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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BACILLUS CEREUS ENOYL-ACYL CARRIER PROTEIN REDUCTASE WITH NADP+ AND INDOLE NAPHTHYRIDINONE (COMPLEX FORM)
 
Authors :  S. J. Kim, B. H. Ha, K. H. Kim, S. K. Hong, S. W. Suh, E. E. Kim
Date :  22 Aug 10  (Deposition) - 08 Sep 10  (Release) - 13 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Enoyl-Acp Reductase, Tetramer, Rossmann Fold, Nad(P) Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. J. Kim, B. H. Ha, K. H. Kim, S. K. Hong, K. J. Shin, S. W. Suh, E. E. Kim
Dimeric And Tetrameric Forms Of Enoyl-Acyl Carrier Protein Reductase From Bacillus Cereus
Biochem. Biophys. Res. Commun. V. 400 517 2010
PubMed-ID: 20800575  |  Reference-DOI: 10.1016/J.BBRC.2010.08.083

(-) Compounds

Molecule 1 - ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE (FABL) (NADPH)
    ChainsA, D, B, C
    EC Number1.3.1.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneBC_1216
    Organism ScientificBACILLUS CEREUS
    Organism Taxid226900
    StrainATCC 14579/DSM31
    SynonymENOYL-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
1IMJ4Ligand/Ion(2E)-N-[(1,2-DIMETHYL-1H-INDOL-3-YL)METHYL]-N-METHYL-3-(7-OXO-5,6,7,8-TETRAHYDRO-1,8-NAPHTHYRIDIN-3-YL)PROP-2-ENAMIDE
2NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:96 , ALA A:97 , TYR A:147 , VAL A:154 , TYR A:157 , SER A:197 , HOH A:271 , NDP A:501BINDING SITE FOR RESIDUE IMJ A 801
2AC2SOFTWAREGLY A:13 , ALA A:15 , SER A:19 , ILE A:20 , ALA A:40 , LEU A:44 , CYS A:65 , ASP A:66 , VAL A:67 , CYS A:93 , ILE A:94 , ALA A:95 , ILE A:120 , LEU A:145 , THR A:146 , TYR A:147 , LYS A:164 , ALA A:190 , GLY A:191 , PRO A:192 , ILE A:193 , THR A:195 , LEU A:196 , SER A:197 , HOH A:267 , HOH A:313 , HOH A:314 , HOH A:315 , HOH A:325 , IMJ A:801BINDING SITE FOR RESIDUE NDP A 501
3AC3SOFTWAREPHE D:96 , ALA D:97 , TYR D:147 , ASN D:156 , TYR D:157 , PRO D:192 , SER D:197 , VAL D:201 , HOH D:272 , NDP D:502BINDING SITE FOR RESIDUE IMJ D 802
4AC4SOFTWAREGLY D:13 , ALA D:15 , SER D:19 , ILE D:20 , ALA D:40 , ARG D:43 , LEU D:44 , CYS D:65 , ASP D:66 , VAL D:67 , CYS D:93 , ILE D:94 , ALA D:95 , ILE D:120 , LEU D:145 , THR D:146 , TYR D:147 , LYS D:164 , ALA D:190 , GLY D:191 , PRO D:192 , ILE D:193 , THR D:195 , SER D:197 , HOH D:270 , HOH D:273 , HOH D:337 , HOH D:338 , HOH D:339 , HOH D:340 , IMJ D:802BINDING SITE FOR RESIDUE NDP D 502
5AC5SOFTWAREPHE B:96 , ALA B:97 , ARG B:99 , TYR B:147 , TYR B:157 , SER B:197 , VAL B:201 , HOH B:291 , HOH B:300 , NDP B:503BINDING SITE FOR RESIDUE IMJ B 803
6AC6SOFTWAREGLY B:13 , ALA B:15 , SER B:19 , ILE B:20 , LEU B:44 , CYS B:65 , ASP B:66 , VAL B:67 , CYS B:93 , ILE B:94 , ALA B:95 , ILE B:120 , LEU B:145 , THR B:146 , LYS B:164 , ALA B:190 , GLY B:191 , PRO B:192 , ILE B:193 , THR B:195 , LEU B:196 , SER B:197 , HOH B:264 , HOH B:282 , HOH B:286 , HOH B:287 , IMJ B:803BINDING SITE FOR RESIDUE NDP B 503
7AC7SOFTWAREPHE C:96 , ALA C:97 , TYR C:147 , ASN C:156 , TYR C:157 , PRO C:192 , SER C:197 , HOH C:307 , NDP C:504BINDING SITE FOR RESIDUE IMJ C 804
8AC8SOFTWAREGLY C:13 , VAL C:14 , ALA C:15 , SER C:19 , ILE C:20 , ALA C:40 , LEU C:44 , CYS C:65 , ASP C:66 , VAL C:67 , CYS C:93 , ILE C:94 , ALA C:95 , ILE C:120 , LEU C:145 , THR C:146 , TYR C:147 , LYS C:164 , ALA C:190 , GLY C:191 , PRO C:192 , ILE C:193 , THR C:195 , LEU C:196 , SER C:197 , HOH C:269 , HOH C:296 , HOH C:310 , HOH C:312 , IMJ C:804BINDING SITE FOR RESIDUE NDP C 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OJF)

