We will use structural biology tools to investigate DNA-processing enzymes from human pathogens, and those relevant to genome integrity or disease process. An area of particular interest is the mechanism of retrovirus integration by the viral integrase (IN), which forms a multimeric complex with both ends of the linear viral DNA genome and captures a cellular target DNA for concerted insertions of the viral DNA termini. The IN-viral DNA complex formed by HIV-1 IN is the target of a class of antiviral drugs called IN strand-transfer inhibitors. Therefore, a better understanding of the IN-DNA interactions is important for improving the clinically used IN inhibitors as well as designing next-generation inhibitors. We are pursuing crystal structures of IN-DNA complexes from HIV-1 and closely related retroviruses, and structure of those in complex with the host co- factor LEDGF/p75. Our preliminary data suggest that the architectures of the multimeric IN complex containing viral and target DNA molecules are distinct between the extensively characterized prototype foamy virus and other retroviruses with smaller 3-domain INs, including Rous sarcoma virus and HIV-1. Besides retrovirus INs, we are interested in the bacterial and pox viral enzymes responsible for regenerating the hairpin telomeres of linear chromosomes by resolving concatemeric replication intermediates. We also study enzymes involved in cleaning damaged DNA ends for error-free repair by end-joining. Through studies of these systems, we intend to learn novel principles in DNA-protein interactions and obtain structural information that can aid in inhibitor development or design of useful engineered enzymes.
Using X-ray crystallography and other structural biology methods, we will investigate DNA-processing enzymes from human pathogens, including the integrase protein from HIV-1. We will also study enzymes important for maintaining genome integrity. The information obtained through this research may help design new drugs useful in treating various human diseases.
|Kurniawan, Fredy; Shi, Ke; Kurahashi, Kayo et al. (2018) Crystal Structure of Entamoeba histolytica Cdc45 Suggests a Conformational Switch that May Regulate DNA Replication. iScience 3:102-109|
|Bohl, Thomas E; Shi, Ke; Lee, John K et al. (2018) Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli. Nat Commun 9:377|
|Ribeiro, Carlos J A; Kankanala, Jayakanth; Shi, Ke et al. (2018) New fluorescence-based high-throughput screening assay for small molecule inhibitors of tyrosyl-DNA phosphodiesterase 2 (TDP2). Eur J Pharm Sci 118:67-79|
|Bohl, Thomas E; Ieong, Pek; Lee, John K et al. (2018) The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release. J Biol Chem 293:7969-7981|
|Shaban, Nadine M; Shi, Ke; Lauer, Kate V et al. (2018) The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism. Mol Cell 69:75-86.e9|
|Bera, Sibes; Pandey, Krishan K; Aihara, Hideki et al. (2018) Differential assembly of Rous sarcoma virus tetrameric and octameric intasomes is regulated by the C-terminal domain and tail region of integrase. J Biol Chem 293:16440-16452|
|Bohl, Thomas E; Aihara, Hideki (2018) Current Progress in the Structural and Biochemical Characterization of Proteins Involved in the Assembly of Lipopolysaccharide. Int J Microbiol 2018:5319146|
|Pandey, Krishan K; Bera, Sibes; Shi, Ke et al. (2017) A C-terminal ""Tail"" Region in the Rous Sarcoma Virus Integrase Provides High Plasticity of Functional Integrase Oligomerization during Intasome Assembly. J Biol Chem 292:5018-5030|
|Bertram, Jonathan H; Mulliner, Kalene M; Shi, Ke et al. (2017) Five Fatty Aldehyde Dehydrogenase Enzymes from Marinobacter and Acinetobacter spp. and Structural Insights into the Aldehyde Binding Pocket. Appl Environ Microbiol 83:|
|Shi, Ke; Carpenter, Michael A; Banerjee, Surajit et al. (2017) Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat Struct Mol Biol 24:131-139|
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