7F1V

Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-homocysteine intermediates

Summary for 7F1V

• Entry DOI: 10.2210/pdb7f1v/pdb
• Descriptor: L-methionine gamma-lyase, (2~{S})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-4-sulfanyl-butanoic acid, 2-AMINO-4-MERCAPTO-BUTYRIC ACID, ... (5 entities in total)
• Functional Keywords: lyase, pseudomonas putida, methionine gamma-lyase, plp enzyme
• Biological source: Pseudomonas putida (Arthrobacter siderocapsulatus); More
• Total number of polymer chains: 4
• Total formula weight: 171854.34

Authors

Okawa, A.,Handa, H.,Yasuda, E.,Murota, M.,Kudo, D.,Tamura, T.,Shiba, T.,Inagaki, K. (deposition date: 2021-06-09, release date: 2022-04-20, Last modification date: 2024-03-13)

Primary citation

Okawa, A.,Handa, H.,Yasuda, E.,Murota, M.,Kudo, D.,Tamura, T.,Shiba, T.,Inagaki, K.
Characterization and application of l-methionine gamma-lyase Q349S mutant enzyme with an enhanced activity toward l-homocysteine.
J.Biosci.Bioeng., 133:213-221, 2022

PubMed Abstract: l-Methionine γ-lyse (MGL), a pyridoxal 5'-phosphate-dependent enzyme, catalyzes the α,γ-elimination of l-methionine (l-Met) and l-homocysteine (l-Hcy) to produce α-keto acids, thiols, and ammonia. Previously, various mutant enzymes of Pseudomonas putida MGL (PpMGL) were prepared to identify a homocysteine (Hcy)-specific enzyme that would assist the diagnosis of homocystinuria. Among the mutat enzymes the Q349S mutant exhibited high degradation activity toward l-Hcy. In the present study, PpMGL Q349S was characterized; the results suggested that it could be applied to determine the amount of l-Hcy. Compared to the wild-type PpMGL, specific activities of the Q349S mutant with l-Hcy and l-Met were 1.5 and 0.7 times, respectively. Additionally, we confirmed that l-Hcy in plasma samples could be accurately detected using the Q349S mutant by preincubating it with cysteine desulfurase (CsdA). Furthermore, we determined the X-ray crystal structure of PpMGL Q349S l-Met or l-Hcy complexes Michaelis complex, germinal diamine, and external aldimine at 2.25-2.40 Å. These 3D structures showed that the interaction partner of the β-hydroxyl group of Thr355 in the wild-type PpMGL was changed to the carboxyl group of the Hcy-PLP external aldimine in the Q349S mutant. The interaction of Ser349 and Arg375 was different between l-Met and l-Hcy recognition, indicating that it was important for the recognition of the carboxyl group of the substrate.

PubMed: 34953671
DOI: 10.1016/j.jbiosc.2021.11.008

Experimental method

X-RAY DIFFRACTION (2.25 Å)