1ET0

CRYSTAL STRUCTURE OF AMINODEOXYCHORISMATE LYASE FROM ESCHERICHIA COLI

Summary for 1ET0

• Entry DOI: 10.2210/pdb1et0/pdb
• Descriptor: 4-AMINO-4-DEOXYCHORISMATE LYASE, PYRIDOXAL-5'-PHOSPHATE (3 entities in total)
• Functional Keywords: pseudo beta barrel, lyase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 29992.17

Authors

Nakai, T.,Mizutani, H.,Miyahara, I.,Hirotsu, K.,Takeda, S.,Jhee, K.H.,Yoshimura, T.,Esaki, N. (deposition date: 2000-04-12, release date: 2000-07-19, Last modification date: 2025-03-26)

Primary citation

Nakai, T.,Mizutani, H.,Miyahara, I.,Hirotsu, K.,Takeda, S.,Jhee, K.H.,Yoshimura, T.,Esaki, N.
Three-dimensional structure of 4-amino-4-deoxychorismate lyase from Escherichia coli.
J.Biochem.(Tokyo), 128:29-38, 2000

PubMed Abstract: 4-Amino-4-deoxychorismate lyase (ADCL) is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. The crystal structure of ADCL from Escherichia coli has been solved using MIR phases in combination with density modification. The structure has been refined to an R-factor of 20.6% at 2.2 A resolution. The enzyme is a homo dimer with a crystallographic twofold axis, and the polypeptide chain is folded into small and large domains with an interdomain loop. The coenzyme, pyridoxal 5'-phosphate, resides at the domain interface, its re-face facing toward the protein. Although the main chain folding of the active site is homologous to those of D-amino acid and L-branched-chain amino acid aminotransferases, no residues in the active site are conserved among them except for Arg59, Lys159, and Glu193, which directly interact with the coenzyme and play critical roles in the catalytic functions. ADC was modeled into the active site of the unliganded enzyme on the basis of the X-ray structures of the unliganded and liganded forms in the D-amino acid and L-branched-chain amino acid aminotransferases. According to this model, the carboxylates of ADC are recognized by Asn256, Arg107, and Lys97, and the cyclohexadiene moiety makes van der Waals contact with the side chain of Leu258. ADC forms a Schiff base with PLP to release the catalytic residue Lys159, which forms a hydrogen bond with Thr38. The neutral amino group of Lys159 eliminates the a-proton of ADC to give a quinonoid intermediate to release a pyruvate in accord with the proton transfer from Thr38 to the olefin moiety of ADC.

PubMed: 10876155

Experimental method

X-RAY DIFFRACTION (2.2 Å)