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1988 …2023
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Research Output 1988 2019

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2019

Structural organization of a Type III-A CRISPR effector subcomplex determined by X-ray crystallography and cryo-EM

Dorsey, B. W., Huang, L. & Mondragon, A., Jan 1 2019, In : Nucleic acids research. 47, 7, p. 3765-3783 19 p.

Research output: Contribution to journalArticle

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Cryoelectron Microscopy
X Ray Crystallography
Guide RNA
RNA Cleavage
2018
4 Citations (Scopus)

CryoEM structures of open dimers of gyrase A in complex with DNA illuminate mechanism of strand passage

Soczek, K. M., Grant, T., Rosenthal, P. B. & Mondragón, A., Nov 1 2018, In : eLife. 7, e41215.

Research output: Contribution to journalArticle

Dimers
DNA
DNA Gyrase
Bacterial DNA
DNA Cleavage
2 Citations (Scopus)

Crystal Structure of Human Rpp20/Rpp25 Reveals Quaternary Level Adaptation of the Alba Scaffold as Structural Basis for Single-stranded RNA Binding

Chan, C. W., Kiesel, B. R. & Mondragon, A., May 11 2018, In : Journal of Molecular Biology. 430, 10, p. 1403-1416 14 p.

Research output: Contribution to journalArticle

Ribonuclease P
Catalytic RNA
Ribonucleoproteins
RNA
Catalytic Domain
5 Citations (Scopus)

Specific structural elements of the t-box riboswitch drive the two-step binding of the tRNA ligand

Zhang, J., Chetnani, B., Cormack, E. D., Alonso, D., Liu, W., Mondragón, A. & Fei, J., Sep 2018, In : eLife. 7, e39518.

Research output: Contribution to journalArticle

Riboswitch
Transfer RNA
Ligands
Aminoacylation
Anticodon
2017
7 Citations (Scopus)
DNA
Type I DNA Topoisomerase
Escherichia coli
Enzymes
Proteins
5 Citations (Scopus)

Molecular envelope and atomic model of an anti-terminated glyQS T-box regulator in complex with tRNAGly

Chetnani, B. & Mondragon, A., Jul 1 2017, In : Nucleic acids research. 45, 13, p. 8079-8090 12 p.

Research output: Contribution to journalArticle

RNA, Transfer, Gly
Transfer RNA
Riboswitch
Structural Models
Bacillus subtilis
4 Citations (Scopus)

Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices

Brahmachari, S., Gunn, K. H., Giuntoli, R. D., Mondragón, A. & Marko, J. F., Oct 31 2017, In : Physical review letters. 119, 18, 188103.

Research output: Contribution to journalArticle

helices
deoxyribonucleic acid
nucleation
buckling
mechanical properties
2016
3 Citations (Scopus)

Methanopyrus kandleri topoisomerase v contains three distinct AP lyase active sites in addition to the topoisomerase active site

Rajan, R., Osterman, A. & Mondragón, A., Feb 22 2016, In : Nucleic acids research. 44, 7, p. 3464-3474 11 p.

Research output: Contribution to journalArticle

DNA-(Apurinic or Apyrimidinic Site) Lyase
Catalytic Domain
DNA Repair
Proteins
X-Rays
2015
55 Citations (Scopus)

Allosteric transcriptional regulation via changes in the overall topology of the core promoter

Philips, S. J., Canalizo-Hernandez, M., Yildirim, I., Schatz, G. C., Mondragón, A. & O'Halloran, T. V., Aug 21 2015, In : Science. 349, 6250, p. 877-881 5 p.

Research output: Contribution to journalArticle

Allosteric Regulation
DNA
DNA-Directed RNA Polymerases
Proteins
A-Form DNA
32 Citations (Scopus)

DNase H Activity of Neisseria meningitidis Cas9

Zhang, Y., Rajan, R., Seifert, H., Mondragon, A. & Sontheimer, E. J., Oct 15 2015, In : Molecular cell. 60, 2, p. 242-255 14 p.

