Structural Characterization of the Hydratase-Aldolases, NahE and PhdJ: Implications for the Specificity, Catalysis, and <i>N</i>-Acetylneuraminate Lyase Subgroup of the Aldolase Superfamily
作者:Jake A. LeVieux、Brenda Medellin、William H. Johnson、Kaci Erwin、Wenzong Li、Ingrid A. Johnson、Yan Jessie Zhang、Christian P. Whitman
DOI:10.1021/acs.biochem.8b00532
日期:2018.6.26
NahE and PhdJ are bifunctional hydratase-aldolases in bacterial catabolic pathways for naphthalene and phenanthrene, respectively. Bacterial species with these pathways can use polycyclic aromatic hydrocarbons (PAHs) as sole sources of carbon and energy. Because of the harmful properties of PAHs and their widespread distribution and persistence in the environment, there is great interest in understanding these degradative pathways, including the mechanisms and specificities of the enzymes found in the pathways. This knowledge can be used to develop and optimize bioremediation techniques. Although hydratase-aldolases catalyze a major step in the PAH degradative pathways, their mechanisms are poorly understood. Sequence analysis identified NahE and PhdJ as members of the N-acetylneuraminate lyase (NAL) subgroup in the aldolase superfamily. Both have a conserved lysine and tyrosine (for Schiff base formation) as well as a GXXGE motif (to bind the pyruvoyl carboxylate group). Herein, we report the structures of NahE, PhdJ, and PhdJ covalently bound to substrate via a Schiff base. Structural analysis and dynamic light scattering experiments show that both enzymes are tetramers. A hydrophobic helix insert, present in the active sites of NahE and PhdJ, might differentiate them from other NAL subgroup members. The individual specificities of NahE and PhdJ are governed by Asn-281/Glu-285 and Ser-278/Asp-282, respectively. Finally, the PhdJ complex structure suggests a potential mechanism for hydration of substrate and subsequent retro-aldol fission. The combined findings fill a gap in our mechanistic understanding of these enzymes and their place in the NAL subgroup.
NahE和PhdJ分别是细菌分解途径中的双功能水合酶-醛缩酶,用于分解萘和菲。具有这些途径的细菌种类可以将多环芳烃(PAHs)作为唯一的碳源和能源。由于PAHs具有有害性质,且在环境中广泛分布和持久存在,因此人们非常关注理解这些降解途径,包括途径中酶的机制和特异性。这些知识可以用于开发和优化生物修复技术。尽管水合酶-醛缩酶在PAH降解途径中催化了一个主要步骤,但其机制了解甚少。通过序列分析,NahE和PhdJ被确定为醛缩酶超家族中N-乙酰神经氨酸裂解酶(NAL)亚组的成员。两者都具有保守的赖氨酸和酪氨酸(用于希夫碱的形成)以及GXXGE基序(用于结合吡咯烷酮羧酸基团)。在此,我们报告了NahE、PhdJ以及通过希夫碱与底物共价结合的PhdJ的结构。结构分析和动态光散射实验表明,这两种酶都是四聚体。NahE和PhdJ活性位点中存在的疏水性螺旋插入可能使它们与NAL亚组的其他成员区分开来。NahE和PhdJ的个体特异性分别由Asn-281/Glu-285和Ser-278/Asp-282控制。最后,PhdJ复合物结构暗示了一种潜在的底物水合作用机制以及随后的逆醛缩裂解。综合发现填补了我们对这些酶机制及其在NAL亚组中位置的理解的空白。