1DJ9

CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and crystallographic studies.

Webster, S.P.Alexeev, D.Campopiano, D.J.Watt, R.M.Alexeeva, M.Sawyer, L.Baxter, R.L.

(2000) Biochemistry 39: 516-528

  • Primary Citation of Related Structures:  1DJE

  • PubMed Abstract: 
  • 8-Amino-7-oxononanoate synthase (also known as 7-keto-8-aminopelargonate synthase, EC 2.3.1.47) is a pyridoxal 5'-phosphate-dependent enzyme which catalyzes the decarboxylative condensation of L-alanine with pimeloyl-CoA in a stereospecific manner to ...

    8-Amino-7-oxononanoate synthase (also known as 7-keto-8-aminopelargonate synthase, EC 2.3.1.47) is a pyridoxal 5'-phosphate-dependent enzyme which catalyzes the decarboxylative condensation of L-alanine with pimeloyl-CoA in a stereospecific manner to form 8(S)-amino-7-oxononanoate. This is the first committed step in biotin biosynthesis. The mechanism of Escherichia coli AONS has been investigated by spectroscopic, kinetic, and crystallographic techniques. The X-ray structure of the holoenzyme has been refined at a resolution of 1.7 A (R = 18.6%, R(free) = 21. 2%) and shows that the plane of the imine bond of the internal aldimine deviates from the pyridine plane. The structure of the enzyme-product external aldimine complex has been refined at a resolution of 2.0 A (R = 21.2%, R(free) = 27.8%) and shows a rotation of the pyridine ring with respect to that in the internal aldimine, together with a significant conformational change of the C-terminal domain and subtle rearrangement of the active site hydrogen bonding. The first step in the reaction, L-alanine external aldimine formation, is rapid (k(1) = 2 x 10(4) M(-)(1) s(-)(1)). Formation of an external aldimine with D-alanine, which is not a substrate, is significantly slower (k(1) = 125 M(-)(1) s(-)(1)). Binding of D-alanine to AONS is enhanced approximately 2-fold in the presence of pimeloyl-CoA. Significant substrate quinonoid formation only occurs upon addition of pimeloyl-CoA to the preformed L-alanine external aldimine complex and is preceded by a distinct lag phase ( approximately 30 ms) which suggests that binding of the pimeloyl-CoA causes a conformational transition of the enzyme external aldimine complex. This transition, which is inferred by modeling to require a rotation around the Calpha-N bond of the external aldimine complex, promotes abstraction of the Calpha proton by Lys236. These results have been combined to form a detailed mechanistic pathway for AONS catalysis which may be applied to the other members of the alpha-oxoamine synthase subfamily.


    Related Citations: 
    • The Crystal Structure of 8-Amino-7-Oxononanoate Synthase: A Bacterial Plp- Dependent, Acyl-Coa-Condensing Enzyme
      ALEXEEV, D.,ALEXEEVA, M.,BAXTER, R.L.,WEBSTER, S.P.,SAWYER, L.
      (1998) J.Mol.Biol. 284: 401


    Organizational Affiliation

    Edinburgh Centre for Protein Technology, Department of Chemistry, University of Edinburgh, King's Buildings, Edinburgh EH9 3JJ, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
8-AMINO-7-OXONONANOATE SYNTHASE
A
384Escherichia coli (strain K12)Gene Names: bioF
EC: 2.3.1.47
Find proteins for P12998 (Escherichia coli (strain K12))
Go to UniProtKB:  P12998
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
KAM
Query on KAM

Download SDF File 
Download CCD File 
A
N-[7-KETO-8-AMINOPELARGONIC ACID]-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
N-PYRIDOXYL-7-KETO-8-AMINOPELARGONIC ACID-5'-MONOPHOSPHATE
C17 H27 N2 O8 P
YXEXNGWPUWJMIT-NSHDSACASA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.212 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 58.890α = 90.00
b = 58.890β = 90.00
c = 201.770γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALEPACKdata scaling
X-PLORmodel building
SHELXL-97refinement
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description