DNA Topoisomerases

  1. Lima, C.D., Wang, J.C., and Mondragón, A. Crystallization of a 67 kDa fragment of Escherichia coli DNA topoisomerase I. J. Mol. Biol. 1993. 232(4):1213-1216.
  2. Lima, C.D., Wang, J.C., and Mondragón, A. Three-dimensional structure of the 67K N-terminal fragment of  E. coli DNA topoisomerase I. Nature 1994. 367(6459):138-146.
  3. Sharma, A., Hanai, R., and Mondragón, A. Crystal Structure of the Amino Terminal Fragment of Vaccinia Virus DNA Topoisomerase I at 1.6 Ĺ Resolution. Structure 1994. 2(8):767-777.
  4. Lue, N., Sharma, A., Mondragón, A., and Wang, J.C. A 26 kDa yeast DNA topoisomerase I fragment: crystallographic structure and mechanistic implications. Structure 1995. 3(12):1315-1322.
  5. Mondragón, A. and DiGate, R. The structure of E. coli DNA topoisomerase III. Structure 1999. 7(11):1373-1383.
  6. Feinberg, H., Lima, C.D., and Mondragón, A. Conformational changes in E. coli DNA topoisomerase I. Nature Struct. Biol. 1999. 6(10):918-922.
  7. Feinberg, H., Changela, A., and Mondragón, A. Protein-nucleotide interactions in E. coli DNA topoisomerase I. Nature Struct. Biol. 1999. 6(10): 961-968.
  8. Li, Z., Mondragón, A., Hiasa, H., Marians, K.J., and DiGate, R.J. Identification of a unique domain essential for Escherichia coli DNA topoisomerase III-catalysed decatenation of replication intermediates. Mol. Microbiol. 2000. 35(4):888-895.
  9. Li, Z., Mondragón, A., and DiGate, R. The mechanism of type IA topoisomerase-mediated DNA topological transformations. Molecular Cell 2001. 7(2):301-307.
  10. Changela, A., DiGate, R. and Mondragón, A. Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule. Nature 2001. 411(6841):1077-1081.
  11. Perry, K. and Mondragón, A. Biochemical Characterization of an Invariant Histidine Involved in Escherichia coli DNA Topoisomerase I Catalysis. J. Biol. Chem. 2002. 277(15):13237-13245.
  12. Perry, K. and Mondragón, A. Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA. Structure 2003. 11(11):1349-1358.
  13. Mondragón, A. Unraveling the mechanistic details of topoisomerases. Structure 2005. 13(4):502-503.
  14. Patel, A., Shuman, S., and Mondragón, A. Crystal structure of bacterial type IB DNA topoisomerase reveals a preassembled active site in the absence of DNA. J. Biol. Chem. 2006. 281(9):6030-6037.
  15. Taneja, B., Patel, A., Slesarev, A., and Mondragón, A. Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases. EMBO J. 2006. 25(2):398-408.
  16. Changela, A., DiGate, R.J., and Mondragón, A. Structural studies of E. coli topoisomerase III-DNA complexes reveal a novel type IA topoisomerase-DNA conformational intermediate. J. Mol. Biol. 2007. 368(1):105-118.
  17. Taneja, B., Schnurr, B., Slesarev, A., Marko, J.F., and Mondragón, A. Topoisomerase V relaxes supercoiled DNA by a constrained swiveling mechanism. Proc. Natl. Acad. Sci. U S A. 2007. 104(37):14670-14675.
  18. Baker, N.M., Rajan, R., and Mondragón, A. Structural studies of type I topoisomerases. Nucleic Acids Res. 2009. 37(3):693-701.
  19. Patel, A., Yakovleva, L., Shuman, S., and Mondragón, A. Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site. Structure 2010. 18(6):725-733.
  20. Rajan, R., Taneja, B., and Mondragón, A. Structures of minimal catalytic fragments of topoisomerase V reveals conformational changes relevant for DNA binding. Structure 2010. 18(7):829-938.
  21. Baker, N.M., Weigand, S., Maar-Mathias, S., and Mondragón, A. Solution structures of DNA-bound gyrase. Nucleic Acids Res. 2011. 39(2):755-766.
  22. Terekhova, K., Gunn, K.H., Marko, J.F., and Mondragón, A. Bacterial topoisomerase I and topoisomerase III relax supercoiled DNA via distinct pathways. Nucleic Acids Res. 2012. 40(20):10432-10440.
  23. Terekhova, K., Marko, J.F., and Mondragón, A. Studies of bacterial topoisomerases I and III at the single-molecule level. Biochem. Soc. Trans. 2013. 41(2):571-575.
  24. Rajan, R., Prasad, R., Taneja, B., Wilson, S.H., and Mondragón, A. Identification of one of the apurinic/apyrimidinic lyase active sites of topoisomerase V by structural and functional studies. Nucleic Acids Res. 2013. 41(1):657-666.
  25. Terekhova, K., Marko, J.F., and Mondragón, A. Single-molecule analysis uncovers the difference between the kinetics of DNA decatenation by bacterial topoisomerases I and III. Nucleic Acids Res. 2014. 42(18):11657-11667.
  26. Rajan, R., Osterman, A.K., Gast, A.T., and Mondragón, A. Biochemical characterization of the topoisomerase domain of Methanopyrus kandleri topoisomerase V. J. Biol. Chem. 2014. 289(42):28898-28909.
  27. Rajan, R., Osterman, A., and Mondragón, A. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site. Nucleic Acids Res. 2016. 44(7):3464-3474.
  28. Gunn, K.H., Marko, J.F., and Mondragón, A. An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases. Nat. Struct. Mol. Biol. 2017. 24(5):484-490.
  29. Gunn, K.H., Marko, J.F., and Mondragón, A. Single-Molecule Magnetic Tweezer Analysis of Topoisomerases. Methods Mol. Biol. 2018. 1703:139-152.
  30. Soczek, K.M., Grant, T., Rosenthal, P.B., and Mondragón, A. CryoEM structures of open dimers of gyrase A in complex with DNA illuminate mechanism of strand passage. Elife 2018. 7: pii: e41215.

