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(-) Description

Title :  STRUCTURE OF 3-KETOACYL-(ACYL-CARRIER-PROTEIN)REDUCTASE (FABG) FROM VIBRIO CHOLERAE O1 COMPLEXED WITH NADP+ (SPACE GROUP P62)
 
Authors :  J. Hou, M. Chruszcz, D. R. Cooper, M. Grabowski, H. Zheng, T. Osinski, I. W. Anderson, W. Minor, Center For Structural Genomics Of Infect Diseases (Csgid)
Date :  02 May 11  (Deposition) - 11 May 11  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Oxireductase, Fabg, Acyl Carrier Protein, Cell Plasma, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Hou, H. Zheng, M. Chruszcz, M. D. Zimmerman, I. A. Shumilin, T. Osinski, M. Demas, S. Grimshaw, W. Minor
Dissecting The Structural Elements For The Activation Of Beta-Ketoacyl-(Acyl Carrier Protein) Reductase From Vibrio Cholerae.
J. Bacteriol. V. 198 463 2015
PubMed-ID: 26553852  |  Reference-DOI: 10.1128/JB.00360-15

(-) Compounds

Molecule 1 - 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE
    Chains: A, B
    EC Number: 1.1.1.100
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 CODONPLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VCD_002346
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid: 243277
    Strain: N16961

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 23)

Asymmetric Unit (4, 23)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3SO411Ligand/IonSULFATE ION
4UNX8Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (4, 46)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3SO422Ligand/IonSULFATE ION
4UNX16Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:133 , ARG A:176BINDING SITE FOR RESIDUE SO4 A 249
02AC2SOFTWAREARG A:19 , GLY A:20 , LYS A:23 , HOH A:277BINDING SITE FOR RESIDUE SO4 A 250
03AC3SOFTWARELYS A:103 , GLU A:104 , LYS A:123BINDING SITE FOR RESIDUE SO4 A 251
04AC4SOFTWAREILE A:93 , ARG A:95 , HOH A:321BINDING SITE FOR RESIDUE SO4 A 252
05AC5SOFTWAREGLY A:83 , LYS A:132BINDING SITE FOR RESIDUE SO4 A 253
06AC6SOFTWAREGLY A:16 , ALA A:17 , SER A:18 , ARG A:19 , ILE A:21 , THR A:41 , LEU A:62 , ASN A:63 , VAL A:64 , ASN A:90 , ALA A:91 , GLY A:92 , VAL A:140 , GLY A:141 , SER A:142 , TYR A:155 , LYS A:159 , PRO A:185 , GLY A:186 , ILE A:188 , THR A:190 , MET A:192 , THR A:193 , HOH A:298 , HOH A:306 , HOH A:309 , HOH A:320 , HOH A:322BINDING SITE FOR RESIDUE NAP A 254
07AC7SOFTWAREILE A:248 , LYS B:167BINDING SITE FOR RESIDUE EDO A 255
08AC8SOFTWAREARG B:19 , GLY B:20 , LYS B:23 , HOH B:278 , HOH B:297BINDING SITE FOR RESIDUE SO4 B 249
09AC9SOFTWARELYS B:103 , GLU B:104BINDING SITE FOR RESIDUE SO4 B 250
10BC1SOFTWARESER A:2 , ARG A:32 , MET B:1 , SER B:2 , ARG B:32BINDING SITE FOR RESIDUE SO4 B 251
11BC2SOFTWAREILE B:93 , ARG B:95 , HOH B:269 , HOH B:309BINDING SITE FOR RESIDUE SO4 B 252
12BC3SOFTWAREARG B:133 , ARG B:176BINDING SITE FOR RESIDUE SO4 B 253
13BC4SOFTWAREGLY B:83 , LYS B:132BINDING SITE FOR RESIDUE SO4 B 254
14BC5SOFTWAREGLY B:16 , SER B:18 , ARG B:19 , ILE B:21 , THR B:41 , LEU B:62 , ASN B:63 , VAL B:64 , ASN B:90 , ALA B:91 , ILE B:93 , VAL B:140 , GLY B:141 , TYR B:155 , LYS B:159 , PRO B:185 , GLY B:186 , ILE B:188 , THR B:190 , HOH B:286 , HOH B:288BINDING SITE FOR RESIDUE NAP B 255
15BC6SOFTWARELYS A:167 , ILE B:248BINDING SITE FOR RESIDUE EDO B 261

