Structure of the antitumour enzyme L-methionine γ-lyase from Pseudomonas putida at 1.8 Å resolution

Daizou Kudou, Shintaro Misaki, Masao Yamashita, Takashi Tamura, Tomoaki Takakura, Takayuki Yoshioka, Shigeo Yagi, Robert M. Hoffman, Akio Takimoto, Nobuyoshi Esaki, Kenji Inagaki

Research output: Contribution to journalArticle

52 Citations (Scopus)

Abstract

l-Methionine γ-lyase (EC 4.4.1.11, MGL_Pp) from Pseudomonas putida is a multifunctional enzyme, which belongs to the γ-family of pyridoxal-5′-phosphate (PLP) dependent enzymes. In this report, we demonstrate that the three-dimensional structure of MGL_Pp has been completely solved by the molecular replacement method to an R-factor of 20.4% at 1.8 Å resolution. Detailed information of the overall structure of MGL_Pp supplies a clear picture of the substrate- and PLP-binding pockets. Tyr59 and Arg61 of neighbouring subunits, which are strongly conserved in other γ-family enzymes, contact the phosphate group of PLP. These residues are important as the main anchor within the active site. Lys240, Asp241 and Arg61 of one partner monomer and Tyr114 and Cys116 of the other partner monomer form a hydrogen-bond network in the MGL active site which is specific for MGLs. It is also suggested that electrostatic interactions at the subunit interface are involved in the stabilization of the structural conformation. The detailed structure will facilitate the development of MGL_Pp as an anticancer drug.

Original languageEnglish
Pages (from-to)535-544
Number of pages10
JournalJournal of Biochemistry
Volume141
Issue number4
DOIs
Publication statusPublished - Apr 2007

Fingerprint

Pseudomonas putida
Lyases
Pyridoxal Phosphate
Methionine
R388
Catalytic Domain
Enzymes
Monomers
Multifunctional Enzymes
Coulomb interactions
Anchors
Static Electricity
Conformations
Hydrogen
Hydrogen bonds
Stabilization
Phosphates
Substrates
Pharmaceutical Preparations

Keywords

  • L-methionine γ-lyase
  • Pyridoxal 5′-phosphate
  • X-ray structure

ASJC Scopus subject areas

  • Biochemistry

Cite this

Structure of the antitumour enzyme L-methionine γ-lyase from Pseudomonas putida at 1.8 Å resolution. / Kudou, Daizou; Misaki, Shintaro; Yamashita, Masao; Tamura, Takashi; Takakura, Tomoaki; Yoshioka, Takayuki; Yagi, Shigeo; Hoffman, Robert M.; Takimoto, Akio; Esaki, Nobuyoshi; Inagaki, Kenji.

In: Journal of Biochemistry, Vol. 141, No. 4, 04.2007, p. 535-544.

Research output: Contribution to journalArticle

Kudou, D, Misaki, S, Yamashita, M, Tamura, T, Takakura, T, Yoshioka, T, Yagi, S, Hoffman, RM, Takimoto, A, Esaki, N & Inagaki, K 2007, 'Structure of the antitumour enzyme L-methionine γ-lyase from Pseudomonas putida at 1.8 Å resolution', Journal of Biochemistry, vol. 141, no. 4, pp. 535-544. https://doi.org/10.1093/jb/mvm055
Kudou, Daizou ; Misaki, Shintaro ; Yamashita, Masao ; Tamura, Takashi ; Takakura, Tomoaki ; Yoshioka, Takayuki ; Yagi, Shigeo ; Hoffman, Robert M. ; Takimoto, Akio ; Esaki, Nobuyoshi ; Inagaki, Kenji. / Structure of the antitumour enzyme L-methionine γ-lyase from Pseudomonas putida at 1.8 Å resolution. In: Journal of Biochemistry. 2007 ; Vol. 141, No. 4. pp. 535-544.
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