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(-) Description

Title :  SYNTHESIS, BIOLOGICAL ACTIVITY, AND X-RAY CRYSTAL STRUCTURAL ANALYSIS OF DIARYL ETHER INHIBITORS OF MALARIAL ENOYL ACP REDUCTASE.
 
Authors :  J. S. Freundlich, H. Shieh, J. W. Anderson, M. Kuo, M. Yu, J. Valderramos L. Karagyozov, H. Tsai, E. Lucumi, W. R. Jacobs Jr. , G. A. Schiehser, D. P. Jacobus, D. A. Fidock, J. C. Sacchettini
Date :  13 Jan 06  (Deposition) - 16 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B,C,D  (2x)
Keywords :  Enoyl Reductase, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Freundlich, F. Wang, H. C. Tsai, M. Kuo, H. M. Shieh, J. W. Anderson L. J. Nkrumah, J. C. Valderramos, M. Yu, T. R. Kumar, S. G. Valderramos, W. R. Jacobs, G. A. Schiehser, D. P. Jacobus, D. A. Fidock, J. C. Sacchettini
X-Ray Structural Analysis Of Plasmodium Falciparum Enoyl Acyl Carrier Protein Reductase As A Pathway Toward The Optimization Of Triclosan Antimalarial Efficacy.
J. Biol. Chem. V. 282 25436 2007
PubMed-ID: 17567585  |  Reference-DOI: 10.1074/JBC.M701813200

(-) Compounds

Molecule 1 - ENOYL-ACYL CARRIER REDUCTASE
    Chains: A, B
    EC Number: 1.3.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3) CODON+-RIL CELLS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL FRAGMENT, RESIDUES 97-216
    Gene: PFENR
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7
 
Molecule 2 - ENOYL-ACYL CARRIER REDUCTASE
    Chains: C, D
    EC Number: 1.3.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3) CODON+-RIL CELLS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL FRAGMENT, RESIDUES 97-156
    Gene: PFENR
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1JPA2Ligand/Ion4-(2,4-DICHLOROPHENOXY)-2'-METHYLBIPHENYL-3-OL
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1JPA2Ligand/Ion4-(2,4-DICHLOROPHENOXY)-2'-METHYLBIPHENYL-3-OL
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1JPA4Ligand/Ion4-(2,4-DICHLOROPHENOXY)-2'-METHYLBIPHENYL-3-OL
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:24 , HOH A:28 , ILE A:105 , GLY A:106 , GLY A:110 , TYR A:111 , TRP A:131 , PHE A:167 , ASP A:168 , ALA A:169 , SER A:170 , SER A:215 , LEU A:216 , ALA A:217 , ASN A:218 , LYS A:240 , LEU A:265 , THR A:266 , LYS A:285 , ALA A:312 , GLY A:313 , PRO A:314 , LEU A:315 , SER A:317 , ALA A:319 , JPA A:500BINDING SITE FOR RESIDUE NAD A 450
2AC2SOFTWAREGLY B:104 , ILE B:105 , GLY B:106 , GLY B:110 , TYR B:111 , TRP B:131 , PHE B:167 , ASP B:168 , ALA B:169 , SER B:170 , SER B:215 , LEU B:216 , ALA B:217 , ASN B:218 , LEU B:265 , THR B:266 , TYR B:267 , LYS B:285 , ALA B:312 , GLY B:313 , PRO B:314 , LEU B:315 , SER B:317 , ALA B:319 , JPA B:501BINDING SITE FOR RESIDUE NAD B 451
3AC3SOFTWAREALA A:217 , ALA A:219 , VAL A:222 , TYR A:267 , TYR A:277 , PRO A:314 , ALA A:319 , ALA A:320 , ILE A:323 , NAD A:450 , PHE C:368 , ILE C:369 , ALA C:372BINDING SITE FOR RESIDUE JPA A 500
4AC4SOFTWAREALA B:217 , ALA B:219 , TYR B:267 , TYR B:277 , PRO B:314 , ALA B:319 , NAD B:451 , PHE D:368 , ALA D:372BINDING SITE FOR RESIDUE JPA B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FOI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FOI)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FOI)

(-) 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:229
 aligned with C6KSZ2_PLAF7 | C6KSZ2 from UniProtKB/TrEMBL  Length:432