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Non-Coding RNA Molecules

  1. Krasilnikov, A.S., Yang, X., Pan, T., and Mondragón, A. Crystal structure of the specificity domain of ribonuclease P. Nature 2003. 421(6924):760-764.
  2. Krasilnikov, A.S. and Mondragón, A. On the occurrence of the T-loop RNA folding motif in large RNA molecules. RNA 2003. 9(6):640-643.
  3. Krasilnikov, A.S., Xiao,Y., Pan,T. and Mondragón, A. Basis for Stuctural Diversity in Homologous RNAs. Science 2004. 306(5693):104-107.
  4. Torres-Larios, A., Swinger, K.K., Krasilnikov, A.S., Pan, T., and Mondragón, A. Crystal structure of the RNA component of bacterial ribonuclease P. Nature 2005. 437(7058):584-587.
  5. Torres-Larios, A., Swinger, K.K., Pan, T., and Mondragón, A. Structure of ribonuclease P--a universal ribozyme. Curr. Opin. Struct. Biol. 2006. 16(3):327-335.
  6. Baird, N.J., Srividya, N., Krasilnikov, A.S., Mondragón, A., Sosnick, T.R., and Pan T. Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium. RNA 2006. 12(4):598-606.
  7. Reiter, N.J., Osterman, A., Torres-Larios, A., Swinger, K.K., Pan, T., and Mondragón, A. Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Nature 2010. 468(7325):784-789.
  8. Reiter, N.J., Chan, C.W., and Mondragón, A. Emerging structural themes in large RNA molecules. Curr. Opin. Struct. Biol. 2011. 21(3):319-326.
  9. Reiter, N.J., Osterman, A., and Mondragón, A. The bacterial ribonuclease P holoenzyme requires specific, conserved residues for efficient catalysis and substrate positioning. Nucleic Acids Res. 2012. 40(20):10384-10393.
  10. Mondragón A. Structural studies of RNase P. Annu. Rev. Biophys. 2013. 42:537-557.
  11. Chetnani, B. and Mondragón, A. Structural biology: RNA exerts self-control. Nature 2013. 500(7462):279-280.
  12. Chan, C.W., Chetnani, B., and Mondragón, A. Structure and function of the T-loop structural motif in noncoding RNAs. Wiley Interdiscip. Rev. RNA. 2013. 4(5):507-522.
  13. Chetnani, B. and Mondragón, A. Molecular envelope and atomic model of an anti-terminated glyQS T-box regulator in complex with tRNAGly. Nucleic Acids Res. 2017. 45(13):8079-8090.
  14. Zhang, J., Chetnani, B., Cormack, E.D., Alonso, D., Liu, W., Mondragón, A., and Fei, J. Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand. Elife 2018. 7: pii: e39518.

