55. Tandukar S, Kwon E, Kim DY (2023) Structural insights into the regulation of peptidoglycan DL-endopeptidases by inhibitory protein IseA. Structure. 31, 619-628.


54. Kwon E*, Dahal P*, Kim DY (2022) Crystal structure and biochemical analysis suggest that YjoB ATPase is a putative substrate-specific molecular chaperone. Proc. Natl. Acad. Sci. USA. 119, e2207856119. (bioRxiv. doi: https://doi.org/10.1101/2022.05.06.490860.) (*These authors contributed equally.)

53. Cha JY, Kim J, Jeong SY, Shin GI, Ji MG, Hwang JW, Khaleda L, Liao X, Ahn G, Park HJ, Kim DY, Pardo JM, Lee SY, Yun DJ, Somers DE, Kim WY (2022) The Na+/H+ antiporter SALT OVERLY SENSITIVE 1 regulates salt compensation of circadian rhythms by stabilizing GIGANTEA in Arabidopsis. Proc. Natl. Acad. Sci. USA. 119, e2207275119.

52. Kwon E*, Pathak D*, Dahal P*, Tandukar S, Jung HS, Kim WY, Kim DY (2022) Structural analysis of the regulation of blue-light receptors by GIGANTEA. Cell Reports. 39, 110700.

51. Dahal P*, Kwon E*, Pathak D*, Kim DY (2022) Crystal structure of a tandem B-box domain from Arabidopsis CONSTANS. Biochem. Biophys. Res. Commun. 599, 38-42.


50. Yeon M, Kim Y, Pathak D, Kwon E, Kim DY, Jeong MS, Jung HS, Jeoung D (2021) The CAGE-MiR-181b-5p-S1PR1 axis regulates anticancer drug resistance and autophagy in gastric cancer cells. Front Cell Dev Biol. 9, 666387.

49. Dahal P, Kim DY, Kwon E (2021) Crystal structure of the DNA-binding domain of Bacillus subtilis CssR. Biochem. Biophys. Res. Commun. 555, 26-31.

48. Sevillano N, Green EM, Votteler J, Kim DY, Ren X, Yang B, Liu X, Lourenço AL, Hurley JH, Farr-Jones S, Gross JD, Cheng Y, Craik CS (2021) Identification of recombinant Fabs for structural and functional characterization of HIV-host factor complexes. PLoS One. 16, e0250318.


47. Pathak D, Kwon E, Kim DY (2020) Selective interactions between mimivirus uracil-DNA glycosylase and inhibitory proteins determined by a single amino acid. Journal of Structural Biology. 211, 107552..

46. Pathak D*, Jin KS*, Tandukar S, Kim JH, Kwon E, Kim DY (2020) Structural insights into the regulation of SigB activity by RsbV and RsbW. IUCrJ. 7, 737-747.

45. Chang HW, Kanegasaki S, Jin F, Deng Y, You Z, Chang JH, Kim DY, Timilshina M, Kim JR, Lee YJ, Toyama-Sorimachi N, Tsuchiya T (2020) A common signaling pathway leading to degranulation in mast cells and its regulation by CCR1-ligand. Allergy. 75, 1371-1381.


44. Kwon, E.*, Pathak, D.*, Kim, H.*, Dahal, P., Ha, S. C., Lee, S. S., Jeong, H., Jeoung, D., Chang, H. W., Jung, H. S.,and Kim, D. Y. (2019) Structural insights into stressosome assembly. IUCrJ. 6, 938-947.

43. Kwon, E., Devkota, S. R., Pathak, D., Dahal, P., and Kim, D. Y. (2019) Structural analysis of the recognition of the -35 promoter element by SigW from Bacillus subtilis. PLoS One. 14, e0221666.

42. Deng, Y., Jin, F., Li, X., Park, S. J., Chang, J. H., Kim, D. Y., Kim, J., A., Nam, J., W., Choi, H., Lee, Y. J., Chang, H. W. (2019) Sauchinone suppresses FcεRI-mediated mast cell signaling and anaphylaxis through regulation of LKB1/AMPK axis and SHP-1-Syk signaling module. Int. Immunopharmacol. 74, 105702.

