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(-) Description

Title :  CRYSTAL STRUCTURE OF ENOYL-ACP REDUCTASES III (FABL) FROM B. SUBTILIS (COMPLEX WITH NADP AND TCL)
 
Authors :  K. -H. Kim, B. H. Ha, S. J. Kim, S. K. Hong, K. Y. Hwang, E. E. Kim
Date :  19 Aug 10  (Deposition) - 05 Jan 11  (Release) - 16 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Fatty Acid Synthesis, Enoyl-Acp Reductases, Fabl, Rossmann-Like Fold, Nadph Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. -H. Kim, B. H. Ha, S. J. Kim, S. K. Hong, K. Y. Hwang, E. E. Kim
Crystal Structures Of Enoyl-Acp Reductases I (Fabi) And Iii (Fabl) From B. Subtilis
J. Mol. Biol. V. 406 403 2011
PubMed-ID: 21185310  |  Reference-DOI: 10.1016/J.JMB.2010.12.003

(-) Compounds

Molecule 1 - ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
    ChainsA, B, C, D
    EC Number1.3.1.10
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneFABL
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    Strain168
    SynonymFABL, ENOYL-ACP REDUCTASES III, ENOYL-ACYL CARRIER PROTEIN REDUCTASE III, NADPH-DEPENDENT ENOYL-ACP REDUCTASE

 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
1NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2TCL4Ligand/IonTRICLOSAN

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:91 , SER A:92 , GLY A:93 , TYR A:151 , ALA A:191 , LEU A:192 , HIS A:194 , PHE A:195 , NDP A:501BINDING SITE FOR RESIDUE TCL A 601
2AC2SOFTWAREGLY A:11 , SER A:13 , ARG A:14 , GLY A:15 , VAL A:16 , ASN A:34 , TYR A:35 , ALA A:36 , ARG A:37 , SER A:38 , ALA A:61 , ASN A:62 , VAL A:63 , ASN A:89 , ALA A:90 , ALA A:91 , ILE A:112 , ILE A:139 , SER A:140 , SER A:141 , LYS A:158 , GLY A:184 , GLY A:185 , ALA A:186 , ILE A:187 , THR A:189 , ALA A:191 , LEU A:192 , HOH A:270 , HOH A:287 , HOH A:316 , HOH A:325 , HOH A:478 , TCL A:601BINDING SITE FOR RESIDUE NDP A 501
3AC3SOFTWARESER B:92 , GLY B:93 , TYR B:151 , ALA B:191 , LEU B:192 , HIS B:194 , PHE B:195 , NDP B:503BINDING SITE FOR RESIDUE TCL B 603
4AC4SOFTWAREGLY B:11 , SER B:13 , ARG B:14 , GLY B:15 , VAL B:16 , ASN B:34 , ALA B:36 , ARG B:37 , SER B:38 , ALA B:61 , ASN B:62 , VAL B:63 , ASN B:89 , ALA B:90 , ALA B:91 , ILE B:112 , ILE B:139 , SER B:140 , SER B:141 , LYS B:158 , GLY B:184 , GLY B:185 , ALA B:186 , ILE B:187 , THR B:189 , ALA B:191 , HOH B:263 , HOH B:278 , HOH B:293 , HOH B:442 , HOH B:443 , HOH B:446 , HOH B:548 , TCL B:603BINDING SITE FOR RESIDUE NDP B 503
5AC5SOFTWAREALA C:91 , SER C:92 , GLY C:93 , TYR C:151 , ALA C:191 , HIS C:194 , PHE C:195 , NDP C:504BINDING SITE FOR RESIDUE TCL C 604
6AC6SOFTWAREGLY C:11 , SER C:13 , ARG C:14 , GLY C:15 , VAL C:16 , ASN C:34 , ALA C:36 , ARG C:37 , SER C:38 , ALA C:61 , ASN C:62 , VAL C:63 , ASN C:89 , ALA C:90 , ALA C:91 , ILE C:112 , ILE C:139 , SER C:140 , SER C:141 , LYS C:158 , GLY C:184 , GLY C:185 , ALA C:186 , ILE C:187 , THR C:189 , ALA C:191 , HOH C:261 , HOH C:281 , HOH C:379 , HOH C:380 , HOH C:381 , HOH C:432 , TCL C:604BINDING SITE FOR RESIDUE NDP C 504
7AC7SOFTWARESER D:92 , GLY D:93 , TYR D:151 , ALA D:191 , LEU D:192 , PHE D:195 , NDP D:502BINDING SITE FOR RESIDUE TCL D 602
8AC8SOFTWAREGLY D:11 , SER D:13 , ARG D:14 , GLY D:15 , VAL D:16 , ASN D:34 , ALA D:36 , ARG D:37 , SER D:38 , ALA D:61 , ASN D:62 , VAL D:63 , ASN D:89 , ALA D:90 , ALA D:91 , ILE D:112 , ILE D:139 , SER D:140 , SER D:141 , LYS D:158 , GLY D:184 , GLY D:185 , ALA D:186 , ILE D:187 , THR D:189 , ALA D:191 , HOH D:262 , HOH D:288 , HOH D:305 , HOH D:326 , HOH D:327 , HOH D:328 , HOH D:329 , TCL D:602BINDING SITE FOR RESIDUE NDP D 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OID)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OID)

