3VK2

Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant.

Summary for 3VK2

• Entry DOI: 10.2210/pdb3vk2/pdb
• Related: 2O7C 3VK3 3VK4
• Descriptor: Methionine gamma-lyase, SULFATE ION (3 entities in total)
• Functional Keywords: plp-dependent enzyme, plp, lyase
• Biological source: Pseudomonas putida
• Total number of polymer chains: 4
• Total formula weight: 172131.20

Authors

Fukumoto, M.,Kudou, D.,Murano, S.,Shiba, T.,Sato, D.,Tamura, T.,Harada, S.,Inagaki, K. (deposition date: 2011-11-07, release date: 2012-09-19, Last modification date: 2023-12-06)

Primary citation

Fukumoto, M.,Kudou, D.,Murano, S.,Shiba, T.,Sato, D.,Tamura, T.,Harada, S.,Inagaki, K.
The role of amino acid residues in the active site of L-methionine gamma-lyase from Pseudomonas putida.
Biosci.Biotechnol.Biochem., 76:1275-1284, 2012

PubMed Abstract: Cys116, Lys240*, and Asp241* (asterisks indicate residues from the second subunit of the active dimer) at the active site of L-methionine γ-lyase of Pseudomonas putida (MGL_Pp) are highly conserved among heterologous MGLs. In a previous study, we found that substitution of Cys116 for His led to a drastic increase in activity toward L-cysteine and a decrease in that toward L-methionine. In this study, we examined some properties of the C116H mutant by kinetic analysis and 3D structural analysis. We assumed that substitution of Cys116 for His broke the original hydrogen-bond network and that this induced a significant effect of Tyr114 as a general acid catalyst, possibly due to the narrow space in the active site. The C116H mutant acquired a novel β-elimination activity and lead a drastic conformation change in the histidine residue at position 116 by binding the substrate, suggesting that this His residue affects the reaction specificity of C116H. Furthermore, we suggest that Lys240* is important for substrate recognition and structural stability and that Asp241* is also involved in substrate specificity in the elimination reaction. Based on this, we suggest that the hydrogen-bond network among Cys116, Lys240*, and Asp241* contributes to substrate specificity that is, to L-methionine recognition at the active site in MGL_Pp.

PubMed: 22785484
DOI: 10.1271/bbb.110906

Experimental method

X-RAY DIFFRACTION (2.3 Å)