(-) 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:257
 aligned with FABI_BACCR | Q81GI3 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:257
                                                                                                                                                                                                                                                                                         256 
                                    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     | 
           FABI_BACCR     1 MELLQGKTFVVMGVANQRSIAWGIARSLHNAGAKLIFTYAGERLERNVRELADTLEGQESLVLPCDVTNDEELTACFETIKQEVGTIHGVAHCIAFANRDDLKGEFVDTSRDGFLLAQNISAFSLTAVAREAKKVMTEGGNILTLTYLGGERVVKNYNVMGVAKASLEASVKYLANDLGQHGIRVNAISAGPIRTLSAKGVGDFNSILREIEERAPLRRTTTQEEVGDTAVFLFSDLARGVTGENIHVDSGYHILG-   -
               SCOP domains d3ojfa_ A: Enoyl-ACP reductase                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee......hhhhhhhhhhhh...eeeeee....hhhhhhhhhhhh......eee....hhhhhhhhhhhhhhhhh...eeee.....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ojf A   1 MELLQGKTFVVMGVANQRSIAWGIARSLHNAGAKLIFTYAGERLERNVRELADTLEGQESLVLPCDVTNDEELTACFETIKQEVGTIHGVAHCIAFANRDDLKGEFVDTSRDGFLLAQNISAFSLTAVAREAKKVMTEGGNILTLTYLGGERVVKNYNVMGVAKASLEASVKYLANDLGQHGIRVNAISAGPIRTLSAKGVGDFNSILREIEERAPLRRTTTQEEVGDTAVFLFSDLARGVTGENIHVDSGYHILGL 257
                                    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 B from PDB  Type:PROTEIN  Length:256
 aligned with FABI_BACCR | Q81GI3 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:256
                                                                                                                                                                                                                                                                                        256 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251    | 
           FABI_BACCR     2 ELLQGKTFVVMGVANQRSIAWGIARSLHNAGAKLIFTYAGERLERNVRELADTLEGQESLVLPCDVTNDEELTACFETIKQEVGTIHGVAHCIAFANRDDLKGEFVDTSRDGFLLAQNISAFSLTAVAREAKKVMTEGGNILTLTYLGGERVVKNYNVMGVAKASLEASVKYLANDLGQHGIRVNAISAGPIRTLSAKGVGDFNSILREIEERAPLRRTTTQEEVGDTAVFLFSDLARGVTGENIHVDSGYHILG-   -
               SCOP domains d3ojfb_ B: Enoyl-ACP reductase                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee......hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh.......eee....hhhhhhhhhhhhhhhhh...eeee.....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ojf B   2 ELLQGKTFVVMGVANQRSIAWGIARSLHNAGAKLIFTYAGERLERNVRELADTLEGQESLVLPCDVTNDEELTACFETIKQEVGTIHGVAHCIAFANRDDLKGEFVDTSRDGFLLAQNISAFSLTAVAREAKKVMTEGGNILTLTYLGGERVVKNYNVMGVAKASLEASVKYLANDLGQHGIRVNAISAGPIRTLSAKGVGDFNSILREIEERAPLRRTTTQEEVGDTAVFLFSDLARGVTGENIHVDSGYHILGL 257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      

