Department of Chemistry, Umeå University, 901 87 Umeå, Sweden.
Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden.
Sci Adv. 2022 Nov 4;8(44):eabm4089. doi: 10.1126/sciadv.abm4089.
Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from (OdinAK). belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be "atypical." On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.
酶催化对选择性、活性位点结构和动力学有严格的依赖性。为了深入了解这些特性的相互作用，我们建立了一种方法，结合 NMR、晶体学和 MD 模拟，专注于从 （OdinAK）中分离出的普遍存在的磷酸转移酶腺苷酸激酶（AK）。属于 Asgard 古菌门，被认为是与真核生物最接近的已知祖先。我们表明，OdinAK 是一种嗜热的三聚体，与其他 AK 家族成员不同，它可以使用所有 NTP 进行磷酸化反应。OdinAK-NTP 复合物的晶体结构揭示了一个通用的 NTP 结合基序，而 F NMR 实验则揭示了一个保守的、限速的动态特征。由于三聚体化，OdinAK 的活性位点缺乏一个关键的催化残基，因此被认为是“非典型的”。基于与人类单体同源物的发现关系，我们的研究结果从酶底物特异性和冷适应的进化角度进行了讨论。