    Alignment length:229
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316         
         C6KSZ2_PLAF7    97 EDICFIAGIGDTNGYGWGIAKELSKRNVKIIFGIWPPVYNIFMKNYKNGKFDNDMIIDKDKKMNILDMLPFDASFDTANDIDEETKNNKRYNMLQNYTIEDVANLIHQKYGKINMLVHSLANAKEVQKDLLNTSRKGYLDALSKSSYSLISLCKYFVNIMKPQSSIISLTYHASQKVVPGYGGGMSSAKAALESDTRVLAYHLGRNYNIRINTISAGPLKSRAATAINK 325
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2foiA00 A:97-325 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhh..hhhhhee...ee..eeeeee......hhhhhhhhhhh..........hhhhhhhhhhhhhh.eeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2foi A  97 EDICFIAGIGDTNGYGWGIAKELSKRNVKIIFGIWPPVYNIFMKNYKNGKFDNDMIIDKDKKMNILDMLPFDASFDTANDIDEETKNNKRYNMLQNYTIEDVANLIHQKYGKINMLVHSLANAKEVQKDLLNTSRKGYLDALSKSSYSLISLCKYFVNIMKPQSSIISLTYHASQKVVPGYGGGMSSAKAALESDTRVLAYHLGRNYNIRINTISAGPLKSRAATAINK 325
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316         


Chain B from PDB  Type:PROTEIN  Length:229
 aligned with C6KSZ2_PLAF7 | C6KSZ2 from UniProtKB/TrEMBL  Length:432

    Alignment length:229
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316         
         C6KSZ2_PLAF7    97 EDICFIAGIGDTNGYGWGIAKELSKRNVKIIFGIWPPVYNIFMKNYKNGKFDNDMIIDKDKKMNILDMLPFDASFDTANDIDEETKNNKRYNMLQNYTIEDVANLIHQKYGKINMLVHSLANAKEVQKDLLNTSRKGYLDALSKSSYSLISLCKYFVNIMKPQSSIISLTYHASQKVVPGYGGGMSSAKAALESDTRVLAYHLGRNYNIRINTISAGPLKSRAATAINK 325
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2foiB00 B:97-325 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhh.......ee...ee..eeeeee......hhhhhhhhhhhh.........hhhhhhhhhhhhhh.eeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2foi B  97 EDICFIAGIGDTNGYGWGIAKELSKRNVKIIFGIWPPVYNIFMKNYKNGKFDNDMIIDKDKKMNILDMLPFDASFDTANDIDEETKNNKRYNMLQNYTIEDVANLIHQKYGKINMLVHSLANAKEVQKDLLNTSRKGYLDALSKSSYSLISLCKYFVNIMKPQSSIISLTYHASQKVVPGYGGGMSSAKAALESDTRVLAYHLGRNYNIRINTISAGPLKSRAATAINK 325
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316         


Chain C from PDB  Type:PROTEIN  Length:60
 aligned with C6KSZ2_PLAF7 | C6KSZ2 from UniProtKB/TrEMBL  Length:432

    Alignment length:60
                                   375       385       395       405       415       425
         C6KSZ2_PLAF7   366 YTFIDYAIEYSEKYAPLRQKLLSTDIGSVASFLLSRESRAITGQTIYVDNGLNIMFLPDD 425
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 2foi C 366 YTFIDYAIEYSEKYAPLRQKLLSTDIGSVASFLLSRESRAITGQTIYVDNGLNIMFLPDD 425
                                   375       385       395       405       415       425


Chain D from PDB  Type:PROTEIN  Length:60
 aligned with C6KSZ2_PLAF7 | C6KSZ2 from UniProtKB/TrEMBL  Length:432

    Alignment length:60
                                   375       385       395       405       415       425
         C6KSZ2_PLAF7   366 YTFIDYAIEYSEKYAPLRQKLLSTDIGSVASFLLSRESRAITGQTIYVDNGLNIMFLPDD 425
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 2foi D 366 YTFIDYAIEYSEKYAPLRQKLLSTDIGSVASFLLSRESRAITGQTIYVDNGLNIMFLPDD 425
                                   375       385       395       405       415       425
   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 2FOI)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (C6KSZ2_PLAF7 | C6KSZ2)
molecular function
    GO:0004318    enoyl-[acyl-carrier-protein] reductase (NADH) activity    Catalysis of the reaction: acyl-[acyl-carrier protein] + NAD+ = trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH + H+.
    GO:0016631    enoyl-[acyl-carrier-protein] reductase activity    Catalysis of the reaction: acyl-[acyl-carrier protein] + NAD(P)+ = trans-2,3-dehydroacyl-[acyl-carrier protein] + NAD(P)H + H+.
    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.
biological process
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    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.
cellular component
    GO:0020011    apicoplast    The plastid organelle found in apicomplexans.

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 Related Entries

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

UniProtKB/TrEMBL
        C6KSZ2_PLAF7 | C6KSZ2: 4ige 4igf

(-) Related Entries Specified in the PDB File

1nhd SAME PROTEIN WITHOUT BOUND INHIBITOR
1nhg SAME PROTEIN BOUND TO TRICLOSAN
1nhw SAME PROTEIN BOUND TO TRICLOSAN ANALOG
1nnu SAME PROTEIN BOUND TO TRICLOSAN ANALOG
1zsn SAME PROTEIN BOUND TO TRICLOSAN ANALOG
1zw1 SAME PROTEIN BOUND TO TRICLOSAN ANALOG