41. Kwon, E., Li, X., Deng, Y., Chang, H. W., and Kim, D. Y. (2019) AMPK is down-regulated by the CRL4A-CRBN axis through the polyubiquitination of AMPKα isoforms. FASEB J. 33, 6539-6550.

40. Jin, F., Li, X., Deng, Y., Timilshina, M., Huang, B., Kim, D. Y., Chang, J. H., Ichinose, H., Baek, S. H., Murakami, M., Lee, Y. J., and Chang, H. W. (2019) The orphan unclear receptor NR4A1 promotes FcεRI-stimulated mast cell activation and anaphylaxis by counteracting the inhibitory LKB1/AMPK axis. Allergy. 74, 1145-1156.


39. Kwon, M. J., Han, M. H., Bagley, J. A., Hyeon. D. Y., Ko, B. S., Lee, Y. M., Cha, I. J., Kim, S. Y., Kim, D. Y., Kim, H. M., Hwang, D., Lee, S. B., and Jan, Y. N. (2018) Coiled-coil structure-dependent interactions between polyQ proteins and Foxo lead to dendrite pathology and behavioral defects. Proc. Natl. Acad. Aci. U S A. 115, E10748-E10757.

38. Nayak, A, Kim, D. Y., Trnka, M. J., Kerr, C. H., Lidsky, P. V., Stanley, D. J., Rivera, B. M., Li, K. H., Burlingame, A. L., Jan, E., Frydman, J., Gross, J. D., and Andino, R. (2018) A viral protein restricts Drosophila RNAi immunity by regulating argonaute activity and stability. Cell Host Microbe. 24, 542-557.

37. Banskota, S., Dahal, S., Kwon, E., Kim, D. Y., and Kim, J. A. (2018) β-Catenin gene promoter hypermethylation by reactive oxygen species correlates with the migratory and invasive potentials of colon cancer cells. Cell Oncol. (Dordr). 41, 569-580.

36. Li, X., Park, S. J., Jin, F., Deng, Y., Yang, J. H., Chang J. H., Kim, D. Y., Kim, J. A., Lee, Y. J., Murakami, M., Son, K. H., and Chang, H. W. (2018) Tanshinone IIA suppresses FcεRI-mediated mast cell signaling and anaphylaxis by activation of the Sirt1/LKB1/AMPK pathway. Biochem. Pharmacol. 152, 362-372.

35. Gautam, J., Banskota, S., Shah, S., Jee, J. G., Kwon, E., Wang, Y., Kim, D. Y., Chang, H. W., and Kim, J. A. (2018) 4-Hydroxynonenal-induced GPR109A (HCA2 receptor) activation elicits bipolar responses, Gαi-mediated anti-inflammatory effects and Gβγ-mediated cell death. Br. J. Pharmacol. 175, 2581-2598.


34. Kwon, E., Pathak, D., Chang, H. W., and , D. Y. (2017) Crystal structure of mimivirus uracil-DNA glycosylase. PLoS One. 12, e0182382.

33. Li, X., Lee, Y. J., Jin, F., Park, Y. N., Deng, Y., Kang, Y., Yang, J. H., Chang, J. H., Kim, D. Y., Kim, J. A., Chang, Y. C., Ko, H. J., Kim, C. H., Murakami, M., and Chang, H. W. (2017) Sirt1 negatively regulates FcεRI-mediated mast cell activation through AMPK- and PTP-B-dependent processes. Sci. Rep. 7, 6444.

32. Kim, D. Y. and Gross, J. D. (2017) CBFb and HIV infection. Adv. Exp. Med. Biol. 962, 415-431.

31. Devkota, S. R.*, Kwon, E.*, Ha, S. C., Chang, H. W.,and Kim, D. Y. (2017) Structural insights into the regulation of Bacillus subtilis SigW activity by anti-sigma RsiW. PLoS One. 12, e0174284.


30. Li, X., Kwon, O., Kim, D. Y., Taketomi, Y., Murakami, M., and Chang, H. W. (2016) NecroX-5 suppresses IgE/Ag-stimulated anaphylaxis and mast cell activation by regulating the SHP-1-Syk signaling module. Allergy. 71, 198-209.


