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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-KETOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE (FABG) FROM VIBRIO CHOLERAE
 
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 :  29 Apr 11  (Deposition) - 18 May 11  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Oxidoreductase, Fabg, Acyl Carrier Protein, Cell Plasma (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-KETOACYL-(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  (5, 23)

Asymmetric Unit (5, 23)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO7Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4PGE2Ligand/IonTRIETHYLENE GLYCOL
5SO412Ligand/IonSULFATE ION
Biological Unit 1 (4, 44)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO14Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4PGE4Ligand/IonTRIETHYLENE GLYCOL
5SO424Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:103 , GLU A:104BINDING SITE FOR RESIDUE SO4 A 249
02AC2SOFTWAREARG A:19 , GLY A:20 , LYS A:23BINDING SITE FOR RESIDUE SO4 A 250
03AC3SOFTWAREGLY A:82 , GLY A:83 , LYS A:132BINDING SITE FOR RESIDUE SO4 A 251
04AC4SOFTWARESER A:18 , ARG A:19 , ALA A:40 , THR A:41 , HOH A:313BINDING SITE FOR RESIDUE SO4 A 252
05AC5SOFTWAREARG A:133 , ARG A:176BINDING SITE FOR RESIDUE SO4 A 253
06AC6SOFTWAREASP A:96 , ALA A:150 , GLY A:151 , HOH A:361BINDING SITE FOR RESIDUE PGE A 254
07AC7SOFTWAREILE A:248 , LYS B:167 , EDO B:259 , HOH B:305BINDING SITE FOR RESIDUE EDO A 255
08AC8SOFTWAREARG A:19 , GLY A:20 , ILE A:21 , GLY A:22 , ASN A:90 , THR A:190 , EDO A:257BINDING SITE FOR RESIDUE EDO A 256
09AC9SOFTWAREARG A:19 , GLY A:20 , THR A:190 , ASP A:191 , EDO A:256BINDING SITE FOR RESIDUE EDO A 257
10BC1SOFTWAREGLU A:8 , SER A:175 , ARG A:176BINDING SITE FOR RESIDUE GOL A 258
11BC2SOFTWARELYS B:103 , GLU B:104 , HOH B:327BINDING SITE FOR RESIDUE SO4 B 249
12BC3SOFTWARESER A:2 , ARG A:32 , SER B:2 , ARG B:32BINDING SITE FOR RESIDUE SO4 B 250
13BC4SOFTWAREARG B:19 , GLY B:20 , LYS B:23 , EDO B:257 , HOH B:352BINDING SITE FOR RESIDUE SO4 B 251
14BC5SOFTWAREGLY B:16 , ALA B:17 , SER B:18 , ALA B:40 , THR B:41 , HOH B:340BINDING SITE FOR RESIDUE SO4 B 252
15BC6SOFTWAREILE B:93 , ARG B:95 , HOH B:331BINDING SITE FOR RESIDUE SO4 B 253
16BC7SOFTWAREARG B:133 , ARG B:176BINDING SITE FOR RESIDUE SO4 B 254
17BC8SOFTWAREGLY B:82 , GLY B:83 , LYS B:132BINDING SITE FOR RESIDUE SO4 B 255
18BC9SOFTWARELYS A:167 , ILE B:248BINDING SITE FOR RESIDUE EDO B 256
19CC1SOFTWAREARG B:19 , GLY B:20 , THR B:190 , ASP B:191 , SO4 B:251 , EDO B:258BINDING SITE FOR RESIDUE EDO B 257
20CC2SOFTWAREGLY B:16 , ARG B:19 , ILE B:21 , GLY B:22 , ASN B:90 , EDO B:257BINDING SITE FOR RESIDUE EDO B 258
21CC3SOFTWAREEDO A:255 , GLY B:145 , ILE B:163 , LYS B:167 , HOH B:305BINDING SITE FOR RESIDUE EDO B 259
22CC4SOFTWAREASP B:96 , ASN B:97 , ALA B:150 , GLY B:151BINDING SITE FOR RESIDUE PGE B 260
23CC5SOFTWARETYR B:155 , LYS B:159BINDING SITE FOR RESIDUE CL B 261

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 3RRO)

(-) 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:247
 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 d3rroa_ 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....hhhhhh.hhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:142-170    ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rro A   2 SQFMNLEGKVALVTGASRGIGKAIAELLAERGAKVIGTATSESGAQAISDYLGDNGKGMALNVTNPESIEAVLKAITDEFGGVDILVNNAGITRDNLLMRMKEEEWSDIMETNLTSIFRLSKAVLRGMMKKRQGRIINVGSVVGTMGNAGQANYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDEQRTATLAQVPAGRLGDPREIASAVAFLASPEAAYITGETLHVNGGMYMI 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       


Chain B from PDB  Type:PROTEIN  Length:247
 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 d3rrob_ B: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------adh_short-3rroB01 B:10-174                                                                                                                                           -------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------adh_short-3rroB02 B:10-174                                                                                                                                           -------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:142-170    ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rro B   2 SQFMNLEGKVALVTGASRGIGKAIAELLAERGAKVIGTATSESGAQAISDYLGDNGKGMALNVTNPESIEAVLKAITDEFGGVDILVNNAGITRDNLLMRMKEEEWSDIMETNLTSIFRLSKAVLRGMMKKRQGRIINVGSVVGTMGNAGQANYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDEQRTATLAQVPAGRLGDPREIASAVAFLASPEAAYITGETLHVNGGMYMI 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
   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 3RRO)

(-) 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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 Related Entries

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

(-) Related Entries Specified in the PDB File

3op4 RELATED ID: IDP90557 RELATED DB: TARGETDB