Structures of a recombinant Kunitz-type serine protease inhibitor from Bauhinia bauhinioides (BbKI) complexed with bovine trypsin were determined in two crystal forms. The crystal structure with the L55R mutant of BbKI was determined in space group P64 at 1.94 Å resolution and that with native BbKI in the monoclinic space group P21 at 3.95 Å resolution. The asymmetric unit of the latter crystals contained 44 independent complexes, thus representing one of the largest numbers of independent objects deposited in the Protein Data Bank. Additionally, the structure of the complex with native BbKI was determined at 2.0 Å resolution from P64 crystals isomorphous to those of the mutant. Since BbKI has previously been found to be a potent inhibitor of the trypsin-like plasma kallikrein, it was also tested against several tissue kallikreins. It was found that BbKI is a potent inhibitor of human tissue kallikrein 4 (KLK4) and the chymotrypsin-like human tissue kallikrein 7 (KLK7). Structures of BbKI complexed with the catalytic domain of human plasma kallikrein were modeled, as well as those with KLK4 and KLK7, and the structures were analyzed in order to identify the interactions that are responsible for inhibitory potency.

Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences 166 10 Prague Czech Republic

Macromolecular Crystallography Laboratory Center for Cancer Research National Cancer Institute Frederick MD 21702 USA

Synchrotron Radiation Research Section Macromolecular Crystallography Laboratory NCI Argonne National Laboratory Argonne IL 60439 USA

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Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C. & Zwart, P. H. (2010). Acta Cryst. D66, 213–221. PubMed PMC

Araújo, A. P. U., Hansen, D., Vieira, D. F., Oliveira, C., Santana, L. A., Beltramini, L. M., Sampaio, C. A. M., Sampaio, M. U. & Oliva, M. L. V. (2005). Biol. Chem. 386, 561–568. PubMed

Batista, I. F. C., Oliva, M. L. V., Araujo, M. S., Sampaio, M. U., Richardson, M., Fritz, H. & Sampaio, C. A. M. (1996). Phytochemistry, 41, 1017–1022. PubMed

Botos, I. & Wlodawer, A. (2007). Curr. Opin. Struct. Biol. 17, 683–690. PubMed PMC

Brito, M. V., de Oliveira, C., Salu, B. R., Andrade, S. A., Malloy, P. M. D., Sato, A. C., Vicente, C. P., Sampaio, M. U., Maffei, F. H. A. & Oliva, M. L. V. (2014). Thromb. Res. 133, 945–951. PubMed

Brünger, A. T. (1992). Nature (London), 355, 472–475. PubMed

Cereda, V., Formica, V., Menghi, A., Pellicori, S. & Roselli, M. (2015). Expert Opin. Investig. Drugs, 24, 929–947. PubMed

Debela, M., Hess, P., Magdolen, V., Schechter, N. M., Steiner, T., Huber, R., Bode, W. & Goettig, P. (2007). Proc. Natl Acad. Sci. USA, 104, 16086–16091. PubMed PMC

De Vonis Bidlingmeyer, U., Leary, T. R. & Laskowski, M. Jr (1972). Biochemistry, 11, 3303–3310. PubMed

Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486–501. PubMed PMC

Fogaça, S. E., Melo, R. L., Pimenta, D. C., Hosoi, K., Juliano, L. & Juliano, M. A. (2004). Biochem. J. 380, 775–781. PubMed PMC

García-Nafría, J., Timm, J., Harrison, C., Turkenburg, J. P. & Wilson, K. S. (2013). Acta Cryst. D69, 1367–1380. PubMed

Helland, R., Otlewski, J., Sundheim, O., Dadlez, M. & Smalås, A. O. (1999). J. Mol. Biol. 287, 923–942. PubMed

Hinkes, S., Wuttke, A., Saupe, S. M., Ivanova, T., Wagner, S., Knörlein, A., Heine, A., Klebe, G. & Steinmetzer, T. (2016). J. Med. Chem. 59, 6370–6386. PubMed

Horn, M., Zbodakova, O., Kasparek, P., Srp, J., Haneckova, R., Hradilek, M., Mares, M. & Sedlacek, R. (2018). Biol. Chem. 399, 1085–1089. PubMed

Humphrey, W., Dalke, A. & Schulten, K. (1996). J. Mol. Graph. 14, 33–38. PubMed

Klauda, J. B., Venable, R. M., Freites, J. A., O’Connor, J. W., Tobias, D. J., Mondragon-Ramirez, C., Vorobyov, I., MacKerell, A. D. Jr & Pastor, R. W. (2010). J. Phys. Chem. B, 114, 7830–7843. PubMed PMC

Kumar, P., Singh, M. & Karthikeyan, S. (2011). Acta Cryst. D67, 131–139. PubMed

Kunitz, M. (1947). J. Gen. Physiol. 30, 311–320. PubMed PMC

Li, Z., Partridge, J., Silva-Garcia, A., Rademacher, P., Betz, A., Xu, Q., Sham, H., Hu, Y., Shan, Y., Liu, B., Zhang, Y., Shi, H., Xu, Q., Ma, X. & Zhang, L. (2017). ACS Med. Chem. Lett. 8, 185–190. PubMed PMC

