2F4Q

Crystal Structure of Deinococcus radiodurans topoisomerase IB

2F4Q の概要

• エントリーDOI: 10.2210/pdb2f4q/pdb
• 分子名称: type I topoisomerase, putative (2 entities in total)
• 機能のキーワード: topoisomerase ib, isomerase
• 由来する生物種: Deinococcus radiodurans
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 39311.87

構造登録者

Patel, A.,Shuman, S.,Mondragon, A. (登録日: 2005-11-23, 公開日: 2005-12-27, 最終更新日: 2024-10-30)

主引用文献

Patel, A.,Shuman, S.,Mondragon, A.
Crystal structure of a bacterial type IB DNA topoisomerase reveals a preassembled active site in the absence of DNA.
J.Biol.Chem., 281:6030-6037, 2006

PubMed Abstract: Type IB DNA topoisomerases are found in all eukarya, two families of eukaryotic viruses (poxviruses and mimivirus), and many genera of bacteria. They alter DNA topology by cleaving and resealing one strand of duplex DNA via a covalent DNA-(3-phosphotyrosyl)-enzyme intermediate. Bacterial type IB enzymes were discovered recently and are described as poxvirus-like with respect to their small size, primary structures, and bipartite domain organization. Here we report the 1.75-A crystal structure of Deinococcus radiodurans topoisomerase IB (DraTopIB), a prototype of the bacterial clade. DraTopIB consists of an amino-terminal (N) beta-sheet domain (amino acids 1-90) and a predominantly alpha-helical carboxyl-terminal (C) domain (amino acids 91-346) that closely resemble the corresponding domains of vaccinia virus topoisomerase IB. The five amino acids of DraTopIB that comprise the catalytic pentad (Arg-137, Lys-174, Arg-239, Asn-280, and Tyr-289) are preassembled into the active site in the absence of DNA in a manner nearly identical to the pentad configuration in human topoisomerase I bound to DNA. This contrasts with the apoenzyme of vaccinia topoisomerase, in which three of the active site constituents are either displaced or disordered. The N and C domains of DraTopIB are splayed apart in an "open" conformation, in which the surface of the catalytic domain containing the active site is exposed for DNA binding. A comparison with the human topoisomerase I-DNA cocrystal structure suggests how viral and bacterial topoisomerase IB enzymes might bind DNA circumferentially via movement of the N domain into the major groove and clamping of a disordered loop of the C domain around the helix.

PubMed: 16368685
DOI: 10.1074/jbc.M512332200

実験手法

X-RAY DIFFRACTION (1.75 Å)