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(-) Description

Title :  CRYSTAL STRUCTURE OF S. AUREUS FABI IN COMPLEX WITH NADPH AND CG400549 (SMALL UNIT CELL)
 
Authors :  J. Schiebel, A. Chang, S. Shah, P. J. Tonge, C. Kisker
Date :  22 Mar 14  (Deposition) - 16 Apr 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Short-Chain Dehydrogenase/Reductase Superfamily, Fatty Acid Biosynthesis, Lipid Synthesis, Safabi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Schiebel, A. Chang, S. Shah, Y. Lu, L. Liu, P. Pan, M. W. Hirschbeck, M. Tareilus, S. Eltschkner, W. Yu, J. E. Cummings, S. E. Knudson, G. R. Bommineni, S. G. Walker, R. A. Slayden, C. A. Sotriffer, P. J. Tonge, C. Kisker
Rational Design Of Broad Spectrum Antibacterial Activity Based On A Clinically Relevant Enoyl-Acyl Carrier Protein (Acp) Reductase Inhibitor.
J. Biol. Chem. V. 289 15987 2014
PubMed-ID: 24739388  |  Reference-DOI: 10.1074/JBC.M113.532804

(-) Compounds

Molecule 1 - ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
    Chains: A, B, C, D
    EC Number: 1.3.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM-11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: N315
    Synonym: ENR, ENOYL-ACP REDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3PT64Ligand/Ion1-(3-AMINO-2-METHYLBENZYL)-4-[2-(THIOPHEN-2-YL)ETHOXY]PYRIDIN-2(1H)-ONE
4SO43Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:13 , ILE A:14 , ALA A:15 , SER A:19 , ILE A:20 , ARG A:40 , LYS A:41 , SER A:44 , ILE A:65 , ASP A:66 , VAL A:67 , SER A:93 , ILE A:94 , ALA A:95 , ILE A:120 , THR A:145 , THR A:146 , TYR A:147 , LYS A:164 , ALA A:190 , PRO A:192 , ILE A:193 , THR A:195 , SER A:197 , PT6 A:1258 , HOH A:2006 , HOH A:2007 , HOH A:2056BINDING SITE FOR RESIDUE NDP A1257
02AC2SOFTWAREGLY B:13 , ILE B:14 , ALA B:15 , SER B:19 , ILE B:20 , ARG B:40 , LYS B:41 , SER B:44 , ILE B:65 , ASP B:66 , VAL B:67 , SER B:93 , ILE B:94 , ALA B:95 , THR B:145 , THR B:146 , TYR B:147 , LYS B:164 , ALA B:190 , GLY B:191 , PRO B:192 , ILE B:193 , THR B:195 , SER B:197 , PT6 B:1258 , HOH B:2012 , HOH B:2013 , HOH B:2014BINDING SITE FOR RESIDUE NDP B1257
03AC3SOFTWAREGLY C:13 , ILE C:14 , ALA C:15 , SER C:19 , ILE C:20 , ARG C:40 , LYS C:41 , SER C:44 , ILE C:65 , ASP C:66 , VAL C:67 , SER C:93 , ILE C:94 , ALA C:95 , ILE C:120 , THR 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 , PHE C:204 , PT6 C:1258 , HOH C:2004 , HOH C:2005 , HOH C:2006BINDING SITE FOR RESIDUE NDP C1257
04AC4SOFTWAREGLY D:13 , ILE D:14 , ALA D:15 , SER D:19 , ILE D:20 , ARG D:40 , LYS D:41 , SER D:44 , ILE D:65 , ASP D:66 , VAL D:67 , SER D:93 , ILE D:94 , ALA D:95 , ILE D:120 , THR D:145 , THR D:146 , TYR D:147 , LYS D:164 , ALA D:190 , PRO D:192 , ILE D:193 , THR D:195 , SER D:197 , PT6 D:1258 , HOH D:2010 , HOH D:2011 , HOH D:2029BINDING SITE FOR RESIDUE NDP D1257
05AC5SOFTWAREALA A:95 , PHE A:96 , ALA A:97 , TYR A:147 , VAL A:154 , GLN A:155 , TYR A:157 , MET A:160 , SER A:197 , NDP A:1257BINDING SITE FOR RESIDUE PT6 A1258
06AC6SOFTWAREALA D:95 , PHE D:96 , ALA D:97 , TYR D:147 , GLN D:155 , TYR D:157 , MET D:160 , SER D:197 , PHE D:204 , NDP D:1257BINDING SITE FOR RESIDUE PT6 D1258
07AC7SOFTWAREALA C:95 , PHE C:96 , ALA C:97 , TYR C:147 , GLN C:155 , TYR C:157 , MET C:160 , SER C:197 , VAL C:201 , GLY C:202 , GLY C:203 , PHE C:204 , ILE C:207 , NDP C:1257BINDING SITE FOR RESIDUE PT6 C1258
08AC8SOFTWAREALA B:95 , PHE B:96 , ALA B:97 , TYR B:147 , GLN B:155 , TYR B:157 , SER B:197 , GLY B:202 , ILE B:207 , NDP B:1257BINDING SITE FOR RESIDUE PT6 B1258
09AC9SOFTWAREVAL B:201 , GLY B:202 , GLY B:203 , PHE B:204 , ASN B:205 , THR B:206BINDING SITE FOR RESIDUE SO4 B1259
10BC1SOFTWAREARG B:40 , LYS B:41 , VAL C:201 , GLY C:202 , GLY C:203 , PHE C:204 , ASN C:205 , THR C:206BINDING SITE FOR RESIDUE SO4 C1259
11BC2SOFTWAREVAL A:201 , GLY A:202 , GLY A:203 , PHE A:204 , ASN A:205 , THR A:206BINDING SITE FOR RESIDUE SO4 A1259
12BC3SOFTWAREALA D:60 , HIS D:61 , LEU D:62 , TYR D:63BINDING SITE FOR RESIDUE EDO D1259
13BC4SOFTWAREGLY B:140 , ASN B:182 , ARG B:184BINDING SITE FOR RESIDUE EDO B1260

