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A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase.

ABSTRACT: The theories for substrate recognition in enzyme catalysis have evolved from lock-key to induced fit, then conformational selection, and conformational selection followed by induced fit. However, the prevalence and consensus of these theories require further examination. Here we use cryogenic electron microscopy and African swine fever virus type 2 topoisomerase (AsfvTop2) to demonstrate substrate binding theories in a joint and ordered manner: catalytic selection by the enzyme, conformational selection by the substrates, then induced fit. The apo-AsfvTop2 pre-exists in six conformers that comply with the two-gate mechanism directing DNA passage and release in the Top2 catalytic cycle. The structures of AsfvTop2-DNA-inhibitor complexes show that substantial induced-fit changes occur locally from the closed apo-conformer that however is too far-fetched for the open apo-conformer. Furthermore, the ATPase domain of AsfvTop2 in the MgAMP-PNP-bound crystal structures coexist in reduced and oxidized forms involving a disulfide bond, which can regulate the AsfvTop2 function.

SUBMITTER: Chang CM

PROVIDER: S-EPMC10901890 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

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A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase.

Chang Chiung-Wen Mary CM Wang Shun-Chang SC Wang Chun-Hsiung CH Pang Allan H AH Yang Cheng-Han CH Chang Yao-Kai YK Wu Wen-Jin WJ Tsai Ming-Daw MD

Communications chemistry 20240228 1

The theories for substrate recognition in enzyme catalysis have evolved from lock-key to induced fit, then conformational selection, and conformational selection followed by induced fit. However, the prevalence and consensus of these theories require further examination. Here we use cryogenic electron microscopy and African swine fever virus type 2 topoisomerase (AsfvTop2) to demonstrate substrate binding theories in a joint and ordered manner: catalytic selection by the enzyme, conformational s ...[more]

PMID: 38418525

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Project description:Type II topoisomerases ubiquitously exist in cellular organisms, where they play an essential role in resolving the topological problems of DNA. The viral type II topoisomerase encoded by the African swine fever virus (ASFV) is critical for viral replication and infection, thus representing an attractive target for antiviral drug development. Here we report two cryo-EM structures of ASFV topoisomerase P1192R in distinct conformations at an overall resolution of 3.16 Å and 3.13 Å, respectively. P1192R assembles as a homodimer with the C-gate formed by the coiled-coil domain adopting a closed or open conformation before reaction, providing the first visual evidence for the dynamic motions of the C-gate of type II topoisomerase. Comparative structural comparisons of eukaryotic homologs and P1192R reveal the unique structural features of P1192R, including the active site configuration, a flexible loop in the TOPRIM domain, an additionally inserted α-helix in the tower domain, and a pin-like structure in the C-terminal coiled-coil domain, which are important for enzyme activity and protein folding. These findings provide important insights into the structure and function of viral topoisomerases and may guide the efficient development of anti-ASFV drugs. Moreover, our study also offers structural evidence to support the scenario of the viral origin of eukaryotic type IIA topoisomerases. IMPORTANCE African swine fever virus (ASFV) is a highly contagious virus that causes lethal hemorrhagic diseases known as African swine fever (ASF) with a case fatality rate of 100%. There is an urgent need to develop anti-ASFV drugs. We determine the first high-resolution structures of viral topoisomerase ASFV P1192R in both the closed and open C-gate forms. P1192R shows a similar overall architecture with eukaryotic and prokaryotic type II topoisomerases, which have been successful targets of many antimicrobials and anticancer drugs, with the most similarity to yeast topo II. P1192R also exhibits differences in the details of active site configuration, which are important to enzyme activity. These two structures offer useful structural information for antiviral drug design and provide structural evidence to support that eukaryotic type IIA topoisomerase likely originated from horizontal gene transfer from the virus.

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A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase.

Publications

A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase.

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