4ZM4

Complex structure of PctV K276R mutant with PMP and 3-dehydroshkimate

Summary for 4ZM4

• Entry DOI: 10.2210/pdb4zm4/pdb
• Related: 4ZM3
• Descriptor: Aminotransferase, PYRIDOXAL-5'-PHOSPHATE, (3E,4R,5R)-4,5-dihydroxy-3-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}cyclohex-1-ene-1-carboxylic acid, ... (4 entities in total)
• Functional Keywords: pyridoxal 5-phosphate, aminotransferase, transferase
• Biological source: Streptomyces pactum
• Total number of polymer chains: 6
• Total formula weight: 288799.82

Authors

Hirayama, A.,Miyanaga, A.,Kudo, F.,Eguchi, T. (deposition date: 2015-05-02, release date: 2015-10-14, Last modification date: 2023-11-08)

Primary citation

Hirayama, A.,Miyanaga, A.,Kudo, F.,Eguchi, T.
Mechanism-Based Trapping of the Quinonoid Intermediate by Using the K276R Mutant of PLP-Dependent 3-Aminobenzoate Synthase PctV in the Biosynthesis of Pactamycin.
Chembiochem, 16:2484-2490, 2015

PubMed Abstract: Mutational analysis of the pyridoxal 5'-phosphate (PLP)-dependent enzyme PctV was carried out to elucidate the multi-step reaction mechanism for the formation of 3-aminobenzoate (3-ABA) from 3-dehydroshikimate (3-DSA). Introduction of mutation K276R led to the accumulation of a quinonoid intermediate with an absorption maximum at 580 nm after the reaction of pyridoxamine 5'-phosphate (PMP) with 3-DSA. The chemical structure of this intermediate was supported by X-ray crystallographic analysis of the complex formed between the K276R mutant and the quinonoid intermediate. These results clearly show that a quinonoid intermediate is involved in the formation of 3-ABA. They also indicate that Lys276 (in the active site of PctV) plays multiple roles, including acid/base catalysis during the dehydration reaction of the quinonoid intermediate.

PubMed: 26426567
DOI: 10.1002/cbic.201500426

Experimental method

X-RAY DIFFRACTION (2.4 Å)