Chain C from PDB  Type:PROTEIN  Length:256
 aligned with FABI_BACCR | Q81GI3 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:256
                                                                                                                                                                                                                                                                                        256 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251    | 
           FABI_BACCR     2 ELLQGKTFVVMGVANQRSIAWGIARSLHNAGAKLIFTYAGERLERNVRELADTLEGQESLVLPCDVTNDEELTACFETIKQEVGTIHGVAHCIAFANRDDLKGEFVDTSRDGFLLAQNISAFSLTAVAREAKKVMTEGGNILTLTYLGGERVVKNYNVMGVAKASLEASVKYLANDLGQHGIRVNAISAGPIRTLSAKGVGDFNSILREIEERAPLRRTTTQEEVGDTAVFLFSDLARGVTGENIHVDSGYHILG-   -
               SCOP domains d3ojfc_ C: Enoyl-ACP reductase                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee......hhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh......eee....hhhhhhhhhhhhhhhh....eeee.....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ojf C   2 ELLQGKTFVVMGVANQRSIAWGIARSLHNAGAKLIFTYAGERLERNVRELADTLEGQESLVLPCDVTNDEELTACFETIKQEVGTIHGVAHCIAFANRDDLKGEFVDTSRDGFLLAQNISAFSLTAVAREAKKVMTEGGNILTLTYLGGERVVKNYNVMGVAKASLEASVKYLANDLGQHGIRVNAISAGPIRTLSAKGVGDFNSILREIEERAPLRRTTTQEEVGDTAVFLFSDLARGVTGENIHVDSGYHILGL 257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      

Chain D from PDB  Type:PROTEIN  Length:256
 aligned with FABI_BACCR | Q81GI3 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:256
                                                                                                                                                                                                                                                                                        256 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251    | 
           FABI_BACCR     2 ELLQGKTFVVMGVANQRSIAWGIARSLHNAGAKLIFTYAGERLERNVRELADTLEGQESLVLPCDVTNDEELTACFETIKQEVGTIHGVAHCIAFANRDDLKGEFVDTSRDGFLLAQNISAFSLTAVAREAKKVMTEGGNILTLTYLGGERVVKNYNVMGVAKASLEASVKYLANDLGQHGIRVNAISAGPIRTLSAKGVGDFNSILREIEERAPLRRTTTQEEVGDTAVFLFSDLARGVTGENIHVDSGYHILG-   -
               SCOP domains d3ojfd_ D: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------adh_short_C2-3ojfD01 D:13-253                                                                                                                                                                                                                    ---- Pfam domains (1)
           Pfam domains (2) -----------adh_short_C2-3ojfD02 D:13-253                                                                                                                                                                                                                    ---- Pfam domains (2)
           Pfam domains (3) -----------adh_short_C2-3ojfD03 D:13-253                                                                                                                                                                                                                    ---- Pfam domains (3)
           Pfam domains (4) -----------adh_short_C2-3ojfD04 D:13-253                                                                                                                                                                                                                    ---- Pfam domains (4)
         Sec.struct. author ......eeeee......hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh........eee....hhhhhhhhhhhhhhhhh...eeee.....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ojf D   2 ELLQGKTFVVMGVANQRSIAWGIARSLHNAGAKLIFTYAGERLERNVRELADTLEGQESLVLPCDVTNDEELTACFETIKQEVGTIHGVAHCIAFANRDDLKGEFVDTSRDGFLLAQNISAFSLTAVAREAKKVMTEGGNILTLTYLGGERVVKNYNVMGVAKASLEASVKYLANDLGQHGIRVNAISAGPIRTLSAKGVGDFNSILREIEERAPLRRTTTQEEVGDTAVFLFSDLARGVTGENIHVDSGYHILGL 257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (FABI_BACCR | Q81GI3)
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: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
        FABI_BACCR | Q81GI33oje

(-) Related Entries Specified in the PDB File

3oje THE BACILLUS CEREUS ENOYL-ACYL CARRIER PROTEIN REDUCTASE (APO FORM)