4K6N

Crystal structure of yeast 4-amino-4-deoxychorismate lyase

Summary for 4K6N

• Entry DOI: 10.2210/pdb4k6n/pdb
• Descriptor: Aminodeoxychorismate lyase, PYRIDOXAL-5'-PHOSPHATE (3 entities in total)
• Functional Keywords: plp-dependent fold type iv enzyme, 4-amino-4-deoxychorismate, 4-aminobenzoate(paba), pyruvate, plp, lyase
• Biological source: Saccharomyces cerevisiae (Baker's yeast)
• Cellular location: Cytoplasm: Q03266
• Total number of polymer chains: 1
• Total formula weight: 44084.17

Authors

Dai, Y.-N.,Chi, C.-B.,Zhou, K.,Cheng, W.,Jiang, Y.-L.,Ren, Y.-M.,Chen, Y.,Zhou, C.-Z. (deposition date: 2013-04-16, release date: 2013-07-10, Last modification date: 2025-03-26)

Primary citation

Dai, Y.-N.,Chi, C.-B.,Zhou, K.,Cheng, W.,Jiang, Y.-L.,Ren, Y.-M.,Ruan, K.,Chen, Y.,Zhou, C.-Z.
Structure and catalytic mechanism of yeast 4-amino-4-deoxychorismate lyase
J.Biol.Chem., 288:22985-22992, 2013

PubMed Abstract: Saccharomyces cerevisiae Abz2 is a pyridoxal 5'-phosphate (PLP)-dependent lyase that converts 4-amino-4-deoxychorismate (ADC) to para-aminobenzoate and pyruvate. To investigate the catalytic mechanism, we determined the 1.9 Å resolution crystal structure of Abz2 complexed with PLP, representing the first eukaryotic ADC lyase structure. Unlike Escherichia coli ADC lyase, whose dimerization is critical to the formation of the active site, the overall structure of Abz2 displays as a monomer of two domains. At the interdomain cleft, a molecule of cofactor PLP forms a Schiff base with residue Lys-251. Computational simulations defined a basic clamp to orientate the substrate ADC in a proper pose, which was validated by site-directed mutageneses combined with enzymatic activity assays. Altogether, we propose a putative catalytic mechanism of a unique class of monomeric ADC lyases led by yeast Abz2.

PubMed: 23818518
DOI: 10.1074/jbc.M113.480335

Experimental method

X-RAY DIFFRACTION (1.9 Å)