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Other Proteins and Protein-Nucleic Acid Complexes

  1. Grum, V.L., Li, D., MacDonald, R.I., and Mondragón, A. Structures of two repeats of spectrin suggest models of flexibility. Cell 1999. 98(4):523-535.
  2. Changela, A., Perry, K., Taneja, B., and Mondragón, A. DNA manipulators: caught in the act. Curr. Opin. Struct. Biol. 2003. 13(1):15-22.
  3. Changela, A., Chen, K., Xue, Y., Holschen, J., Outten, C.E., O'Halloran, T.V., and Mondragón, A. Molecular basis of metal-ion selectivity and zeptomolar sensitivity by CueR. Science 2003. 301(5638):1383-1387.
  4. Kusunoki, H., MacDonald, R.I., and Mondragón, A. Structural Insights into the Stability and Flexibility of Unusual Erythroid Spectrin Repeats. Structure 2004. 12(4):645-656.
  5. Kusunoki, H., Minasov, G., MacDonald, R.I., and Mondragón, A. Independent Movement, Dimerization and Stability of Tandem Repeats of Chicken Brain alpha-Spectrin. J. Mol. Biol. 2004. 344(2):495-511.
  6. Changela, A., Martins, A., Shuman, S., and Mondragón, A. Crystal structure of baculovirus RNA triphosphatase complexed with phosphate. J. Biol. Chem. 2005. 280(18):17848-17856.
  7. Ipsaro, J.J., Huang, L., and Mondragón, A. Structures of the spectrin-ankyrin interaction binding domains. Blood 2009. 113(22):5385-5393.
  8. Ipsaro, J.J. and Mondragón, A. Structural basis for spectrin recognition by ankyrin. Blood 2010. 115(20):4093-4101.
  9. Ipsaro, J.J., Harper, S.L., Messick, T.E., Marmorstein, R., Mondragón, A., and Speicher, D.W. Crystal structure and functional interpretation of the erythrocyte spectrin tetramerization domain complex. Blood 2010. 115(23):4843-4852.
  10. Godley, L.A. and Mondragón, A. Molecular biology. Preference by exclusion. Science 2011. 331(6020):1017-1018.
  11. Yasunaga, M., Ipsaro, J.J., and Mondragón, A. Structurally similar but functionally diverse ZU5 domains in human erythrocyte ankyrin. J. Mol. Biol. 2012. 417(4):336-350.
  12. Clark, M.D., Marcum, R., Graveline, R., Chan, C.W., Xie, T., Chen, Z., Ding, Y., Zhang, Y., Mondragón, A., David, G., and Radhakrishnan, I. Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex. Proc. Natl. Acad. Sci. U S A 2015. 112(28):E3669-E3678.
  13. Brahmachari, S., Gunn, K.H., Giuntoli, R.D., Mondragón, A., and Marko, J.F. Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices. Phys. Rev. Lett. 2017. 119(18):188103.
  14. Chan, C.W., Kiesel, B.R., and Mondragón, A. Crystal Structure of Human Rpp20/Rpp25 Reveals Quaternary Level Adaptation of the Alba Scaffold as Structural Basis for Single-stranded RNA Binding. J. Mol. Biol. 2018. 430(10):1403-1416.
  15. Dorsey, B.W., Huang, L., and Mondragón, A. Structural organization of a Type III-A CRISPR effector subcomplex determined by X-ray crystallography and cryo-EM. Nucleic Acids Res. 2019. 47(7):3765-3783.

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