29. Li, X., Yang, J. H., Jin, Y., Jin, F., Kim, D. Y., Chang, J. H., Kim, J. A., Son, J. K., Moon, T. C., Son, K. H., and Chang, H. W. (2015) 15, 16-Dihydrotanshinone I suppresses IgE-Ag stimulated mouse bone marrow-derived mast cell activation by inhibiting Syk kinase. J. Ethnopharmacol. 169, 138-144.

28. Kim, D. Y. (2015) Two stress sensor proteins for the expression of sigmaE regulon: DegS and RseB. J. Micorbiol. 53, 306-310.

27. Kim, D. Y. (2015) The assembly of Vif ubiquitin E3 ligase for APOBEC3 degradation. Arch. Pharm. Res. 38, 435-445.


26. Kim, D. Y.*, Kwon, E.*, Harley, P. D.*, Crosby, D. C., Mann, S., Krogan, N. J., and Gross, J. D. (2013) CBFb stabilizes HIV Vif to promote APOBEC3 ubiquitination at the expense of RUNX1 mediated gene expression. Molecular Cell. 49, 632-644. (* contributed equally)


25. Stanley, D. J., Bartholomeeusen, K., Crosby, D. C., Kim, D. Y., Kwon, E., Yen, L., Cartozo, N. C., Li, M., Jager, S., Mason-Herr, J., Hayashi, F., Yokoyama, S., Krogan, N. J., Harris, R. S., Peterlin, B. M. and Gross, J. D. (2012) Inhibition of a NEDD8 cascade restores restriction of HIV-1 by APOBEC3G. PLoS Pathogens. e1003085.

24. Kwon, E., Kim, D. Y., Ngo, T. D., Gross, C. A., Gross, J. D. and Kim, K. K. (2012) Crystal structure of the periplasmic domain of Vibrio parahaemolyticus CpxA. Protein Sci. 21, 1334-1343.

23. Jager, S.*, Kim, D. Y.*, Hultquist, J. F.*, Shindo K., LaRue, R. S., Kwon, E., Li, M., Anderson, B. D., Yen, L., Stanley, D., Mahon, C., Kane J., Franks-Skiba, K., Cimermancic, P., Burlingame, A., Sali, A., Craik, C. S., Harris, R. S., Gross, J. D., and Krogan, N. J. (2012) Vif hijacks CBF-b to degrade APOBEC3G and promote HIV-1 infection. Nature. 481, 371-375. (* contributed equally)


22. Kwon, E., Kim, D. Y., Gross, C. A., Gross, J. D. and Kim, K. K. (2010) Crystal structure Escherichia coli Spy. Protein Sci. 19, 2252-2259.

21. Kim, D. Y., Kwon, E., Choi, J., Hwang, H. Y. and Kim, K. K. (2010) Structural basis for the negative regulation of bacterial stress response by RseB. Protein Sci. 19, 1258-1263.

20. Kim, D., San, B. H., Moh, S. H., Park, H., Kim, D. Y., Lee, S. and Kim, K. K. (2010) Structural basis for the substrate specificity of PepA from Streptococcus pneumoniae, a dodecameric tetrahedral protease. Biochem Biophys Res Commun. 391, 431-436.


19. Kim, D., Reddy, S., Kim, D. Y., Rich, A., Lee, S., Kim, K. K. and Kim, Y. G. (2009) Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA. Nucleic Acids Res. 37, 4353-4359.


18. Kim, D. Y. and Kim, K. K. (2008) The structural basis for the activation and peptide recognition of bacterial ClpP. J. Mol. Biol. 379, 760-771.

17. Jin, K. S.*, Kim, D. Y. *, Rho, Y., Le, V. B., Kwon, E., Kim, K. K. and Ree M. (2008) Solution structures of RseA and its complex with RseB. J. Synchrotron Radiat. 15, 219-222. (* contributed equally)

16. Kim, D. Y., Kwon, E., Shin, Y. K., Kweon, D. H. and Kim, K. K. (2008) The mechanism of temperature-induced bacterial HtrA activation. J. Mol. Biol. 377, 410-420.

15. Kim, H., Chu, T. T., Kim, D. Y., Kim, D. R., Nguyen, C. M., Choi, J., Lee, J. R., Hahn, M. J. and Kim, K. K. (2008) The crystal structure of guamerin in complex with chymotrypsin and the development of an elastase-specific inhibitor. J. Mol. Biol. 376, 184-192.