MacKerell, A. D. Jr, Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiórkiewicz-Kuczera, J., Yin, D. & Karplus, M. (1998). J. Phys. Chem. B, 102, 3586–3616. PubMed

Majumder, S., Khamrui, S., Dasgupta, J., Dattagupta, J. K. & Sen, U. (2012). Biochim. Biophys. Acta, 1824, 882–890. PubMed

Mavridis, K., Avgeris, M. & Scorilas, A. (2014). Expert Opin. Ther. Targets, 18, 365–383. PubMed

McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). J. Appl. Cryst. 40, 658–674. PubMed PMC

Murafuji, H., Sakai, H., Goto, M., Imajo, S., Sugawara, H. & Muto, T. (2017). Bioorg. Med. Chem. Lett. 27, 5272–5276. PubMed

Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst. D67, 355–367. PubMed PMC

Nakahata, A. M., Mayer, B., Neth, P., Hansen, D., Sampaio, M. U. & Oliva, M. L. V. (2013). Planta Med. 79, 227–235. PubMed

Odei-Addo, F., Frost, C., Smith, N., Ogawa, T., Muramoto, K., Oliva, M. L. V., Gráf, L. & Naude, R. (2014). J. Enzyme Inhib. Med. Chem. 29, 633–638. PubMed

Oliva, M. L. V., Mendes, C. R., Juliano, M. A., Chagas, J. R., Rosa,J. C., Greene, L. J., Sampaio, M. U. & Sampaio, C. A. M. (1999). Immunopharmacology, 45, 163–169. PubMed

Oliva, M. L. V., Mendes, C. R., Santomauro-Vaz, E. M., Juliano, M. A., Mentele, R., Auerswald, E. A., Sampaio, M. U. & Sampaio, C. A. M. (2001). Curr. Med. Chem. 8, 977–984. PubMed

Oliva, M. L. V. & Sampaio, U. M. (2008). Biol. Chem. 389, 1007–1013. PubMed

Oliva, M. L. V., Silva, M. C. C., Sallai, R. C., Brito, M. V. & Sampaio, M. U. (2010). Biochimie, 92, 1667–1673. PubMed

Otwinowski, Z. & Minor, W. (1997). Methods Enzymol. 276, 307–326. PubMed

Pampalakis, G. & Sotiropoulou, G. (2007). Biochim. Biophys. Acta, 1776, 22–31. PubMed

Patil, D. N., Chaudhary, A., Sharma, A. K., Tomar, S. & Kumar, P. (2012). FEBS J. 279, 4547–4564. PubMed

Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L. & Schulten, K. (2005). J. Comput. Chem. 26, 1781–1802. PubMed PMC

Prassas, I., Eissa, A., Poda, G. & Diamandis, E. P. (2015). Nature Rev. Drug Discov. 14, 183–202. PubMed

Renko, M., Sabotič, J. & Turk, D. (2012). Biol. Chem. 393, 1043–1054. PubMed

Riley, B. T., Ilyichova, O., Costa, M. G. S., Porebski, B. T., de Veer, S. J., Swedberg, J. E., Kass, I., Harris, J. M., Hoke, D. E. & Buckle, A. M. (2016). Sci. Rep. 6, 35385. PubMed PMC

Scheidig, A. J., Hynes, T. R., Pelletier, L. A., Wells, J. A. & Kossiakoff, A. A. (1997). Protein Sci. 6, 1806–1824. PubMed PMC

Song, H. K. & Suh, S. W. (1998). J. Mol. Biol. 275, 347–363. PubMed

Sotiropoulou, G. & Pampalakis, G. (2012). Trends Pharmacol. Sci. 33, 623–634. PubMed

Souza-Pinto, J. C., Oliva, M. L. V., Sampaio, C. A. M., Damas, J., Auerswald, E. A., Limãos, E., Fritz, H. & Sampaio, M. U. (1996). Immunopharmacology, 33, 330–332. PubMed

Swedberg, J. E., de Veer, S. J., Sit, K. C., Reboul, C. F., Buckle, A. M. & Harris, J. M. (2011). PLoS One, 6, e19302. PubMed PMC

Tanaka, S., Sawaya, M. R. & Yeates, T. O. (2010). Science, 327, 81–84. PubMed

Turk, B. (2006). Nature Rev. Drug Discov. 5, 785–799. PubMed

Vadivel, K., Ponnuraj, S. M., Kumar, Y., Zaiss, A. K., Bunce, M. W., Camire, R. M., Wu, L., Evseenko, D., Herschman, H. R., Bajaj, M. S. & Bajaj, S. P. (2014). J. Biol. Chem. 289, 31647–31661. PubMed PMC

Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A. & Wilson, K. S. (2011). Acta Cryst. D67, 235–242. PubMed PMC

Zhou, D., Hansen, D., Shabalin, I. G., Gustchina, A., Vieira, D. F., de Brito, M. V., Araújo, A. P. U., Oliva, M. L. V. & Wlodawer, A. (2015). Acta Cryst. F71, 1055–1062. PubMed PMC

Zhou, D., Lobo, Y. A., Batista, I. F. C., Marques-Porto, R., Gustchina, A., Oliva, M. L. V. & Wlodawer, A. (2013). PLoS One, 8, e62252. PubMed PMC

Structural studies of complexes of kallikrein 4 with wild-type and mutated forms of the Kunitz-type inhibitor BbKI