Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them

References

First citationAfonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H. & Adams, P. D. (2012). Acta Cryst. D68, 352–367.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationAgirre, J., Atanasova, M., Bagdonas, H., Ballard, C. B., Baslé, A., Beilsten-Edmands, J., Borges, R. J., Brown, D. G., Burgos-Mármol, J. J., Berrisford, J. M., Bond, P. S., Caballero, I., Catapano, L., Chojnowski, G., Cook, A. G., Cowtan, K. D., Croll, T. I., Debreczeni, J. É., Devenish, N. E., Dodson, E. J., Drevon, T. R., Emsley, P., Evans, G., Evans, P. R., Fando, M., Foadi, J., Fuentes-Montero, L., Garman, E. F., Gerstel, M., Gildea, R. J., Hatti, K., Hekkelman, M. L., Heuser, P., Hoh, S. W., Hough, M. A., Jenkins, H. T., Jiménez, E., Joosten, R. P., Keegan, R. M., Keep, N., Krissinel, E. B., Kolenko, P., Kovalevskiy, O., Lamzin, V. S., Lawson, D. M., Lebedev, A. A., Leslie, A. G. W., Lohkamp, B., Long, F., Malý, M., McCoy, A. J., McNicholas, S. J., Medina, A., Millán, C., Murray, J. W., Murshudov, G. N., Nicholls, R. A., Noble, M. E. M., Oeffner, R., Pannu, N. S., Parkhurst, J. M., Pearce, N., Pereira, J., Perrakis, A., Powell, H. R., Read, R. J., Rigden, D. J., Rochira, W., Sammito, M., Sánchez Rodríguez, F., Sheldrick, G. M., Shelley, K. L., Simkovic, F., Simpkin, A. J., Skubak, P., Sobolev, E., Steiner, R. A., Stevenson, K., Tews, I., Thomas, J. M. H., Thorn, A., Valls, J. T., Uski, V., Usón, I., Vagin, A., Velankar, S., Vollmar, M., Walden, H., Waterman, D., Wilson, K. S., Winn, M. D., Winter, G., Wojdyr, M. & Yamashita, K. (2023). Acta Cryst. D79, 449–461.  Web of Science CrossRef IUCr Journals Google Scholar
First citationAnderson, K. S. (2017). Protein Eng. Des. Sel. 30, 255–264.  CrossRef CAS Google Scholar
First citationAnderson, W. F. (2022). IUCrJ, 9, 536–537.  CrossRef CAS PubMed IUCr Journals Google Scholar
First citationBaker, P., Carere, J. & Seah, S. Y. K. (2012). Biochemistry, 51, 4558–4567.  CrossRef CAS PubMed Google Scholar
First citationBarends, T. R., Dunn, M. F. & Schlichting, I. (2008). Curr. Opin. Chem. Biol. 12, 593–600.  CrossRef PubMed CAS Google Scholar
First citationBarycki, J. J., O'Brien, L. K., Strauss, A. W. & Banaszak, L. J. (2000). J. Biol. Chem. 275, 27186–27196.  Web of Science CrossRef PubMed CAS Google Scholar
First citationBoby, M. L., Fearon, D., Ferla, M., Filep, M., Koekemoer, L., Robinson, M. C., The COVID Moonshot Consortium, Chodera, J. D., Lee, A. A., London, N., Von Delft, A. & Von Delft, F. (2023). Science, 382, eabo7201.  CrossRef PubMed Google Scholar
First citationBosken, Y. K., Ai, R., Hilario, E., Ghosh, R. K., Dunn, M. F., Kan, S.-H., Niks, D., Zhou, H., Ma, W., Mueller, L. J., Fan, L. & Chang, C. A. (2022). Protein Sci. 31, 432–442.  CrossRef CAS PubMed Google Scholar
First citationCarbery, A., Skyner, R., von Delft, F. & Deane, C. M. (2022). J. Med. Chem. 65, 11404–11413.  CrossRef CAS PubMed Google Scholar
First citationChen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12–21.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationCole, S. T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S. V., Eiglmeier, K., Gas, S., Barry, C. E., Tekaia, F., Badcock, K., Basham, D., Brown, D., Chillingworth, T., Connor, R., Davies, R., Devlin, K., Feltwell, T., Gentles, S., Hamlin, N., Holroyd, S., Hornsby, T., Jagels, K., Krogh, A., McLean, J., Moule, S., Murphy, L., Oliver, K., Osborne, J., Quail, M. A., Rajandream, M. A., Rogers, J., Rutter, S., Seeger, K., Skelton, J., Squares, R., Squares, S., Sulston, J. E., Taylor, K., Whitehead, S. & Barrell, B. G. (1998). Nature, 393, 537–544.  Web of Science CrossRef CAS PubMed Google Scholar
First citationCzub, M. P., Stewart, A. J., Shabalin, I. G. & Minor, W. (2022). IUCrJ, 9, 551–561.  Web of Science CrossRef CAS PubMed IUCr Journals Google Scholar
