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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM BERGHEI ENOYL-ACYL-CARRIER-PROTEIN REDUCTASE WITH TRICLOSAN
 
Authors :  J. C. Sacchettini, H. -C. Tsai
Date :  31 Oct 08  (Deposition) - 02 Mar 10  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pbenr, Pbfabi, Triclosan, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Yu, T. R. Kumar, L. J. Nkrumah, A. Coppi, S. Retzlaff, C. D. Li, B. J. Kelly, P. A. Moura, V. Lakshmanan, J. S. Freundlich, J. C. Valderramos, C. Vilcheze, M. Siedner, J. H. Tsai, B. Falkard, A. B. Sidhu, L. A. Purcell, P. Gratraud, L. Kremer, A. P. Waters, G. Schiehser, D. P. Jacobus, C. J. Janse, A. Ager, W. R. Jacobs, J. C. Sacchettini, V. Heussler, P. Sinnis, D. A. Fidock
The Fatty Acid Biosynthesis Enzyme Fabi Plays A Key Role In The Development Of Liver-Stage Malarial Parasites.
Cell Host Microbe V. 4 567 2008
PubMed-ID: 19064257  |  Reference-DOI: 10.1016/J.CHOM.2008.11.001

(-) Compounds

Molecule 1 - ENOYL-ACYL CARRIER PROTEIN REDUCTASE
    Chains: A, B, C, D
    EC Number: 1.3.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP16
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 75 TO 396
    Gene: PBFABI
    Organism Scientific: PLASMODIUM BERGHEI
    Organism Taxid: 5821

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2TCL4Ligand/IonTRICLOSAN

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:30 , HOH A:58 , GLY A:87 , VAL A:88 , GLY A:89 , GLY A:93 , TYR A:94 , TRP A:114 , LEU A:152 , ASP A:153 , ALA A:154 , SER A:200 , LEU A:201 , ALA A:202 , ASN A:203 , LEU A:250 , THR A:251 , LYS A:270 , ALA A:297 , GLY A:298 , PRO A:299 , LEU A:300 , SER A:302 , ARG A:303 , ALA A:304 , TCL A:400 , HOH A:418 , HOH A:421 , HOH A:441 , HOH A:454BINDING SITE FOR RESIDUE NAD A 450
2AC2SOFTWAREALA A:202 , GLY A:204 , TYR A:252 , TYR A:262 , LYS A:270 , ALA A:304 , ALA A:305 , ILE A:308 , NAD A:450BINDING SITE FOR RESIDUE TCL A 400
3AC3SOFTWAREHOH D:45 , GLY D:87 , GLY D:89 , GLY D:93 , TYR D:94 , TRP D:114 , LEU D:152 , ASP D:153 , ALA D:154 , SER D:200 , LEU D:201 , ALA D:202 , ASN D:203 , LYS D:225 , LEU D:250 , THR D:251 , LYS D:270 , ALA D:297 , GLY D:298 , PRO D:299 , LEU D:300 , SER D:302 , ALA D:304 , HOH D:401 , HOH D:413 , HOH D:438 , HOH D:441 , HOH D:443 , TCL D:500BINDING SITE FOR RESIDUE NAD D 550
4AC4SOFTWAREALA D:202 , ASN D:203 , GLY D:204 , TYR D:252 , TYR D:262 , ALA D:304 , NAD D:550BINDING SITE FOR RESIDUE TCL D 500
5AC5SOFTWAREHOH C:44 , GLY C:87 , VAL C:88 , GLY C:89 , GLY C:93 , TYR C:94 , TRP C:114 , LEU C:152 , ASP C:153 , ALA C:154 , SER C:200 , LEU C:201 , ALA C:202 , LEU C:250 , THR C:251 , LYS C:270 , ALA C:297 , GLY C:298 , PRO C:299 , LEU C:300 , SER C:302 , ALA C:304 , TCL C:400 , HOH C:408 , HOH C:411 , HOH C:431 , HOH C:440BINDING SITE FOR RESIDUE NAD C 450
6AC6SOFTWAREGLY C:204 , TYR C:252 , TYR C:262 , ALA C:304 , ALA C:305 , NAD C:450BINDING SITE FOR RESIDUE TCL C 400
7AC7SOFTWAREHOH B:35 , VAL B:88 , GLY B:89 , GLY B:93 , TYR B:94 , TRP B:114 , LEU B:152 , ASP B:153 , ALA B:154 , SER B:200 , LEU B:201 , ALA B:202 , ASN B:203 , LEU B:250 , THR B:251 , LYS B:270 , ALA B:297 , GLY B:298 , PRO B:299 , LEU B:300 , SER B:302 , ALA B:304 , HOH B:403 , HOH B:411 , HOH B:416 , HOH B:417 , TCL B:500BINDING SITE FOR RESIDUE NAD B 550
8AC8SOFTWAREALA B:202 , GLY B:204 , TYR B:252 , TYR B:262 , ALA B:304 , ALA B:305 , NAD B:550BINDING SITE FOR RESIDUE TCL B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F4B)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asn B:137 -Asn B:138
2Asp B:139 -Asn B:140
3Asn B:140 -Ser B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F4B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F4B)

