6M4Y

Structure of a R371A mutant of a Group II PLP dependent decarboxylase from Methanocaldococcus jannaschii

6M4Y の概要

• エントリーDOI: 10.2210/pdb6m4y/pdb
• 関連するPDBエントリー: 6JY1 6LDR 6LDS 6LDT
• 分子名称: L-tyrosine/L-aspartate decarboxylase, SULFATE ION, GLYCEROL, ... (4 entities in total)
• 機能のキーワード: plp dependent decarboxylase, catalytic mutant, protein conformation, llp, internal aldimine, tyrosine, tyrosine decarboxylase, structure-activity relationship, lyase
• 由来する生物種: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 48141.15

構造登録者

Manoj, N.,Chellam Gayathri, S. (登録日: 2020-03-09, 公開日: 2020-12-02, 最終更新日: 2023-11-29)

主引用文献

Gayathri, S.C.,Manoj, N.
Crystallographic Snapshots of the Dunathan and Quinonoid Intermediates provide Insights into the Reaction Mechanism of Group II Decarboxylases.
J.Mol.Biol., 432:166692-166692, 2020

PubMed Abstract: PLP-dependent enzymes catalyze a plethora of chemical reactions affecting diverse physiological functions. Here we report the structural determinants of the reaction mechanism in a Group II PLP-dependent decarboxylase by assigning two early intermediates. The in-crystallo complexes of the PLP bound form, and the Dunathan and quinonoid intermediates, allowed direct observation of the active site interactions. The structures reveal that a subtle rearrangement of a conserved Arg residue in concert with a water-mediated interaction with the carboxylate of the Dunathan intermediate, appears to directly stabilize the alignment and facilitate the release of CO to yield the quinonoid. Modeling indicates that the conformational change of a dynamic catalytic loop to a closed form controls a conserved network of hydrogen bond interactions between catalytic residues to protonate the quinonoid. Our results provide a structural framework to elucidate mechanistic roles of residues that govern reaction specificity and catalysis in PLP-dependent decarboxylation.

PubMed: 33122004
DOI: 10.1016/j.jmb.2020.10.026

実験手法

X-RAY DIFFRACTION (2.1 Å)