14. Wu, C., Lokanath, N. K., Kim, D. Y., Nguyen L. D. and Kim, K. K. (2008) Crystallization and preliminary X-ray studies of SdiA from Escherichia coli. Acta Crystallogr Sect F 64, 19-21.

13. Kwon, E., Kim, D. Y., Suh, S. W., and Kim, K. K. (2008) Crystal structure of the mouse p53 core domain in zinc-free state. Proteins 70, 280-283.


12. Le, B. V., Lee, H. S., Cho, Y., Kang, S. G., Kim, D. Y., Kim, Y. G. and Kim, K. K. (2007) Crystallization and preliminary X-ray studies of TON_1713 from Thermococcus onnurineus NA1, a putative member of the haloacid dehalogenase superfamily. Acta Crystallogr Sect F 63, 1048-1050.

11. Kim, D. Y., Jin, K. S., Kwon, E., Ree, M. and Kim, K. K. (2007) Crystal structure of RseB and a model of its binding mode to RseA. Proc. Natl. Acad. Sci. U. S. A. 104, 8779-8784.


10. Wu, C. A., Lokanath, N. K., Kim, D. Y., Park, H. J., Hwang, H. Y., Kim, S. T., Suh, S. W. and Kim, K. K. (2005) Structure of inorganic pyrophosphatase from Helicobacter pylori. Acta Crystallogr D Biol Crystallogr. 61, 1459-1464.

9. Kim, D. Y. and Kim, K. K. (2005) Structure and Function of HtrA family proteins, the key players in protein quality control. J Biochem Mol Biol. 38, 266-274 Review.

8. Han, Y. H., Kim, Y. G., Kim, D. Y., Ha, S. C., Lokanath, N. K. and Kim, K. K. (2005) The target of RNAIII-activating protein (TRAP) from Staphylococcus aureus: purification, crystallization and preliminary X-ray analysis. Biochim Biophys Acta. 1748, 134-136.


7. Kim, H., Wu, C. A., Kim, D. Y., Han, Y. H., Ha, S. C., Kim, C. S., Suh, S. W. and Kim, K. K. (2004) Crystallization and preliminary X-ray crystallographic study of UDP-glucose pyrophosphorylase (UGPase) from Helicobacter pylori. Acta Crystallogr D Biol Crystallogr. 60, 1447-1449.

6. Kim, D. R., Kim, D. Y., Chu, T. T., Jung, K. H. and Kim, K. K. (2004) Crystallization and preliminary X-ray crystallographic study of the leech protease inhibitor guamerin and its complex with bovine pancreatic chymotrypsin. Biochim Biophys Acta. 1699, 285-287.


5. Kim, D. Y. and Kim, K. K. (2003) Crystal structure of ClpX molecular chaperone from Helicobacter pylori. J. Biol. Chem. 278, 50664-50670.

4. Kim, D. Y., Wu, C. A., Kim, D. R., Ha, S. C., Han, Y. H. and Kim, K. K. (2003) Purification, crystallization and preliminary X-ray studies of ClpX from Helicobacter pylori. Acta Crystallogr D Biol Crystallogr. 59, 1642-164.

3. Kim, D. Y., Kim, D. R., Ha, S. C., Lokanath, N. K., Lee, C. J., Hwang, H. Y. and Kim, K. K. (2003) Crystal structure of the protease domain of a heat-shock protein HtrA from Thermotoga maritima. J. Biol. Chem. 278, 6543-6551.


2. Lee, I., Lokanath, N. K., Min, K., Ha, S. C., Kim, D. Y. and Kim, K. K. (2002) Cloning, purification, crystallization and preliminary X-ray studies of RFC boxes II-VIII of replication factor C from Methanococcus jannaschii. Acta Crystallogr D Biol Crystallogr. 58, 519-521.

1. Kim, D. Y., and Kim, K. K. (2002) Crystallization and preliminary X-ray studies of the protease domain of the heat-shock protein HtrA from Thermotoga maritima. Acta Crystallogr D Biol Crystallogr. 58, 170-172.