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(-) Description

Title :  SP21 DOUBLE MUTANT P. VIVAX DIHYDROFOLATE REDUCTASE IN COMPLEX WITH DES-CHLOROPYRIMETHAMINE
 
Authors :  P. Kongsaeree, P. Khongsuk, U. Leartsakulpanich, P. Chitnumsub, B. Tarnchompoo, M. D. Walkinshaw, Y. Yuthavong
Date :  03 Mar 05  (Deposition) - 07 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Dihydrofolate Reductase, Plasmodium Vivax, Malaria, Drug Resistance, Thymidylate Synthase, Pyrimethamine, Double Mutant, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Kongsaeree, P. Khongsuk, U. Leartsakulpanich, P. Chitnumsub, B. Tarnchompoo, M. D. Walkinshaw, Y. Yuthavong
Crystal Structure Of Dihydrofolate Reductase From Plasmodium Vivax: Pyrimethamine Displacement Linked With Mutation-Induced Resistance.
Proc. Natl. Acad. Sci. Usa V. 102 13046 2005
PubMed-ID: 16135570  |  Reference-DOI: 10.1073/PNAS.0501747102

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE
    ChainsA
    EC Number1.5.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificPLASMODIUM VIVAX
    Organism Taxid5855
    SynonymDIHYDROFOLATE REDUCTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CP71Ligand/Ion6-ETHYL-5-PHENYLPYRIMIDINE-2,4-DIAMINE
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:14 , ALA A:15 , LEU A:39 , GLY A:40 , GLY A:43 , THR A:44 , GLY A:114 , ARG A:115 , SER A:116 , ASN A:117 , LEU A:136 , SER A:137 , LYS A:138 , THR A:139 , ASP A:153 , SER A:154 , ILE A:173 , GLY A:174 , GLY A:175 , ALA A:176 , GLN A:177 , VAL A:178 , TYR A:179 , CP7 A:1240 , HOH A:2117 , HOH A:2172 , HOH A:2207 , HOH A:2208 , HOH A:2209BINDING SITE FOR RESIDUE NDP A1239
2AC2SOFTWAREILE A:13 , CYS A:14 , ALA A:15 , ASP A:53 , MET A:54 , PHE A:57 , ASN A:117 , ILE A:173 , THR A:194 , NDP A:1239BINDING SITE FOR RESIDUE CP7 A1240
3AC3SOFTWAREMET A:54 , ARG A:58 , ARG A:131BINDING SITE FOR RESIDUE MES A1241

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:126 -Pro A:127
2Gly A:174 -Gly A:175

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_DRTS_PLAVI_001 *S58RDRTS_PLAVI  ---  ---AR58R
2UniProtVAR_DRTS_PLAVI_002 *S117NDRTS_PLAVI  ---  ---AN117N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHFR_2PS51330 Dihydrofolate reductase (DHFR) domain profile.DRTS_PLAVI9-237  1A:9-237
2DHFR_1PS00075 Dihydrofolate reductase (DHFR) domain signature.DRTS_PLAVI38-61  1A:38-61

(-) Exons   (0, 0)

(no "Exon" information available for 2BLC)

(-) 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:215
 aligned with DRTS_PLAVI | O02604 from UniProtKB/Swiss-Prot  Length:623

