Publications

Found 47 results
Filters: Author is Shi, Ke  [Clear All Filters]
2019
Tang, H., Shi, K., Shi, C., Aihara, H., Zhang, J., and Du, G. (2019) Enhancing subtilisin thermostability through a modified normalized B-factor analysis and loop-grafting strategy. J Biol Chem. 10.1074/jbc.RA119.010658
Tang, H., Zhang, J., Shi, K., Aihara, H., and Du, G. (2019) Insight into subtilisin E-S7 cleavage pattern based on crystal structure and hydrolysates peptide analysis. Biochem Biophys Res Commun. 10.1016/j.bbrc.2019.03.064
2018
Shaban, N. M., Shi, K., Lauer, K. V., Carpenter, M. A., Richards, C. M., Salamango, D., Wang, J., Lopresti, M. W., Banerjee, S., Levin-Klein, R., Brown, W. L., Aihara, H., and Harris, R. S. (2018) The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism. Mol Cell. 69, 75-86.e9
Kurniawan, F., Shi, K., Kurahashi, K., Bielinsky, A. - K., and Aihara, H. (2018) Crystal Structure of Cdc45 Suggests a Conformational Switch that May Regulate DNA Replication. iScience. 3, 102-109
Bohl, T. E., Shi, K., Lee, J. K., and Aihara, H. (2018) Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli. Nat Commun. 9, 377
Lee, J. K., Bosnakovski, D., Toso, E. A., Dinh, T., Banerjee, S., Bohl, T. E., Shi, K., Orellana, K., Kyba, M., and Aihara, H. (2018) Crystal Structure of the Double Homeodomain of DUX4 in Complex with DNA. Cell Rep. 25, 2955-2962.e3
Ribeiro, C. J. A., Kankanala, J., Shi, K., Kurahashi, K., Kiselev, E., Ravji, A., Pommier, Y., Aihara, H., and Wang, Z. (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
Xing, Q., Shi, K., Portaliou, A., Rossi, P., Economou, A., and Kalodimos, C. G. (2018) Structures of chaperone-substrate complexes docked onto the export gate in a type III secretion system. Nat Commun. 9, 1773
Bohl, T. E., Ieong, P., Lee, J. K., Lee, T., Kankanala, J., Shi, K., Demir, Ö., Kurahashi, K., Amaro, R. E., Wang, Z., and Aihara, H. (2018) The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release. J Biol Chem. 10.1074/jbc.RA118.002503
Shi, K., Bohl, T. E., Park, J., Zasada, A., Malik, S., Banerjee, S., Tran, V., Li, N., Yin, Z., Kurniawan, F., Orellana, K., and Aihara, H. (2018) T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction. Nucleic Acids Res. 10.1093/nar/gky776
2017
Shi, K., Demir, Ö., Carpenter, M. A., Wagner, J., Kurahashi, K., Harris, R. S., Amaro, R. E., and Aihara, H. (2017) Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B. Sci Rep. 7, 17415
Bertram, J. H., Mulliner, K. M., Shi, K., Plunkett, M. H., Nixon, P., Serratore, N. A., Douglas, C. J., Aihara, H., and Barney, B. M. (2017) Five Fatty Aldehyde Dehydrogenase Enzymes from Marinobacter and Acinetobacter spp. and Structural Insights into the Aldehyde Binding Pocket. Appl Environ Microbiol. 10.1128/AEM.00018-17
Shi, K., Carpenter, M. A., Banerjee, S., Shaban, N. M., Kurahashi, K., Salamango, D. J., McCann, J. L., Starrett, G. J., Duffy, J. V., Demir, Ö., Amaro, R. E., Harki, D. A., Harris, R. S., and Aihara, H. (2017) Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat Struct Mol Biol. 24, 131-139
2016
Shaban, N. M., Shi, K., Li, M., Aihara, H., and Harris, R. S. (2016) 1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure. J Mol Biol. 428, 2307-16
Yin, Z., Shi, K., Banerjee, S., Pandey, K. K., Bera, S., Grandgenett, D. P., and Aihara, H. (2016) Crystal structure of the Rous sarcoma virus intasome. Nature. 530, 362-6
Chen, X., Randles, L., Shi, K., Tarasov, S. G., Aihara, H., and Walters, K. J. (2016) Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome. Structure. 24, 1257-70
2015
Shi, K., Carpenter, M. A., Kurahashi, K., Harris, R. S., and Aihara, H. (2015) Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain. J Biol Chem. 290, 28120-30
2013
Shi, K., Huang, W. Mun, and Aihara, H. (2013) An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation. PLoS Biol. 11, e1001472
Shi, K., Pandey, K. K., Bera, S., Vora, A. C., Grandgenett, D. P., and Aihara, H. (2013) A possible role for the asymmetric C-terminal domain dimer of Rous sarcoma virus integrase in viral DNA binding. PLoS One. 8, e56892
Chen, L., Shi, K., Yin, Z., and Aihara, H. (2013) Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution. Nucleic Acids Res. 41, 648-56
2012
Huang, W. Mun, DaGloria, J., Fox, H., Ruan, Q., Tillou, J., Shi, K., Aihara, H., Aron, J., and Casjens, S. (2012) Linear chromosome-generating system of Agrobacterium tumefaciens C58: protelomerase generates and protects hairpin ends. J Biol Chem. 287, 25551-63
Shi, K., Kurahashi, K., Gao, R., Tsutakawa, S. E., Tainer, J. A., Pommier, Y., and Aihara, H. (2012) Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2. Nat Struct Mol Biol. 19, 1372-7

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