Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in complex with the cis isomer of amiclenomycin

2-AMINO-4-(4-AMINO-CYCLOHEXA-2,5-DIENYL)-BUTYRIC ACID

Structural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin

7,8-diamino-pelargonic acid aminotransferase

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, DAPA aminotransferase

PEG4000, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Structure of the substrate complex with the WT enzyme

1mlz contains the same enzyme complexed with the trans-isomer of amiclenomycin

sequence
The crystallized protein differs from the Swissprot
sequence at residue 14. In the Swissprot sequence number
14 is a tryptophan while here it is a leucin. This is
confirmed by DNA sequencing and was also reported for
the original WT structure (1qj5).

In both subunits the cofactor pyridoxal-5'-phosphate forms a covalent adduct with the inhibitor amiclenomycin, followed by aromatization of amiclenomycin hexadiene ring. The binding mode for the inhibitor is different in the two subunits. The electron density for the covalent adduct between amiclenomycin and pyridoxal-5'-phosphate is better in monomer A. For details see the primary citation.

In monomer A two stretches of residues are disordered, 159-168 and 180-189 resp. In monomer B three stretches of residues are disordered, 159-168, 180-189 and 299-303 resp. Residue 429 was excluded from both monomers. A number of side chains on the surface of the protein are disordered. The occupancy for these is estimated to 0 in most cases. In four cases the side chains are given the occupancy 0.5.

7,8-diamino-pelargonic acid aminotransferase(E.C.2.6.1.62)

Aminotransferase, Fold type I, subclass II, amiclenomycin, TRANSFERASE