1DJE

CRYSTAL STRUCTURE OF THE PLP-BOUND FORM OF 8-AMINO-7-OXONANOATE SYNTHASE

Summary for 1DJE

• Entry DOI: 10.2210/pdb1dje/pdb
• Related: 1BS0 1DJ9
• Descriptor: 8-AMINO-7-OXONANOATE SYNTHASE, SULFATE ION, PYRIDOXAL-5'-PHOSPHATE, ... (4 entities in total)
• Functional Keywords: biotin biosynthesis, 8-amino-7-oxonanoate synthase, 8-amino-7-ketopelargonate synthase, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 42074.39

Authors

Webster, S.P.,Alexeev, D.,Campopiano, D.J.,Watt, R.M.,Alexeeva, M.,Sawyer, L.,Baxter, R.L. (deposition date: 1999-12-02, release date: 2000-12-04, Last modification date: 2018-01-24)

Primary citation

Webster, S.P.,Alexeev, D.,Campopiano, D.J.,Watt, R.M.,Alexeeva, M.,Sawyer, L.,Baxter, R.L.
Mechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and crystallographic studies.
Biochemistry, 39:516-528, 2000

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 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.

PubMed: 10642176
DOI: 10.1021/bi991620j

Experimental method

X-RAY DIFFRACTION (1.71 Å)