Research output: Contribution to journalArticle

Neisseria meningitidis
Clustered Regularly Interspaced Short Palindromic Repeats
Deoxyribonucleases
RNA
DNA
12 Citations (Scopus)

Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex

Clark, M. D., Marcum, R., Graveline, R., Chan, C. W., Xie, T., Chen, Z., Ding, Y., Zhang, Y., Mondragón, A., David, G. & Radhakrishnan, I., Jul 14 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 28, p. E3669-E3678

Research output: Contribution to journalArticle

Co-Repressor Proteins
Histone Deacetylases
Chromatin
Mi-2 Nucleosome Remodeling and Deacetylase Complex
Protein Interaction Domains and Motifs
2014
3 Citations (Scopus)

Biochemical characterization of the topoisomerase domain of Methanopyrus kandleri topoisomerase V

Rajan, R., Osterman, A. K., Gast, A. T. & Mondragón, A., Oct 17 2014, In : Journal of Biological Chemistry. 289, 42, p. 28898-28909 12 p.

Research output: Contribution to journalArticle

Catalytic Domain
DNA
Enzymes
Amino Acids
DNA Cleavage
13 Citations (Scopus)

Single-molecule analysis uncovers the difference between the kinetics of DNA decatenation by bacterial topoisomerases i and III

Terekhova, K., Marko, J. F. & Mondragón, A., Oct 13 2014, In : Nucleic acids research. 42, 18, p. 11657-11667 11 p.

Research output: Contribution to journalArticle

Type I DNA Topoisomerase
DNA
Proteins
Escherichia coli
DNA topoisomerase III
46 Citations (Scopus)

Structural and Mechanistic Basis of Zinc Regulation Across the E. coli Zur Regulon

Gilston, B. A., Wang, S., Marcus, M. D., Canalizo-Hernández, M. A., Swindell, E. P., Xue, Y., Mondragon, A. & O'Halloran, T. V., Jan 1 2014, In : PLoS biology. 12, 11

Research output: Contribution to journalArticle

Regulon
regulon
Escherichia coli
Zinc
zinc
2013
4 Citations (Scopus)

Identification of one of the apurinic/apyrimidinic lyase active sites of topoisomerase v by structural and functional studies

Rajan, R., Prasad, R., Taneja, B., Wilson, S. H. & Mondragón, A., Jan 1 2013, In : Nucleic acids research. 41, 1, p. 657-666 10 p.

Research output: Contribution to journalArticle

Lyases
Catalytic Domain
DNA Repair
Deoxyribonuclease I
Proteins
33 Citations (Scopus)

Structural studies of RNase P

Mondragon, A., May 1 2013, In : Annual Review of Biophysics. 42, 1, p. 537-557 21 p.

Research output: Contribution to journalArticle

Ribonuclease P
RNA
Catalytic RNA
Molecules
Catalysis
2012
22 Citations (Scopus)

Bacterial topoisomerase i and topoisomerase III relax supercoiled DNA via distinct pathways

Terekhova, K., Gunn, K. H., Marko, J. F. & Mondragón, A., Nov 1 2012, In : Nucleic acids research. 40, 20, p. 10432-10440 9 p.

Research output: Contribution to journalArticle

Superhelical DNA
DNA
Type I DNA Topoisomerase
Single-Stranded DNA
DNA topoisomerase III
12 Citations (Scopus)

Structurally similar but functionally diverse ZU5 domains in human erythrocyte ankyrin

Yasunaga, M., Ipsaro, J. J. & Mondragón, A., Apr 6 2012, In : Journal of Molecular Biology. 417, 4, p. 336-350 15 p.

Research output: Contribution to journalArticle

Ankyrins
Spectrin
Erythrocytes
Proteins
Tandem Repeat Sequences
9 Citations (Scopus)

The bacterial ribonuclease P holoenzyme requires specific, conserved residues for efficient catalysis and substrate positioning

Reiter, N. J., Osterman, A. K. & Mondragón, A., Nov 1 2012, In : Nucleic acids research. 40, 20, p. 10384-10393 10 p.

Research output: Contribution to journalArticle

Ribonuclease P
Holoenzymes
Catalysis
Catalytic Domain
RNA Precursors
2011
26 Citations (Scopus)

Solution structures of DNA-bound gyrase

Baker, N. M., Weigand, S., Maar-Mathias, S. & Mondragón, A., Jan 1 2011, In : Nucleic acids research. 39, 2, p. 755-766 12 p.