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CV0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CV0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CV0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CV0)

(-) Exons   (0, 0)

(no "Exon" information available for 4CV0)

(-) 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:254
 aligned with A0A0H3JLH9_S | A0A0H3JLH9 from UniProtKB/TrEMBL  Length:256

    Alignment length:254
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252    
         A0A0H3JLH9_S     3 NLENKTYVIMGIANKRSIAFGVAKVLDQLGAKLVFTYRKERSRKELEKLLEQLNQPEAHLYQIDVQSDEEVINGFEQIGKDVGNIDGVYHSIAFANMEDLRGRFSETSREGFLLAQDISSYSLTIVAHEAKKLMPEGGSIVATTYLGGEFAVQNYNVMGVAKASLEANVKYLALDLGPDNIRVNAISAGPIRTLSAKGVGGFNTILKEIEERAPLKRNVDQVEVGKTAAYLLSDLSSGVTGENIHVDSGFHAIK 256
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh......eee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhh.ee..hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.............hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhh.ee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cv0 A   3 NLENKTYVIMGIANKRSIAFGVAKVLDQLGAKLVFTYRKERSRKELEKLLEQLNQPEAHLYQIDVQSDEEVINGFEQIGKDVGNIDGVYHSIAFANMEDLRGRFSETSREGFLLAQDISSYSLTIVAHEAKKLMPEGGSIVATTYLGGEFAVQNYNVMGVAKASLEANVKYLALDLGPDNIRVNAISAGPIRTLSAKGVGGFNTILKEIEERAPLKRNVDQVEVGKTAAYLLSDLSSGVTGENIHVDSGFHAIK 256
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252    


Chain B from PDB  Type:PROTEIN  Length:255
 aligned with A0A0H3JLH9_S | A0A0H3JLH9 from UniProtKB/TrEMBL  Length:256

    Alignment length:255
                                    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     
         A0A0H3JLH9_S     2 LNLENKTYVIMGIANKRSIAFGVAKVLDQLGAKLVFTYRKERSRKELEKLLEQLNQPEAHLYQIDVQSDEEVINGFEQIGKDVGNIDGVYHSIAFANMEDLRGRFSETSREGFLLAQDISSYSLTIVAHEAKKLMPEGGSIVATTYLGGEFAVQNYNVMGVAKASLEANVKYLALDLGPDNIRVNAISAGPIRTLSAKGVGGFNTILKEIEERAPLKRNVDQVEVGKTAAYLLSDLSSGVTGENIHVDSGFHAIK 256
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee......hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh........eee....hhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhh.ee..hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee............hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhh.ee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cv0 B   2 VNLENKTYVIMGIANKRSIAFGVAKVLDQLGAKLVFTYRKERSRKELEKLLEQLNQPEAHLYQIDVQSDEEVINGFEQIGKDVGNIDGVYHSIAFANMEDLRGRFSETSREGFLLAQDISSYSLTIVAHEAKKLMPEGGSIVATTYLGGEFAVQNYNVMGVAKASLEANVKYLALDLGPDNIRVNAISAGPIRTLSAKGVGGFNTILKEIEERAPLKRNVDQVEVGKTAAYLLSDLSSGVTGENIHVDSGFHAIK 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     