(-) 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:249
 aligned with FABL_BACSU | P71079 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:249
                                                                                                                                                                                                                                                                                 250 
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       | 
           FABL_BACSU     3 QNKCALVTGSSRGVGKAAAIRLAENGYNIVINYARSKKAALETAEEIEKLGVKVLVVKANVGQPAKIKEMFQQIDETFGRLDVFVNNAASGVLRPVMELEETHWDWTMNINAKALLFCAQEAAKLMEKNGGGHIVSISSLGSIRYLENYTTVGVSKAALEALTRYLAVELSPKQIIVNAVSGGAIDTDALKHFPNREDLLEDARQNTPAGRMVEIKDMVDTVEFLVSSKADMIRGQTIIVDGGRSLLV-   -
               SCOP domains d3oida_ A: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee....hhhhhhh.hhhhhhhhhhhhh......hhhhhhhhhhhhh..........eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oid A   3 QNKCALVTGSSRGVGKAAAIRLAENGYNIVINYARSKKAALETAEEIEKLGVKVLVVKANVGQPAKIKEMFQQIDETFGRLDVFVNNAASGVLRPVMELEETHWDWTMNINAKALLFCAQEAAKLMEKNGGGHIVSISSLGSIRYLENYTTVGVSKAALEALTRYLAVELSPKQIIVNAVSGGAIDTDALKHFPNREDLLEDARQNTPAGRMVEIKDMVDTVEFLVSSKADMIRGQTIIVDGGRSLLVL 251
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242         

Chain B from PDB  Type:PROTEIN  Length:251
 aligned with FABL_BACSU | P71079 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:251
                                                                                                                                                                                                                                                                                   250 
                                    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 
           FABL_BACSU     1 MEQNKCALVTGSSRGVGKAAAIRLAENGYNIVINYARSKKAALETAEEIEKLGVKVLVVKANVGQPAKIKEMFQQIDETFGRLDVFVNNAASGVLRPVMELEETHWDWTMNINAKALLFCAQEAAKLMEKNGGGHIVSISSLGSIRYLENYTTVGVSKAALEALTRYLAVELSPKQIIVNAVSGGAIDTDALKHFPNREDLLEDARQNTPAGRMVEIKDMVDTVEFLVSSKADMIRGQTIIVDGGRSLLV-   -
               SCOP domains d3oidb_ B: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee....hhhhhhh.hhhhhhhhhhhhh......hhhhhhhhhhhhh..........eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oid B   1 MEQNKCALVTGSSRGVGKAAAIRLAENGYNIVINYARSKKAALETAEEIEKLGVKVLVVKANVGQPAKIKEMFQQIDETFGRLDVFVNNAASGVLRPVMELEETHWDWTMNINAKALLFCAQEAAKLMEKNGGGHIVSISSLGSIRYLENYTTVGVSKAALEALTRYLAVELSPKQIIVNAVSGGAIDTDALKHFPNREDLLEDARQNTPAGRMVEIKDMVDTVEFLVSSKADMIRGQTIIVDGGRSLLVL 251
                                    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 