(-) Exons   (0, 0)

(no "Exon" information available for 3F4B)

(-) 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:284
 aligned with Q6TEI5_PLABE | Q6TEI5 from UniProtKB/TrEMBL  Length:396

    Alignment length:310
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389
         Q6TEI5_PLABE    80 NEICFIAGVGDSNGYGWGIAKELSKRNVKVIFGVWPPVYNIFIKNLESGKFDKDMIINNDNSKRMQILDVLPLDAGFDNYDDIDEDTKNNKRYNNLKNYSIEEVANLIYNKYGKISMLVHSLANGREVQKSLLDTSRDGYLDAISKSSYSLISLCKHFCKFMNSGGSVVSLTYQASQKVVPGYGGGMSSAKAALESDTRVLAYYLGRKYNIRINTISAGPLKSRAATAINKFNNNQKNNMNSSGETDKQNYSFIDYAIDYSEKYAPLKKKLLSTDVGSVASFLLSKESSAVTGQTIYVDNGLNIMFGPDD 389
               SCOP domains d3f4ba_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhh..hhhhhh.-----....eeeeee......hhhhhhhhhhh..........hhhhhhhhhhhhhh.eeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhh..---------------------hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f4b A  80 NEICFIAGVGDSNGYGWGIAKELSKRNVKVIFGVWPPVYNIFIKNLESGKFDKDMII-----KRMQILDVLPLDAGFDNYDDIDEDTKNNKRYNNLKNYSIEEVANLIYNKYGKISMLVHSLANGREVQKSLLDTSRDGYLDAISKSSYSLISLCKHFCKFMNSGGSVVSLTYQASQKVVPGYGGGMSSAKAALESDTRVLAYYLGRKYNIRINTISAGPLKSRAATAIN---------------------SFIDYAIDYSEKYAPLKKKLLSTDVGSVASFLLSKESSAVTGQTIYVDNGLNIMFGPDD 389
                                    89        99       109       119       129      |  -  |    149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309         -         - |     339       349       359       369       379       389
                                                                                  136   142                                                                                                                                                                    309                   331                                                          


Chain B from PDB  Type:PROTEIN  Length:289
 aligned with Q6TEI5_PLABE | Q6TEI5 from UniProtKB/TrEMBL  Length:396

    Alignment length:310
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389
         Q6TEI5_PLABE    80 NEICFIAGVGDSNGYGWGIAKELSKRNVKVIFGVWPPVYNIFIKNLESGKFDKDMIINNDNSKRMQILDVLPLDAGFDNYDDIDEDTKNNKRYNNLKNYSIEEVANLIYNKYGKISMLVHSLANGREVQKSLLDTSRDGYLDAISKSSYSLISLCKHFCKFMNSGGSVVSLTYQASQKVVPGYGGGMSSAKAALESDTRVLAYYLGRKYNIRINTISAGPLKSRAATAINKFNNNQKNNMNSSGETDKQNYSFIDYAIDYSEKYAPLKKKLLSTDVGSVASFLLSKESSAVTGQTIYVDNGLNIMFGPDD 389
               SCOP domains d3f4bb_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhhh...eeeeeehhhhhhhhhhhhh........ee.....ee..eeeeee...........hhhhhh..........hhhhhhhhhhhhhh.eeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhh.---------------------.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f4b B  80 NEICFIAGVGDSNGYGWGIAKELSKRNVKVIFGVWPPVYNIFIKNLESGKFDKDMIINNDNSKRMQILDVLPLDAGFDNYDDIDEDTKNNKRYNNLKNYSIEEVANLIYNKYGKISMLVHSLANGREVQKSLLDTSRDGYLDAISKSSYSLISLCKHFCKFMNSGGSVVSLTYQASQKVVPGYGGGMSSAKAALESDTRVLAYYLGRKYNIRINTISAGPLKSRAATAI---------------------YSFIDYAIDYSEKYAPLKKKLLSTDVGSVASFLLSKESSAVTGQTIYVDNGLNIMFGPDD 389
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299        |-         -         -|      339       349       359       369       379       389
                                                                                                                                                                                                                                                              308                   330                                                           