First citationDalwani, S., Lampela, O., Leprovost, P., Schmitz, W., Juffer, A. H., Wierenga, R. K. & Venkatesan, R. (2021). J. Struct. Biol. 213, 107776.  CrossRef PubMed Google Scholar
First citationD'Amico, R. N. & Boehr, D. D. (2023). Curr. Opin. Struct. Biol. 82, 102657.  PubMed Google Scholar
First citationDaniel, E., Maksimainen, M. M., Smith, N., Ratas, V., Biterova, E., Murthy, S. N., Rahman, M. T., Kiema, T.-R., Sridhar, S., Cordara, G., Dalwani, S., Venkatesan, R., Prilusky, J., Dym, O., Lehtiö, L., Koski, M. K., Ashton, A. W., Sussman, J. L. & Wierenga, R. K. (2021). Acta Cryst. D77, 151–163.  Web of Science CrossRef IUCr Journals Google Scholar
First citationDavies, D. R., Begley, D. W., Hartley, R. C., Staker, B. L. & Stewart, L. J. (2011). Methods Enzymol. 493, 91–114.  Web of Science CrossRef CAS PubMed Google Scholar
First citationDiaz, D. B. & Yudin, A. K. (2017). Nat. Chem. 9, 731–742.  CrossRef CAS PubMed Google Scholar
First citationEmsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486–501.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationErlanson, D. A., Fesik, S. W., Hubbard, R. E., Jahnke, W. & Jhoti, H. (2016). Nat. Rev. Drug Discov. 15, 605–619.  Web of Science CrossRef CAS PubMed Google Scholar
First citationEvans, P. R. & Murshudov, G. N. (2013). Acta Cryst. D69, 1204–1214.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationFeng, Z., Westbrook, J. D., Sala, R., Smart, O. S., Bricogne, G., Matsubara, M., Yamada, I., Tsuchiya, S., Aoki-Kinoshita, K. F., Hoch, J. C., Kurisu, G., Velankar, S., Burley, S. K. & Young, J. Y. (2021). Structure, 29, 393–400.  Web of Science CrossRef CAS PubMed Google Scholar
First citationHarijan, R. K., Dalwani, S., Kiema, T., Venkatesan, R. & Wierenga, R. K. (2023). Annu. Rev. Biochem. 92, 351–384.   CrossRef CAS PubMed Google Scholar
First citationHeightman, T. D., Berdini, V., Braithwaite, H., Buck, I. M., Cassidy, M., Castro, J., Courtin, A., Day, J. E. H., East, C., Fazal, L., Graham, B., Griffiths-Jones, C. M., Lyons, J. F., Martins, V., Muench, S., Munck, J. M., Norton, D., O'Reilly, M., Palmer, N., Pathuri, P., Reader, M., Rees, D. C., Rich, S. J., Richardson, C., Saini, H., Thompson, N. T., Wallis, N. G., Walton, H., Wilsher, N. E., Woolford, A. J.-A., Cooke, M., Cousin, D., Onions, S., Shannon, J., Watts, J. & Murray, C. W. (2018). J. Med. Chem. 61, 4978–4992.  CrossRef CAS PubMed Google Scholar
First citationHilario, E., Caulkins, B. G., Huang, Y.-M. M., You, W., Chang, C. A., Mueller, L. J., Dunn, M. F. & Fan, L. (2016). Biochim. Biophys. Acta, 1864, 268–279.  CrossRef CAS PubMed Google Scholar
First citationHuschmann, F. U., Linnik, J., Sparta, K., Ühlein, M., Wang, X., Metz, A., Schiebel, J., Heine, A., Klebe, G., Weiss, M. S. & Mueller, U. (2016). Acta Cryst. F72, 346–355.  Web of Science CrossRef IUCr Journals Google Scholar
First citationIncardona, M.-F., Bourenkov, G. P., Levik, K., Pieritz, R. A., Popov, A. N. & Svensson, O. (2009). J. Synchrotron Rad. 16, 872–879.  Web of Science CrossRef IUCr Journals Google Scholar
First citationIshikawa, M., Tsuchiya, D., Oyama, T., Tsunaka, Y. & Morikawa, K. (2004). EMBO J. 23, 2745–2754.  Web of Science CrossRef PubMed CAS Google Scholar
First citationJoosten, R. P., Joosten, K., Cohen, S. X., Vriend, G. & Perrakis, A. (2011). Bioinformatics, 27, 3392–3398.  Web of Science CrossRef CAS PubMed Google Scholar
First citationKabsch, W. (2010). Acta Cryst. D66, 125–132.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationKrissinel, E. & Henrick, K. (2004). Acta Cryst. D60, 2256–2268.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationKrojer, T., Fraser, J. S. & von Delft, F. (2020). Curr. Opin. Struct. Biol. 65, 209–216.  Web of Science CrossRef CAS PubMed Google Scholar
First citationKrug, M., Weiss, M. S., Heinemann, U. & Mueller, U. (2012). J. Appl. Cryst. 45, 568–572.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationLiang, K., Li, N., Wang, X., Dai, J., Liu, P., Wang, C., Chen, X.-W., Gao, N. & Xiao, J. (2018). Proc. Natl Acad. Sci. USA, 115, 7039–7044.  CrossRef CAS PubMed Google Scholar
