Singh K, Modak M J
Dept of Biochemistry and Molecular Biology, UMD-New Jersey Medical School, Newark 07103, USA.
Trends Biochem Sci. 1998 Aug;23(8):277-81. doi: 10.1016/s0968-0004(98)01250-x.
Crystal structures of various DNA polymerases show a common structural topology that resembles a right hand and has distinct finger, palm and thumb subdomains. Early models of the klenow fragment (KF) of Escherichia coli polymerase I showed DNA entering a large cleft that faces the palm subdomain where the catalytic site is situated1,2. However, subsequent resolution of the structures of HIV-1 reverse transcriptase, KF and polymerase beta (pol beta) bound to DNA3-5 yielded conflicting data that suggested a different orientation for DNA bound to pol beta compared with DNA bound to other polymerases. The debate, on the correct orientation of the template-primer DNA, that followed failed to reach a consensus. Using an alternative superposition scheme, we now provide convincing evidence for a common DNA-binding mode that is applicable to all polymerases, including pol beta.
各种DNA聚合酶的晶体结构显示出一种常见的结构拓扑，类似于右手，具有不同的手指、手掌和拇指亚结构域。大肠杆菌聚合酶I的klenow片段（KF）的早期模型显示，DNA进入一个面对催化位点所在的手掌亚结构域的大裂缝1,2。然而，随后对与DNA结合的HIV-1逆转录酶、KF和聚合酶β（pol beta）结构的解析3-5产生了相互矛盾的数据，表明与结合到其他聚合酶的DNA相比，结合到pol beta的DNA具有不同的方向。随后关于模板-引物DNA正确方向的争论未能达成共识。现在，我们使用一种替代的叠加方案，为适用于所有聚合酶（包括pol beta）的常见DNA结合模式提供了令人信服的证据。