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.FABG_VIBCH138-166
 		  2A:142-170
B:142-170
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.FABG_VIBCH138-166
 		  4A:142-170
B:142-170

(-) Exons   (0, 0)

(no "Exon" information available for 3RSH)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:244
 aligned with FABG_VIBCH | Q9KQH7 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:247
                               1                                                                                                                                                                                                                                                   
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       
           FABG_VIBCH     - ---MNLEGKVALVTGASRGIGKAIAELLAERGAKVIGTATSESGAQAISDYLGDNGKGMALNVTNPESIEAVLKAITDEFGGVDILVNNAGITRDNLLMRMKEEEWSDIMETNLTSIFRLSKAVLRGMMKKRQGRIINVGSVVGTMGNAGQANYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDEQRTATLAQVPAGRLGDPREIASAVAFLASPEAAYITGETLHVNGGMYMI 244
               SCOP domains d3rsha_ A: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........---hhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:142-170    ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rsh A   2 SQFMNLEGKVALVTGASRGIGKAIAELLAERGAKVIGTATSESGAQAISDYLGDNGKGMALNVTNPESIEAVLKAITDEFGGVDILVNNAGITRDNLLMRMKEEEWSDIMETNLTSIFRLSKAVLRGMMKKRQGRIINVGSVVGTMGNAGQANYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTK---DEQRTATLAQVPAGRLGDPREIASAVAFLASPEAAYITGETLHVNGGMYMI 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  |   |201       211       221       231       241       
                                                                                                                                                                                                                          194 198                                                  


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with FABG_VIBCH | Q9KQH7 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:248
                                1                                                                                                                                                                                                                                                   
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236        
           FABG_VIBCH     - ----MNLEGKVALVTGASRGIGKAIAELLAERGAKVIGTATSESGAQAISDYLGDNGKGMALNVTNPESIEAVLKAITDEFGGVDILVNNAGITRDNLLMRMKEEEWSDIMETNLTSIFRLSKAVLRGMMKKRQGRIINVGSVVGTMGNAGQANYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDEQRTATLAQVPAGRLGDPREIASAVAFLASPEAAYITGETLHVNGGMYMI 244
               SCOP domains d3rshb_ B: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------adh_short-3rshB01 B:10-174                                                                                                                                           -------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------adh_short-3rshB02 B:10-174                                                                                                                                           -------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........-.hhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:142-170    ------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rsh B   1 MSQFMNLEGKVALVTGASRGIGKAIAELLAERGAKVIGTATSESGAQAISDYLGDNGKGMALNVTNPESIEAVLKAITDEFGGVDILVNNAGITRDNLLMRMKEEEWSDIMETNLTSIFRLSKAVLRGMMKKRQGRIINVGSVVGTMGNAGQANYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTK-LNDEQRTATLAQVPAGRLGDPREIASAVAFLASPEAAYITGETLHVNGGMYMI 248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   | | 200       210       220       230       240        
                                                                                                                                                                                                                           194 |                                                    
                                                                                                                                                                                                                             196
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FABG_VIBCH | Q9KQH7)
molecular function
    GO:0004316    3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity    Catalysis of the reaction: (3R)-3-hydroxyacyl-[acyl-carrier protein] + NADP+ = 3-oxoacyl-[acyl-carrier protein] + NADPH + H+.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    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: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.

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        FABG_VIBCH | Q9KQH7: 3rro 3u09 4i08 4wjz 5end

(-) Related Entries Specified in the PDB File

3op4
3rro RELATED ID: IDP90557 RELATED DB: TARGETDB