8FDB

CRYSTAL STRUCTURE OF NAGB-II PHOSPHOSUGAR ISOMERASE FROM Shewanella denitrificans OS217 IN COMPLEX WITH GLUCITOLAMINE-6-PHOSPHATE AT 3.06 A RESOLUTION.

8FDB の概要

• エントリーDOI: 10.2210/pdb8fdb/pdb
• 分子名称: Glutamine-fructose-6-phosphate transaminase (Isomerizing), 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE, MAGNESIUM ION, ... (6 entities in total)
• 機能のキーワード: deaminase isomerization-deamination amino-sugar metabolism positive cooperativity and allosteric activation sugar-isomerase domain, isomerase
• 由来する生物種: Shewanella denitrificans OS217; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 72274.39

構造登録者

Rodriguez-Romero, A.,Rodriguez-Hernandez, A.,Marcos-Viquez, J.,Bustos-Jaimes, I. (登録日: 2022-12-02, 公開日: 2023-05-17, 最終更新日: 2023-06-07)

主引用文献

Marcos-Viquez, J.,Rodriguez-Hernandez, A.,Alvarez-Anorve, L.I.,Medina-Garcia, A.,Plumbridge, J.,Calcagno, M.L.,Rodriguez-Romero, A.,Bustos-Jaimes, I.
Substrate binding in the allosteric site mimics homotropic cooperativity in the SIS-fold glucosamine-6-phosphate deaminases.
Protein Sci., 32:e4651-e4651, 2023

PubMed Abstract: Glucosamine-6-phosphate (GlcN6P) deaminases from Escherichia coli (EcNagBI) and Shewanella denitrificans (SdNagBII) are special examples of what constitute nonhomologous isofunctional enzymes due to their convergence, not only in catalysis, but also in cooperativity and allosteric properties. Additionally, we found that the sigmoidal kinetics of SdNagBII cannot be explained by the existing models of homotropic activation. This study describes the regulatory mechanism of SdNagBII using enzyme kinetics, isothermal titration calorimetry (ITC), and X-ray crystallography. ITC experiments revealed two different binding sites with distinctive thermodynamic signatures: a single binding site per monomer for the allosteric activator N-acetylglucosamine 6-phosphate (GlcNAc6P) and two binding sites per monomer for the transition-state analog 2-amino-2-deoxy-D-glucitol 6-phosphate (GlcNol6P). Crystallographic data demonstrated the existence of an unusual allosteric site that can bind both GlcNAc6P and GlcNol6P, implying that the homotropic activation of this enzyme arises from the occupation of the allosteric site by the substrate. In this work we describe the presence of this novel allosteric site in the SIS-fold deaminases, which is responsible for the homotropic and heterotropic activation of SdNagBII by GlcN6P and GlcNAc6P, respectively. This study unveils an original mechanism to generate a high degree of homotropic activation in SdNagBII, mimicking the allosteric and cooperative properties of hexameric EcNagBI but with a reduced number of subunits.

PubMed: 37145875
DOI: 10.1002/pro.4651

実験手法

X-RAY DIFFRACTION (3.06 Å)