Research output: Contribution to journalArticle

DNA Gyrase
DNA
X-Rays
Hydrodynamics
Adenosine Triphosphatases
2010
52 Citations (Scopus)

Crystal structure and functional interpretation of the erythrocyte spectrin tetramerization domain complex

Ipsaro, J. J., Harper, S. L., Messick, T. E., Marmorstein, R., Mondragón, A. & Speicher, D. W., Jun 10 2010, In : Blood. 115, 23, p. 4843-4852 10 p.

Research output: Contribution to journalArticle

Spectrin
Erythrocytes
Crystal structure
Mutation
Anemia
18 Citations (Scopus)

Crystal Structure of a Bacterial Topoisomerase IB in Complex with DNA Reveals a Secondary DNA Binding Site

Patel, A., Yakovleva, L., Shuman, S. & Mondragón, A., Jun 1 2010, In : Structure. 18, 6, p. 725-733 9 p.

Research output: Contribution to journalArticle

Bacterial Structures
Binding Sites
DNA
Enzymes
DNA Topoisomerases
61 Citations (Scopus)

Structural basis for spectrin recognition by ankyrin

Ipsaro, J. J. & Mondragón, A., May 20 2010, In : Blood. 115, 20, p. 4093-4101 9 p.

Research output: Contribution to journalArticle

Ankyrins
Spectrin
Proteins
Membrane Proteins
Hereditary Elliptocytosis
169 Citations (Scopus)

Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA

Reiter, N. J., Osterman, A., Torres-Larios, A., Swinger, K. K., Pan, T. & Mondragon, A., Dec 9 2010, In : Nature. 468, 7325, p. 784-791 8 p.

Research output: Contribution to journalArticle

Ribonuclease P
Bacterial Structures
Holoenzymes
Transfer RNA
RNA
5 Citations (Scopus)

Structures of Minimal Catalytic Fragments of Topoisomerase V Reveals Conformational Changes Relevant for DNA Binding

Rajan, R., Taneja, B. & Mondragon, A., Jul 1 2010, In : Structure. 18, 7, p. 829-838 10 p.

Research output: Contribution to journalArticle

Catalytic Domain
Type I DNA Topoisomerase
DNA
Proteins
DNA Repair
97 Citations (Scopus)

Tetrathiomolybdate inhibits copper trafficking proteins through metal cluster formation

Alvarez, H. M., Xue, Y., Robinson, C. D., Canalizo-Hernández, M. A., Marvin, R. G., Kelly, R. A., Mondragón, A., Penner-Hahn, J. E. & O'Halloran, T. V., Jan 15 2010, In : Science. 327, 5963, p. 331-334 4 p.

Research output: Contribution to journalArticle

Protein Transport
Copper
Metals
Metallochaperones
Molybdoferredoxin
2009
65 Citations (Scopus)

Structures of the spectrin-ankyrin interaction binding domains

Ipsaro, J. J., Huang, L. & Mondragon, A., Nov 17 2009, In : Blood. 113, 22, p. 5385-5393 9 p.

Research output: Contribution to journalArticle

Ankyrins
Spectrin
Ankyrin Repeat
Consensus Sequence
Erythrocyte Membrane
2007
27 Citations (Scopus)

Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate

Changela, A., DiGate, R. J. & Mondragon, A., Apr 20 2007, In : Journal of Molecular Biology. 368, 1, p. 105-118 14 p.

Research output: Contribution to journalArticle

Type I DNA Topoisomerase
Single-Stranded DNA
Escherichia coli
Catalytic Domain
DNA
42 Citations (Scopus)

Topoisomerase V relaxes supercoiled DNA by a constrained swiveling mechanism

Taneja, B., Schnurr, B., Slesarev, A., Marko, J. F. & Mondragón, A., Sep 11 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, 37, p. 14670-14675 6 p.

Research output: Contribution to journalArticle

Superhelical DNA
Type I DNA Topoisomerase
Enzymes
Friction
DNA
2006
20 Citations (Scopus)

Crystal structure of a bacterial type IB DNA topoisomerase reveals a preassembled active site in the absence of DNA

Patel, A., Shuman, S. & Mondragón, A., Mar 3 2006, In : Journal of Biological Chemistry. 281, 9, p. 6030-6037 8 p.