First citationLiebschner, D., Afonine, P. V., Baker, M. L., Bunkóczi, G., Chen, V. B., Croll, T. I., Hintze, B., Hung, L.-W., Jain, S., McCoy, A. J., Moriarty, N. W., Oeffner, R. D., Poon, B. K., Prisant, M. G., Read, R. J., Richardson, J. S., Richardson, D. C., Sammito, M. D., Sobolev, O. V., Stockwell, D. H., Terwilliger, T. C., Urzhumtsev, A. G., Videau, L. L., Williams, C. J. & Adams, P. D. (2019). Acta Cryst. D75, 861–877.  Web of Science CrossRef IUCr Journals Google Scholar
First citationMartin, M. P. & Noble, M. E. M. (2022). Acta Cryst. D78, 1294–1302.  Web of Science CrossRef IUCr Journals Google Scholar
First citationMcCoy, 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.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationMcNicholas, S., Potterton, E., Wilson, K. S. & Noble, M. E. M. (2011). Acta Cryst. D67, 386–394.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationMetzger, V. T., Eun, C., Kekenes-Huskey, P. M., Huber, G. & McCammon, J. A. (2014). Biophys. J. 107, 2394–2402.  CrossRef CAS PubMed Google Scholar
First citationMi, J., Gong, W. & Wu, X. (2022). Biomed. Res. Int. 2022, 5099312.  PubMed Google Scholar
First citationMoriarty, N. W., Draizen, E. J. & Adams, P. D. (2017). Acta Cryst. D73, 123–130.  Web of Science CrossRef IUCr Journals Google Scholar
First citationMurshudov, 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.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationNada, M. A., Rhead, W. J., Sprecher, H., Schulz, H. & Roe, C. R. (1995). J. Biol. Chem. 270, 530–535.  CrossRef CAS PubMed Web of Science Google Scholar
First citationNicholls, R. A., Joosten, R. P., Long, F., Wojdyr, M., Lebedev, A., Krissinel, E., Catapano, L., Fischer, M., Emsley, P. & Murshudov, G. N. (2021). Acta Cryst. D77, 712–726.  Web of Science CrossRef IUCr Journals Google Scholar
First citationPotterton, L., Agirre, J., Ballard, C., Cowtan, K., Dodson, E., Evans, P. R., Jenkins, H. T., Keegan, R., Krissinel, E., Stevenson, K., Lebedev, A., McNicholas, S. J., Nicholls, R. A., Noble, M., Pannu, N. S., Roth, C., Sheldrick, G., Skubak, P., Turkenburg, J., Uski, V., von Delft, F., Waterman, D., Wilson, K., Winn, M. & Wojdyr, M. (2018). Acta Cryst. D74, 68–84.  Web of Science CrossRef IUCr Journals Google Scholar
First citationPrice, A. J., Howard, S. & Cons, B. D. (2017). Essays Biochem. 61, 475–484.  Web of Science CrossRef PubMed Google Scholar
First citationRadeva, N., Schiebel, J., Wang, X., Krimmer, S. G., Fu, K., Stieler, M., Ehrmann, F. R., Metz, A., Rickmeyer, T., Betz, M., Winquist, J., Park, A. Y., Huschmann, F. U., Weiss, M. S., Mueller, U., Heine, A. & Klebe, G. (2016). J. Med. Chem. 59, 9743–9759.  Web of Science CrossRef CAS PubMed Google Scholar
First citationRohde, K. H., Veiga, D. F. T., Caldwell, S., Balázsi, G. & Russell, D. G. (2012). PLoS Pathog. 8, e1002769.  CrossRef PubMed Google Scholar
First citationSah-Teli, S. K., Hynönen, M. J., Schmitz, W., Geraets, J. A., Seitsonen, J., Pedersen, J. S., Butcher, S. J., Wierenga, R. K. & Venkatesan, R. (2019). Biochem. J. 476, 1975–1994.  Web of Science CAS PubMed Google Scholar
First citationSah-Teli, S. K., Hynönen, M. J., Sulu, R., Dalwani, S., Schmitz, W., Wierenga, R. K. & Venkatesan, R. (2020). J. Struct. Biol. 210, 107494.  Web of Science PubMed Google Scholar
First citationSah-Teli, S. K., Pinkas, M., Hynönen, M. J., Butcher, S. J., Wierenga, R. K., Novacek, J. & Venkatesan, R. (2023). Structure, 31, 812–825.  CAS PubMed Google Scholar
First citationSchiebel, J., Radeva, N., Krimmer, S. G., Wang, X., Stieler, M., Ehrmann, F. R., Fu, K., Metz, A., Huschmann, F. U., Weiss, M. S., Mueller, U., Heine, A. & Klebe, G. (2016). ACS Chem. Biol.

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