Hajredini Fatlum, Ghose Ranajeet
Department of Chemistry and Biochemistry, The City College of New York, New York, NY, United States.
PhD Program in Biochemistry, The Graduate Center of CUNY, New York, NY, United States.
Front Mol Biosci. 2021 Oct 1;8:747206. doi: 10.3389/fmolb.2021.747206. eCollection 2021.
Bacterial tyrosine kinases (BY-kinases) and shikimate kinases (SKs) comprise two structurally divergent P-loop containing enzyme families that share similar catalytic site geometries, most notably with respect to their Walker-A, Walker-B, and DxD motifs. We had previously demonstrated that in BY-kinases, a specific interaction between the Walker-A and Walker-B motifs, driven by the conserved "catalytic" lysine housed on the former, leads to a conformation that is unable to efficiently coordinate Mg•ATP and is therefore incapable of chemistry. Here, using enhanced sampling molecular dynamics simulations, we demonstrate that structurally similar interactions between the Walker-A and Walker-B motifs, also mediated by the catalytic lysine, stabilize a state in SKs that deviates significantly from one that is necessary for the optimal coordination of Mg•ATP. This structural role of the Walker-A lysine is a general feature in SKs and is found to be present in members that encode a Walker-B sequence characteristic of the family ( SK), and in those that do not ( SK). Thus, the structural role of the Walker-A lysine in stabilizing an inactive state, distinct from its catalytic function, is conserved between two distantly related P-loop containing kinase families, the SKs and the BY-kinases. The universal conservation of this element, and of the key characteristics of its associated interaction partners within the Walker motifs of P-loop containing enzymes, suggests that this structural role of the Walker-A lysine is perhaps a widely deployed regulatory mechanism within this ancient family.
细菌酪氨酸激酶（BY激酶）和莽草酸激酶（SK）构成了两个结构上不同的含P环酶家族，它们具有相似的催化位点几何结构，最显著的是在其沃克A、沃克B和DxD基序方面。我们之前已经证明，在BY激酶中，由前者上保守的“催化”赖氨酸驱动的沃克A和沃克B基序之间的特定相互作用，导致一种无法有效配位Mg•ATP的构象，因此无法进行化学反应。在这里，我们使用增强采样分子动力学模拟表明，沃克A和沃克B基序之间结构相似的相互作用，同样由催化赖氨酸介导，在SK中稳定了一种状态，该状态与Mg•ATP最佳配位所需的状态有显著偏差。沃克A赖氨酸的这种结构作用是SK中的一个普遍特征，并且发现在编码该家族特征性沃克B序列的成员中存在，在不编码的成员中也存在。因此，沃克A赖氨酸在稳定非活性状态方面的结构作用，与其催化功能不同，在两个远亲的含P环激酶家族SK和BY激酶之间是保守的。该元素及其在含P环酶的沃克基序内相关相互作用伙伴的关键特征的普遍保守性表明，沃克A赖氨酸的这种结构作用可能是这个古老家族中广泛应用的一种调节机制。
