1NFG

Structure of D-hydantoinase

1NFG の概要

• エントリーDOI: 10.2210/pdb1nfg/pdb
• 分子名称: D-hydantoinase, ZINC ION (3 entities in total)
• 機能のキーワード: tim barrel, hydrolase
• 由来する生物種: Ralstonia pickettii
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 200682.51

構造登録者

Xu, Z.,Yang, Y.,Jiang, W.,Arnold, E.,Ding, J. (登録日: 2002-12-14, 公開日: 2003-07-15, 最終更新日: 2023-11-15)

主引用文献

Xu, Z.,Liu, Y.,Yang, Y.,Jiang, W.,Arnold, E.,Ding, J.
Crystal Structure of D-Hydantoinase from Burkholderia pickettii at a Resolution of 2.7 Angstroms: Insights into the Molecular Basis of Enzyme Thermostability.
J.Bacteriol., 185:4038-4049, 2003

PubMed Abstract: D-Hydantoinase (D-HYD) is an industrial enzyme that is widely used in the production of D-amino acids which are precursors for semisynthesis of antibiotics, peptides, and pesticides. This report describes the crystal structure of D-hydantoinase from Burkholderia pickettii (HYD(Bp)) at a 2.7-A resolution. The structure of HYD(Bp) consists of a core (alpha/beta)(8) triose phosphate isomerase barrel fold and a beta-sheet domain, and the catalytic active site consists of two metal ions and six highly conserved amino acid residues. Although HYD(Bp) shares only moderate sequence similarity with D-HYDs from Thermus sp. (HYD(Tsp)) and Bacillus stearothermophilus (HYD(Bst)), whose structures have recently been solved, the overall structure and the structure of the catalytic active site are strikingly similar. Nevertheless, the amino acids that compose the substrate-binding site are less conserved and have different properties, which might dictate the substrate specificity. Structural comparison has revealed insights into the molecular basis of the differential thermostability of D-HYDs. The more thermostable HYD(Tsp) contains more aromatic residues in the interior of the structure than HYD(Bp) and HYD(Bst). Changes of large aromatic residues in HYD(Tsp) to smaller residues in HYD(Bp) or HYD(Bst) decrease the hydrophobicity and create cavities inside the structure. HYD(Tsp) has more salt bridges and hydrogen-bonding interactions and less oxidation susceptible Met and Cys residues on the protein surface than HYD(Bp) and HYD(Bst). Besides, HYD(Tsp) also contains more rigid Pro residues. These factors are likely to make major contributions to the varying thermostability of these enzymes. This information could be exploited in helping to engineer more thermostable mesophilic enzymes.

PubMed: 12837777
DOI: 10.1128/JB.185.14.4038-4049.2003

実験手法

X-RAY DIFFRACTION (2.7 Å)