5BY5

High resolution structure of the ectoine synthase from the cold-adapted marine bacterium Sphingopyxis alaskensis

5BY5 の概要

• エントリーDOI: 10.2210/pdb5by5/pdb
• 関連するPDBエントリー: 5BXX
• 分子名称: L-ectoine synthase, S-1,2-PROPANEDIOL (3 entities in total)
• 機能のキーワード: compatible solute - osmostress protectant - chemical chaperone - enzyme - ectoine synthesis - cupin - x-ray analysis, lyase
• 由来する生物種: Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 16860.00

構造登録者

Widderich, N.,Kobus, S.,Hoeppner, A.,Bremer, E.,Smits, S.H.J. (登録日: 2015-06-10, 公開日: 2016-04-27, 最終更新日: 2024-05-08)

主引用文献

Widderich, N.,Kobus, S.,Hoppner, A.,Riclea, R.,Seubert, A.,Dickschat, J.S.,Heider, J.,Smits, S.H.,Bremer, E.
Biochemistry and Crystal Structure of Ectoine Synthase: A Metal-Containing Member of the Cupin Superfamily.
Plos One, 11:e0151285-e0151285, 2016

PubMed Abstract: Ectoine is a compatible solute and chemical chaperone widely used by members of the Bacteria and a few Archaea to fend-off the detrimental effects of high external osmolarity on cellular physiology and growth. Ectoine synthase (EctC) catalyzes the last step in ectoine production and mediates the ring closure of the substrate N-gamma-acetyl-L-2,4-diaminobutyric acid through a water elimination reaction. However, the crystal structure of ectoine synthase is not known and a clear understanding of how its fold contributes to enzyme activity is thus lacking. Using the ectoine synthase from the cold-adapted marine bacterium Sphingopyxis alaskensis (Sa), we report here both a detailed biochemical characterization of the EctC enzyme and the high-resolution crystal structure of its apo-form. Structural analysis classified the (Sa)EctC protein as a member of the cupin superfamily. EctC forms a dimer with a head-to-tail arrangement, both in solution and in the crystal structure. The interface of the dimer assembly is shaped through backbone-contacts and weak hydrophobic interactions mediated by two beta-sheets within each monomer. We show for the first time that ectoine synthase harbors a catalytically important metal co-factor; metal depletion and reconstitution experiments suggest that EctC is probably an iron-dependent enzyme. We found that EctC not only effectively converts its natural substrate N-gamma-acetyl-L-2,4-diaminobutyric acid into ectoine through a cyclocondensation reaction, but that it can also use the isomer N-alpha-acetyl-L-2,4-diaminobutyric acid as its substrate, albeit with substantially reduced catalytic efficiency. Structure-guided site-directed mutagenesis experiments targeting amino acid residues that are evolutionarily highly conserved among the extended EctC protein family, including those forming the presumptive iron-binding site, were conducted to functionally analyze the properties of the resulting EctC variants. An assessment of enzyme activity and iron content of these mutants give important clues for understanding the architecture of the active site positioned within the core of the EctC cupin barrel.

PubMed: 26986827
DOI: 10.1371/journal.pone.0151285

実験手法

X-RAY DIFFRACTION (1.2 Å)