Singleton M R, Håkansson K, Timson D J, Wigley D B
Sir William Dunn School of Pathology, University of Oxford, South ParksRoad, Oxford OX1 3RE, UK.
Structure. 1999 Jan 15;7(1):35-42. doi: 10.1016/s0969-2126(99)80007-0.
DNA ligases catalyse phosphodiester bond formation between adjacent bases in nicked DNA, thereby sealing the nick. A key step in the catalytic mechanism is the formation of an adenylated DNA intermediate. The adenyl group is derived from either ATP (in eucaryotes and archaea) or NAD+4 (in bacteria). This difference in cofactor specificity suggests that DNA ligase may be a useful antibiotic target.
The crystal structure of the adenylation domain of the NAD+-dependent DNA ligase from Bacillus stearothermophilus has been determined at 2.8 A resolution. Despite a complete lack of detectable sequence similarity, the fold of the central core of this domain shares homology with the equivalent region of ATP-dependent DNA ligases, providing strong evidence for the location of the NAD+-binding site.
Comparison of the structure of the NAD+4-dependent DNA ligase with that of ATP-dependent ligases and mRNA-capping enzymes demonstrates the manifold utilisation of a conserved nucleotidyltransferase domain within this family of enzymes. Whilst this conserved core domain retains a common mode of nucleotide binding and activation, it is the additional domains at the N terminus and/or the C terminus that provide the alternative specificities and functionalities in the different members of this enzyme superfamily.
DNA连接酶催化缺口DNA中相邻碱基之间磷酸二酯键的形成，从而封闭缺口。催化机制中的关键步骤是形成腺苷酸化的DNA中间体。腺苷基团来源于ATP（真核生物和古细菌中）或NAD⁺（细菌中）。这种辅因子特异性的差异表明DNA连接酶可能是一个有用的抗生素靶点。
嗜热脂肪芽孢杆菌依赖NAD⁺的DNA连接酶腺苷化结构域的晶体结构已在2.8 Å分辨率下确定。尽管完全缺乏可检测到的序列相似性，但该结构域中心核心的折叠与依赖ATP的DNA连接酶的等效区域具有同源性，为NAD⁺结合位点的定位提供了有力证据。
将依赖NAD⁺的DNA连接酶的结构与依赖ATP的连接酶及mRNA加帽酶的结构进行比较，证明了该酶家族中保守的核苷酸转移酶结构域的多种用途。虽然这个保守的核心结构域保留了核苷酸结合和激活的共同模式，但正是N端和/或C端的额外结构域在该酶超家族的不同成员中提供了不同的特异性和功能。
