPLEXED WITH PYRIMETHAMINE, NADPH, AND DUMP
1j3k QUADRUPLE MUTANT PFDHFR-TS(N51I+C59R+S108N+I164L) COMPLEXED WITH WR99210, NADPH, AND DUMP
3dg8 QUADRUPLE MUTANT PFDHFR-TS(N51I+C59R+S108N+I164L) COMPLEXED WITH RJF670, NADPH, AND DUMP
3dga WILD-TYPE PFDHFR-TS COMPLEXED WITH RJF01302, NADPH, AND DUMP
3jsu QUADRUPLE MUTANT(N51I+C59R+S108N+I164L) PLASMODIUM FALCIPARUM DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE(PFDHFR-TS) COMPLEXED WITH QN254, NADPH, AND DUMP
3qfx
3qg2
3rg9