Chain C from PDB  Type:PROTEIN  Length:248
 aligned with FABL_BACSU | P71079 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:248
                                                                                                                                                                                                                                                                                250 
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243      | 
           FABL_BACSU     4 NKCALVTGSSRGVGKAAAIRLAENGYNIVINYARSKKAALETAEEIEKLGVKVLVVKANVGQPAKIKEMFQQIDETFGRLDVFVNNAASGVLRPVMELEETHWDWTMNINAKALLFCAQEAAKLMEKNGGGHIVSISSLGSIRYLENYTTVGVSKAALEALTRYLAVELSPKQIIVNAVSGGAIDTDALKHFPNREDLLEDARQNTPAGRMVEIKDMVDTVEFLVSSKADMIRGQTIIVDGGRSLLV-   -
               SCOP domains d3oidc_ C: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee....hhhhhhh.hhhhhhhhhhhhh......hhhhhhhhhhhhh..........eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oid C   4 NKCALVTGSSRGVGKAAAIRLAENGYNIVINYARSKKAALETAEEIEKLGVKVLVVKANVGQPAKIKEMFQQIDETFGRLDVFVNNAASGVLRPVMELEETHWDWTMNINAKALLFCAQEAAKLMEKNGGGHIVSISSLGSIRYLENYTTVGVSKAALEALTRYLAVELSPKQIIVNAVSGGAIDTDALKHFPNREDLLEDARQNTPAGRMVEIKDMVDTVEFLVSSKADMIRGQTIIVDGGRSLLVL 251
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243        

Chain D from PDB  Type:PROTEIN  Length:248
 aligned with FABL_BACSU | P71079 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:248
                                                                                                                                                                                                                                                                                250 
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243      | 
           FABL_BACSU     4 NKCALVTGSSRGVGKAAAIRLAENGYNIVINYARSKKAALETAEEIEKLGVKVLVVKANVGQPAKIKEMFQQIDETFGRLDVFVNNAASGVLRPVMELEETHWDWTMNINAKALLFCAQEAAKLMEKNGGGHIVSISSLGSIRYLENYTTVGVSKAALEALTRYLAVELSPKQIIVNAVSGGAIDTDALKHFPNREDLLEDARQNTPAGRMVEIKDMVDTVEFLVSSKADMIRGQTIIVDGGRSLLV-   -
               SCOP domains d3oidd_ D: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------adh_short_C2-3oidD01 D:10-247                                                                                                                                                                                                                 ---- Pfam domains (1)
           Pfam domains (2) ------adh_short_C2-3oidD02 D:10-247                                                                                                                                                                                                                 ---- Pfam domains (2)
           Pfam domains (3) ------adh_short_C2-3oidD03 D:10-247                                                                                                                                                                                                                 ---- Pfam domains (3)
           Pfam domains (4) ------adh_short_C2-3oidD04 D:10-247                                                                                                                                                                                                                 ---- Pfam domains (4)
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee....hhhhhhh.hhhhhhhhhhhhh......hhhhhhhhhhhhh..........eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oid D   4 NKCALVTGSSRGVGKAAAIRLAENGYNIVINYARSKKAALETAEEIEKLGVKVLVVKANVGQPAKIKEMFQQIDETFGRLDVFVNNAASGVLRPVMELEETHWDWTMNINAKALLFCAQEAAKLMEKNGGGHIVSISSLGSIRYLENYTTVGVSKAALEALTRYLAVELSPKQIIVNAVSGGAIDTDALKHFPNREDLLEDARQNTPAGRMVEIKDMVDTVEFLVSSKADMIRGQTIIVDGGRSLLVL 251
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243        

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (FABL_BACSU | P71079)
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: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: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:0030497    fatty acid elongation    The elongation of a fatty acid chain by the sequential addition of two-carbon units.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    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:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FABL_BACSU | P710793oic

(-) Related Entries Specified in the PDB File

3oic ENOYL-ACP REDUCTASES III, APO-FORM
3oif ENOYL-ACP REDUCTASES I IN COMPLEX WITH NAD AND TRICLOSAN
3oig ENOYL-ACP REDUCTASES I IN COMPLEX WITH NAD AND INHIBITOR