Research output: Contribution to journalArticle

Bacterial Structures
Type I DNA Topoisomerase
Deinococcus
Catalytic Domain
Crystal structure
19 Citations (Scopus)

Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium

Baird, N. J., Srividya, N., Krasilnikov, A. S., Mondragon, A., Sosnick, T. R. & Pan, T., Apr 1 2006, In : RNA. 12, 4, p. 598-606 9 p.

Research output: Contribution to journalArticle

RNA Stability
Thermus thermophilus
Escherichia coli
Bacteria
Ribonuclease P
36 Citations (Scopus)

Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases

Taneja, B., Patel, A., Slesarev, A. & Mondragón, A., Jan 25 2006, In : EMBO Journal. 25, 2, p. 398-408 11 p.

Research output: Contribution to journalArticle

Archaea
Catalytic Domain
DNA
Eukaryota
Conservation
2005
20 Citations (Scopus)

Crystal structure of baculovirus RNA triphosphatase complexed with phosphate

Changela, A., Martins, A., Shuman, S. & Mondragón, A., May 6 2005, In : Journal of Biological Chemistry. 280, 18, p. 17848-17856 9 p.

Research output: Contribution to journalArticle

Baculoviridae
Crystal structure
Phosphates
mRNA guanylyltransferase
Phosphoric Monoester Hydrolases
167 Citations (Scopus)

Crystal structure of the RNA component of bacterial ribonuclease P

Torres-Larios, A., Swinger, K. K., Krasilnikov, A. S., Pan, T. & Mondragon, A., Sep 22 2005, In : Nature. 437, 7058, p. 584-587 4 p.

Research output: Contribution to journalArticle

Bacterial RNA
Ribonuclease P
Catalytic RNA
Transfer RNA
RNA
2004
113 Citations (Scopus)

Basis for structural diversity in homologous RNAs

Krasilnikov, A. S., Xiao, Y., Pan, T. & Mondragon, A., Oct 1 2004, In : Science. 306, 5693, p. 104-107 4 p.

Research output: Contribution to journalArticle

Catalytic RNA
RNA
85 Citations (Scopus)

Independent movement, dimerization and stability of tandem repeats of chicken brain α-spectrin

Kusunoki, H., Minasov, G., MacDonald, R. I. & Mondragón, A., Nov 19 2004, In : Journal of Molecular Biology. 344, 2, p. 495-511 17 p.

Research output: Contribution to journalArticle

Spectrin
Tandem Repeat Sequences
Dimerization
Chickens
Brain
64 Citations (Scopus)

Structural insights into the stability and flexibility of unusual erythroid spectrin repeats

Kusunoki, H., MacDonald, R. I. & Mondragon, A., Apr 1 2004, In : Structure. 12, 4, p. 645-656 12 p.

Research output: Contribution to journalArticle

Spectrin
Tandem Repeat Sequences
Elasticity
Tryptophan
Cell Membrane
2003
184 Citations (Scopus)

Crystal structure of the specificity domain of ribonuclease P

Krasilnikov, A. S., Yang, X., Pan, T. & Mondragon, A., Feb 13 2003, In : Nature. 421, 6924, p. 760-764 5 p.

Research output: Contribution to journalArticle

Ribonuclease P
Catalytic RNA
Transfer RNA
Bacterial RNA
RNA
409 Citations (Scopus)

Molecular basis of metal-ion selectivity and zeptomolar sensitivity by CueR

Changela, A., Chen, K., Xue, Y., Holschen, J., Outten, C. E., O'Halloran, T. V. & Mondragon, A., Sep 5 2003, In : Science. 301, 5638, p. 1383-1387 5 p.

Research output: Contribution to journalArticle

Metals
Ions
Metalloproteins
Hydrogen Bonding
Thermodynamics
65 Citations (Scopus)

On the occurrence of the T-loop RNA folding motif in large RNA molecules

Krasilnikov, A. S. & Mondragon, A., Jun 1 2003, In : RNA. 9, 6, p. 640-643 4 p.