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           DRTS_PLAVI     2 EDLSDVFDIYAICACCKVAPTSEGTKNEPFSPRTFRGLGNKGTLPWKCNSVDMKYFSSVTTYVDESKYEKLKWKRERYLRMEASQGGGDNTSGGDNTHGGDNADKLQNVVVMGRSSWESIPKQYKPLPNRINVVLSKTLTKEDVKEKVFIIDSIDDLLLLLKKLKYYKCFIIGGAQVYRECLSRNLIKQIYFTRINGAYPCDVFFPEFDESQFRVTSVSEVYNSKGTTLDFLVYSKV 238
               SCOP domains d2blca_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2blcA00 A:2-238 Dihydrofolate Reductase, subunit A                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.eeeeeeeeee................eeeee.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh----------------------....eeeeehhhhhhhhhhhh.....eeeee.............eee.hhhhhhhhhhh.....eee..hhhhhhhhhhh....eeeeeeeeeee...ee....hhh...............eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------R----------------------------------------------------------N------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------DHFR_2  PDB: A:9-237 UniProt: 9-237                                                                                                                                                                                                  - PROSITE (1)
                PROSITE (2) ------------------------------------DHFR_1  PDB: A:38-61    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2blc A   2 ENLSDVFDIYAICACCKVAPTSEGTKNEPFSPRTFRGLGNKGTLPWKCNSVDMKYFRSVTTYVDESKYEKLKWKRERYLRME----------------------KLQNVVVMGRSNWESIPKQYKPLPNRINVVLSKTLTKEDVKEKVFIIDSIDDLLLLLKKLKYYKCFIIGGAQVYRECLSRNLIKQIYFTRINGAYPCDVFFPEFDESEFRVTSVSEVYNSKGTTLDFLVYSKV 238
                                    11        21        31        41        51        61        71        81 |       -         -    |  111       121       131       141       151       161       171       181       191       201       211       221       231       
                                                                                                            83                    106                                                                                                                                    

Chain A from PDB  Type:PROTEIN  Length:215
 aligned with Q5U9H1_PLAVI | Q5U9H1 from UniProtKB/TrEMBL  Length:237

    Alignment length:237
                                                                                                                                                                                                                                                                     237 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     | 
         Q5U9H1_PLAVI     2 EDLSDVFDIYAICACCKVAPTSEGTKNEPFSPRTFRGLGNKGTLPWKCNSVDMKYFRSVTTYVDESKYEKLKWKRERYLRMEASQGGGDNTSGGDNTSGGDNADKLQNVVVMGRSNWESIPKQYKPLPNRINVVLSKTLTKEDVKEKVFIIDSIDDLLLLLKKLKYYKCFIIGGAQVYRECLSRNLIKQIYFTRINGAYPCDVFFPEFDESQFRVTSVSEVYNSKGTTLDFLVYSK-   -
               SCOP domains d2blca_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2blcA00 A:2-238 Dihydrofolate Reductase, subunit A                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.eeeeeeeeee................eeeee.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh----------------------....eeeeehhhhhhhhhhhh.....eeeee.............eee.hhhhhhhhhhh.....eee..hhhhhhhhhhh....eeeeeeeeeee...ee....hhh...............eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------R----------------------------------------------------------N------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2blc A   2 ENLSDVFDIYAICACCKVAPTSEGTKNEPFSPRTFRGLGNKGTLPWKCNSVDMKYFRSVTTYVDESKYEKLKWKRERYLRME----------------------KLQNVVVMGRSNWESIPKQYKPLPNRINVVLSKTLTKEDVKEKVFIIDSIDDLLLLLKKLKYYKCFIIGGAQVYRECLSRNLIKQIYFTRINGAYPCDVFFPEFDESEFRVTSVSEVYNSKGTTLDFLVYSKV 238
                                    11        21        31        41        51        61        71        81 |       -         -    |  111       121       131       141       151       161       171       181       191       201       211       221       231       
                                                                                                            83                    106                                                                                                                                    

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BLC)

(-) Gene Ontology  (15, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5U9H1_PLAVI | Q5U9H1)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0004146    dihydrofolate reductase activity    Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
    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.
biological process
    GO:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    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: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.

Chain A   (DRTS_PLAVI | O02604)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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: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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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/Swiss-Prot
        DRTS_PLAVI | O026042bl9 2bla 2blb
        Q5U9H1_PLAVI | Q5U9H12bla

(-) Related Entries Specified in the PDB File

2bl9 X-RAY CRYSTAL STRUCTURE OF PLASMODIUM VIVAX DIHYDROFOLATE REDUCTASE IN COMPLEX WITH PYRIMETHAMINE AND ITS DERIVATIVE
2bla SP21 DOUBLE MUTANT P. VIVAX DIHYDROFOLATE REDUCTASE IN COMPLEX WITH PYRIMETHAMINE
2blb X-RAY CRYSTAL STRUCTURE OF PLASMODIUM VIVAX DIHYDROFOLATE REDUCTASE IN COMPLEX WITH PYRIMETHAMINE AND ITS DERIVATIVE