Chain C from PDB  Type:PROTEIN  Length:254
 aligned with A0A0H3JLH9_S | A0A0H3JLH9 from UniProtKB/TrEMBL  Length:256

    Alignment length:254
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252    
         A0A0H3JLH9_S     3 NLENKTYVIMGIANKRSIAFGVAKVLDQLGAKLVFTYRKERSRKELEKLLEQLNQPEAHLYQIDVQSDEEVINGFEQIGKDVGNIDGVYHSIAFANMEDLRGRFSETSREGFLLAQDISSYSLTIVAHEAKKLMPEGGSIVATTYLGGEFAVQNYNVMGVAKASLEANVKYLALDLGPDNIRVNAISAGPIRTLSAKGVGGFNTILKEIEERAPLKRNVDQVEVGKTAAYLLSDLSSGVTGENIHVDSGFHAIK 256
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhh.ee..hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhh.ee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cv0 C   3 NLENKTYVIMGIANKRSIAFGVAKVLDQLGAKLVFTYRKERSRKELEKLLEQLNQPEAHLYQIDVQSDEEVINGFEQIGKDVGNIDGVYHSIAFANMEDLRGRFSETSREGFLLAQDISSYSLTIVAHEAKKLMPEGGSIVATTYLGGEFAVQNYNVMGVAKASLEANVKYLALDLGPDNIRVNAISAGPIRTLSAKGVGGFNTILKEIEERAPLKRNVDQVEVGKTAAYLLSDLSSGVTGENIHVDSGFHAIK 256
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252    


Chain D from PDB  Type:PROTEIN  Length:254
 aligned with A0A0H3JLH9_S | A0A0H3JLH9 from UniProtKB/TrEMBL  Length:256

    Alignment length:254
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252    
         A0A0H3JLH9_S     3 NLENKTYVIMGIANKRSIAFGVAKVLDQLGAKLVFTYRKERSRKELEKLLEQLNQPEAHLYQIDVQSDEEVINGFEQIGKDVGNIDGVYHSIAFANMEDLRGRFSETSREGFLLAQDISSYSLTIVAHEAKKLMPEGGSIVATTYLGGEFAVQNYNVMGVAKASLEANVKYLALDLGPDNIRVNAISAGPIRTLSAKGVGGFNTILKEIEERAPLKRNVDQVEVGKTAAYLLSDLSSGVTGENIHVDSGFHAIK 256
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh........eeee....hhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhh.ee..hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee............hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhh.ee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cv0 D   3 NLENKTYVIMGIANKRSIAFGVAKVLDQLGAKLVFTYRKERSRKELEKLLEQLNQPEAHLYQIDVQSDEEVINGFEQIGKDVGNIDGVYHSIAFANMEDLRGRFSETSREGFLLAQDISSYSLTIVAHEAKKLMPEGGSIVATTYLGGEFAVQNYNVMGVAKASLEANVKYLALDLGPDNIRVNAISAGPIRTLSAKGVGGFNTILKEIEERAPLKRNVDQVEVGKTAAYLLSDLSSGVTGENIHVDSGFHAIK 256
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252
   Legend:   → Mismatch (orange background)
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  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 4CV0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CV0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CV0)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4CV0)

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 Related Entries

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

UniProtKB/TrEMBL
        A0A0H3JLH9_S | A0A0H3JLH9: 4ali 4alj 4alk 4all 4alm 4aln 4bnf 4bng 4bnh 4bni 4bnj 4bnk 4bnl 4bnm 4bnn 4cuz 4cv1

(-) Related Entries Specified in the PDB File

4cuz CRYSTAL STRUCTURE OF S. AUREUS FABI IN COMPLEX WITH NADPH AND PT173
4cv1 CRYSTAL STRUCTURE OF S. AUREUS FABI IN COMPLEX WITH NADPH AND CG400549
4cv2 CRYSTAL STRUCTURE OF E. COLI FABI IN COMPLEX WITH NADH AND CG400549
4cv3 CRYSTAL STRUCTURE OF E. COLI FABI IN COMPLEX WITH NADH AND PT166