Research output: Contribution to journalArticle

RNA Folding
Nucleotide Motifs
Base Pairing
RNA
Ribonuclease P
30 Citations (Scopus)

Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA

Perry, K. & Mondragon, A., Jan 1 2003, In : Structure. 11, 11, p. 1349-1358 10 p.

Research output: Contribution to journalArticle

Type I DNA Topoisomerase
Single-Stranded DNA
Catalytic Domain
Escherichia coli
Enzymes

Structure of the Bacillus subtilis YYCN Protein: A Putative N-Acetyltransferase

Taneja, B., Maar, S., Shuvalova, L., Collart, F., Anderson, W. & Mondragón, A., Dec 1 2003, In : Proteins: Structure, Function and Genetics. 53, 4, p. 950-952 3 p.

Research output: Contribution to journalArticle

Arylamine N-Acetyltransferase
Acetyltransferases
Molecular Models
Bacterial Proteins
X ray crystallography
2002
23 Citations (Scopus)

Biochemical characterization of an invariant histidine involved in Escherichia coli DNA topoisomerase I catalysis

Perry, K. & Mondragon, A., Apr 12 2002, In : Journal of Biological Chemistry. 277, 15, p. 13237-13245 9 p.

Research output: Contribution to journalArticle

Type I DNA Topoisomerase
Catalysis
Histidine
Escherichia coli
DNA
2001
79 Citations (Scopus)

Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule

Changela, A., DiGate, R. J. & Mondragon, A., Jun 28 2001, In : Nature. 411, 6841, p. 1077-1081 5 p.

Research output: Contribution to journalArticle

Single-Stranded DNA
Enzymes
Catalytic Domain
Escherichia coli
Phosphotyrosine
72 Citations (Scopus)

Structure and mechanism of the RNA triphosphatase component of mammalian mRNA capping enzyme

Changela, A., Ho, C. K., Martins, A., Shuman, S. & Mondragon, A., May 15 2001, In : EMBO Journal. 20, 10, p. 2575-2586 12 p.

Research output: Contribution to journalArticle

mRNA guanylyltransferase
Phosphoric Monoester Hydrolases
Cysteine
Phosphoprotein Phosphatases
RNA Precursors
32 Citations (Scopus)

The mechanism of type IA topoisomerase-mediated DNA topological transformations

Li, Z., Mondragon, A. & DiGate, R. J., Jan 1 2001, In : Molecular cell. 7, 2, p. 301-307 7 p.

Research output: Contribution to journalArticle

Type I DNA Topoisomerase
DNA
Disulfides
DNA Topoisomerases
Single-Stranded DNA
2000
30 Citations (Scopus)

Identification of a unique domain essential for Escherichia coli DNA topoisomerase III-catalysed decatenation of replication intermediates

Li, Z., Mondragón, A., Hiasa, H., Marians, K. J. & DiGate, R. J., Mar 4 2000, In : Molecular Microbiology. 35, 4, p. 888-895 8 p.

Research output: Contribution to journalArticle

Type II DNA Topoisomerase
Escherichia coli
DNA Replication
Plasmids
Superhelical DNA
1999
35 Citations (Scopus)

Conformational changes in E. coli DNA topoisomerase I

Feinberg, H., Lima, C. D. & Mondragon, A., Oct 13 1999, In : Nature Structural Biology. 6, 10, p. 918-922 5 p.

Research output: Contribution to journalArticle

DNA Topoisomerases
Type I DNA Topoisomerase
Escherichia coli
Double-Stranded DNA Breaks
Conformations
22 Citations (Scopus)

Protein-nucleotide interactions in E. coli DNA topoisomerase I

Feinberg, H., Changela, A. & Mondragon, A., Oct 13 1999, In : Nature Structural Biology. 6, 10, p. 961-968 8 p.

Research output: Contribution to journalArticle

Type I DNA Topoisomerase
Escherichia coli
Nucleotides
DNA
Proteins
203 Citations (Scopus)

Structures of two repeats of spectrin suggest models of flexibility

Grum, V. L., Li, D., MacDonald, R. I. & Mondragón, A., Aug 20 1999, In : Cell. 98, 4, p. 523-535 13 p.

Research output: Contribution to journalArticle

Spectrin
Cytoskeleton
Scaffolds
Chickens
Brain