Chain C from PDB  Type:PROTEIN  Length:282
 aligned with Q6TEI5_PLABE | Q6TEI5 from UniProtKB/TrEMBL  Length:396

    Alignment length:310
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389
         Q6TEI5_PLABE    80 NEICFIAGVGDSNGYGWGIAKELSKRNVKVIFGVWPPVYNIFIKNLESGKFDKDMIINNDNSKRMQILDVLPLDAGFDNYDDIDEDTKNNKRYNNLKNYSIEEVANLIYNKYGKISMLVHSLANGREVQKSLLDTSRDGYLDAISKSSYSLISLCKHFCKFMNSGGSVVSLTYQASQKVVPGYGGGMSSAKAALESDTRVLAYYLGRKYNIRINTISAGPLKSRAATAINKFNNNQKNNMNSSGETDKQNYSFIDYAIDYSEKYAPLKKKLLSTDVGSVASFLLSKESSAVTGQTIYVDNGLNIMFGPDD 389
               SCOP domains d3f4bc_ C: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh..hhhhhh.------...eeeeee......hhhhhhhhhhh..........hhhhhhhhhhhhhh.eeeeee...............hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhh.----------------------hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f4b C  80 NEICFIAGVGDSNGYGWGIAKELSKRNVKVIFGVWPPVYNIFIKNLESGKFDKDMII------RMQILDVLPLDAGFDNYDDIDEDTKNNKRYNNLKNYSIEEVANLIYNKYGKISMLVHSLANGREVQKSLLDTSRDGYLDAISKSSYSLISLCKHFCKFMNSGGSVVSLTYQASQKVVPGYGGGMSSAKAALESDTRVLAYYLGRKYNIRINTISAGPLKSRAATAI----------------------SFIDYAIDYSEKYAPLKKKLLSTDVGSVASFLLSKESSAVTGQTIYVDNGLNIMFGPDD 389
                                    89        99       109       119       129      |  -   |   149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299        |-         -         - |     339       349       359       369       379       389
                                                                                  136    143                                                                                                                                                                  308                    331                                                          


Chain D from PDB  Type:PROTEIN  Length:289
 aligned with Q6TEI5_PLABE | Q6TEI5 from UniProtKB/TrEMBL  Length:396

    Alignment length:310
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389
         Q6TEI5_PLABE    80 NEICFIAGVGDSNGYGWGIAKELSKRNVKVIFGVWPPVYNIFIKNLESGKFDKDMIINNDNSKRMQILDVLPLDAGFDNYDDIDEDTKNNKRYNNLKNYSIEEVANLIYNKYGKISMLVHSLANGREVQKSLLDTSRDGYLDAISKSSYSLISLCKHFCKFMNSGGSVVSLTYQASQKVVPGYGGGMSSAKAALESDTRVLAYYLGRKYNIRINTISAGPLKSRAATAINKFNNNQKNNMNSSGETDKQNYSFIDYAIDYSEKYAPLKKKLLSTDVGSVASFLLSKESSAVTGQTIYVDNGLNIMFGPDD 389
               SCOP domains d3f4bd_ D: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhh.hhhhh...........eeeeee......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhh.---------------------.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f4b D  80 NEICFIAGVGDSNGYGWGIAKELSKRNVKVIFGVWPPVYNIFIKNLESGKFDKDMIINNDNSKRMQILDVLPLDAGFDNYDDIDEDTKNNKRYNNLKNYSIEEVANLIYNKYGKISMLVHSLANGREVQKSLLDTSRDGYLDAISKSSYSLISLCKHFCKFMNSGGSVVSLTYQASQKVVPGYGGGMSSAKAALESDTRVLAYYLGRKYNIRINTISAGPLKSRAATAI---------------------YSFIDYAIDYSEKYAPLKKKLLSTDVGSVASFLLSKESSAVTGQTIYVDNGLNIMFGPDD 389
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299        |-         -         -|      339       349       359       369       379       389
                                                                                                                                                                                                                                                              308                   330
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F4B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F4B)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q6TEI5_PLABE | Q6TEI5)
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: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.

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 Related Entries

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1nhg