PDBsum entry: 1dj9

Transferase

PDB id: 1dj9

Contents

Protein chain

383 a.a. *

Ligands

SO4 ×2

KAM

Metals

_MG

Waters ×337

* Residue conservation analysis

PDB id:

1dj9

Name:

Transferase

Title:

Crystal structure of 8-amino-7-oxonanoate synthase (or 7-ket 8aminipelargonate or kapa synthase) complexed with plp and product 8(s)-amino-7-oxonanonoate (or kapa). The enzyme of biosynthetic pathway.

Structure:

8-amino-7-oxononanoate synthase. Chain: a. Synonym: 7-kap synthetase. Ec: 2.3.1.47

Source:

Escherichia coli. Organism_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.212 R-free: 0.278

Authors:

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

Key ref:

S.P.Webster et al. (2000). Mechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and crystallographic studies. Biochemistry, 39, 516-528. PubMed id: 10642176 DOI: 10.1021/bi991620j

Date:

02-Dec-99 Release date: 06-Dec-00

Protein chain

P12998  (BIOF_ECOLI) -  8-amino-7-oxononanoate synthase

Seq: 384 a.a.

Struc: 383 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.3.1.47 - 8-amino-7-oxononanoate synthase.
• Reaction: 6-carboxyhexanoyl-CoA + L-alanine = 8-amino-7-oxononanoate + CoA + CO₂
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = KAM) matches with 51.72% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (5 terms)

reference

DOI no: 10.1021/bi991620j

Biochemistry 39:516-528 (2000)

PubMed id: 10642176

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

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

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.