6OFU

X-ray crystal structure of the YdjI aldolase from Escherichia coli K12

6OFU の概要

• エントリーDOI: 10.2210/pdb6ofu/pdb
• 分子名称: YdjI aldolase, ZINC ION, CHLORIDE ION, ... (4 entities in total)
• 機能のキーワード: aldolase, lyase
• 由来する生物種: Escherichia coli (strain K12)
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 128261.62

構造登録者

Dopkins, B.J.,Thoden, J.B.,Huddleston, J.P.,Narindoshvili, T.,Fose, B.,Rachel, F.M.,Holden, H.M. (登録日: 2019-04-01, 公開日: 2019-04-24, 最終更新日: 2023-11-15)

主引用文献

Huddleston, J.P.,Thoden, J.B.,Dopkins, B.J.,Narindoshvili, T.,Fose, B.J.,Holden, H.M.,Raushel, F.M.
Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity inEscherichia coliK12.
Biochemistry, 58:3340-3353, 2019

PubMed Abstract: The gene cluster is found in 80% of sequenced genomes and other closely related species in the human microbiome. On the basis of the annotations of the enzymes located in this cluster, it is expected that together they catalyze the catabolism of an unknown carbohydrate. The focus of this investigation is on YdjI, which is in the gene cluster of K-12. It is predicted to be a class II aldolase of unknown function. Here we describe a structural and functional characterization of this enzyme. YdjI catalyzes the hydrogen/deuterium exchange of the pro- hydrogen at C3 of dihydroxyacetone phosphate (DHAP). In the presence of DHAP, YdjI catalyzes an aldol condensation with a variety of aldo sugars. YdjI shows a strong preference for higher-order (seven-, eight-, and nine-carbon) monosaccharides with specific hydroxyl stereochemistries and a negatively charged terminus (carboxylate or phosphate). The best substrate is l-arabinuronic acid with an apparent of 3.0 s. The product, l--l--octuluronate-1-phosphate, has a / value of 2.1 × 10 M s in the retro-aldol reaction with YdjI. This is the first recorded synthesis of l--l--octuluronate-1-phosphate and six similar carbohydrates. The crystal structure of YdjI, determined to a nominal resolution of 1.75 Å (Protein Data Bank entry 6OFU ), reveals unusual positions for two arginine residues located near the active site. Computational docking was utilized to distinguish preferable binding orientations for l--l--octuluronate-1-phosphate. These results indicate a possible alternative binding orientation for l--l--octuluronate-1-phosphate compared to that observed in other class II aldolases, which utilize shorter carbohydrate molecules.

PubMed: 31322866
DOI: 10.1021/acs.biochem.9b00326

実験手法

X-RAY DIFFRACTION (1.75 Å)