5BK7

The structure of MppP E15A mutant soaked with the substrate L-arginine

5BK7 の概要

• エントリーDOI: 10.2210/pdb5bk7/pdb
• 分子名称: PLP-Dependent L-Arginine Hydroxylase MppP, (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine (3 entities in total)
• 機能のキーワード: dimer, substrate binding in e15a mutant, oxidase, plp, hydrolase-antibiotic complex, oxidoreductase
• 由来する生物種: Streptomyces wadayamensis
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 335064.38

構造登録者

Han, L.,Silvaggi, N.R. (登録日: 2018-01-27, 公開日: 2018-09-05, 最終更新日: 2023-09-27)

主引用文献

Han, L.,Vuksanovic, N.,Oehm, S.A.,Fenske, T.G.,Schwabacher, A.W.,Silvaggi, N.R.
Streptomyces wadayamensis MppP is a PLP-Dependent Oxidase, Not an Oxygenase.
Biochemistry, 57:3252-3264, 2018

PubMed Abstract: The PLP-dependent l-arginine hydroxylase/deaminase MppP from Streptomyces wadayamensis (SwMppP) is involved in the biosynthesis of l-enduracididine, a nonproteinogenic amino acid found in several nonribosomally produced peptide antibiotics. SwMppP uses only PLP and molecular oxygen to catalyze a 4-electron oxidation of l-arginine to form a mixture of 2-oxo-4(S)-hydroxy-5-guanidinovaleric acid and 2-oxo-5-guanidinovaleric acid. Steady-state kinetics analysis in the presence and absence of catalase shows that one molecule of peroxide is formed for every molecule of dioxygen consumed in the reaction. Moreover, for each molecule of 2-oxo-4(S)-hydroxy-5-guanidinovaleric acid produced, two molecules of dioxygen are consumed, suggesting that both the 4-hydroxy and 2-keto groups are derived from water. This was confirmed by running the reactions using either O or HO and analyzing the products by ESI-MS. Incorporation of O was only observed when the reaction was performed in HO. Crystal structures of SwMppP with l-arginine, 2-oxo-4(S)-hydroxy-5-guanidinovaleric acid, or 2-oxo-5-guanidinovaleric acid bound were determined at resolutions of 2.2, 1.9. and 1.8 Å, respectively. The structural data show that the N-terminal portion of the protein is disordered unless substrate or product is bound in the active site, in which case it forms a well-ordered helix that covers the catalytic center. This observation suggested that the N-terminal helix may have a role in substrate binding and/or catalysis. Our structural and kinetic characterizations of N-terminal variants show that the N-terminus is critical for catalysis. In light of this new information, we have refined our previously proposed mechanism of the SwMppP-catalyzed oxidation of l-arginine.

PubMed: 29473729
DOI: 10.1021/acs.biochem.8b00130

実験手法

X-RAY DIFFRACTION (2.196 Å)