Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)-Ib From Campylobacter fetus subsp. fetus.
Campylobacter fetus subsp. fetus
aminoglycoside
aminoglycoside modifying enzyme
aminoglycoside nucleotidyltransferase‐6
streptomycin
Journal
Proteins
ISSN: 1097-0134
Titre abrégé: Proteins
Pays: United States
ID NLM: 8700181
Informations de publication
Date de publication:
09 Sep 2024
09 Sep 2024
Historique:
revised:
13
08
2024
received:
30
05
2024
accepted:
26
08
2024
medline:
9
9
2024
pubmed:
9
9
2024
entrez:
9
9
2024
Statut:
aheadofprint
Résumé
Aminoglycoside antibiotics have played a critical role in the treatment of both Gram-negative and Gram-positive bacterial infections. However, antibiotic resistance has severely compromised the efficacy of aminoglycosides. A leading cause of aminoglycoside resistance is mediated by bacterial enzymes that inactivate these drugs via chemical modification. Aminoglycoside nucleotidyltransferase-6 (ANT(6)) enzymes inactivate streptomycin by transferring an adenyl group from ATP to position 6 on the antibiotic. Despite the clinical significance of this activity, ANT(6) enzymes remain relatively uncharacterized. Here, we report the first high resolution x-ray crystallographic structure of ANT(6)-Ib from Campylobacter fetus subsp. fetus bound with streptomycin. Structural modeling and gel filtration chromatography experiments suggest that the enzyme exists as a dimer in which both subunits contribute to the active site. Moreover, superposition of the ANT(6)-Ib structure with the structurally related enzyme lincosamide nucleotidyltransferase B (LinB) permitted the identification of a putative nucleotide binding site. These data also suggest that residues D44 and D46 coordinate essential divalent metal ions and D102 functions as the catalytic base.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : S3 Ott-Stiner Endowed Fellowship in Chemistry and Natural Sciences
Organisme : Office of Undergraduate Research and Scholarship
Organisme : Development Office at Grand Valley State University
Informations de copyright
© 2024 Wiley Periodicals LLC.
Références
A. Schatz, E. Bugie, and S. A. Waksman, “Streptomycin, a Substance Exhibiting Antibiotic Activity Against Gram‐Positive and Gram‐Negative Bacteria. 1944,” Clinical Orthopaedics and Related Research 437 (August 2005): 3–6, https://doi.org/10.1097/01.blo.0000175887.98112.fe.
K. M. Krause, A. W. Serio, T. R. Kane, and L. E. Connolly, “Aminoglycosides: An Overview,” Cold Spring Harbor Perspectives in Medicine 6, no. 6 (June 2016): a027029, https://doi.org/10.1101/cshperspect.a027029.
L. P. Kotra, J. Haddad, and S. Mobashery, “Aminoglycosides: Perspectives on Mechanisms of Action and Resistance and Strategies to Counter Resistance,” Antimicrobial Agents and Chemotherapy 44, no. 12 (December 2000): 3249–3256, https://doi.org/10.1128/AAC.44.12.3249‐3256.2000.
M. S. Ramirez and M. E. Tolmasky, “Aminoglycoside Modifying Enzymes,” Drug Resistance Updates 13, no. 6 (December 2010): 151–171, https://doi.org/10.1016/j.drup.2010.08.003.
L. Hormeno, M. Ugarte‐Ruiz, G. Palomo, et al., “ant(6)‐I Genes Encoding Aminoglycoside O‐Nucleotidyltransferases Are Widely Spread Among Streptomycin Resistant Strains of Campylobacter jejuni and Campylobacter coli,” Frontiers in Microbiology 9 (2018): 2515, https://doi.org/10.3389/fmicb.2018.02515.
J. Lu, Y. Sha, M. Gao, et al., “Identification and Characterization of a Novel Aminoglycoside O‐Nucleotidyltransferase ANT(6)‐if From Paenibacillus thiaminolyticus PATH554,” Frontiers in Microbiology 14 (2023): 1184349, https://doi.org/10.3389/fmicb.2023.1184349.
L. C. Pedersen, M. M. Benning, and H. M. Holden, “Structural Investigation of the Antibiotic and ATP‐Binding Sites in Kanamycin Nucleotidyltransferase,” Biochemistry 34, no. 41 (October 1995): 13305–13311, https://doi.org/10.1021/bi00041a005.
G. Cox, P. J. Stogios, A. Savchenko, and G. D. Wright, “Structural and Molecular Basis for Resistance to Aminoglycoside Antibiotics by the Adenylyltransferase ANT(2″)‐Ia,” MBio 6, no. 1 (January 2015): e02180‐14, https://doi.org/10.1128/mBio.02180‐14.
C. Semper, P. Stogios, D. Meziane‐Cherif, E. Evdokimova, P. Courvalin, and A. Savchenko, “Structural Characterization of Aminoglycoside 4'‐O‐Adenylyltransferase ANT(4′)‐IIb From Pseudomonas aeruginosa,” Protein Science 29, no. 3 (March 2020): 758–767, https://doi.org/10.1002/pro.3815.
A. L. Stern, S. E. Van der Verren, P. S. Kanchugal, J. Nasvall, H. Gutierrez‐de‐Teran, and M. Selmer, “Structural Mechanism of AadA, a Dual‐Specificity Aminoglycoside Adenylyltransferase From Salmonella enterica,” Journal of Biological Chemistry 293, no. 29 (July 2018): 11481–11490, https://doi.org/10.1074/jbc.RA118.003989.
P. S. Kanchugal and M. Selmer, “Structural Recognition of Spectinomycin by Resistance Enzyme ANT(9) From Enterococcus faecalis,” Antimicrobial Agents and Chemotherapy 64, no. 6 (May 2020): e00371‐20, https://doi.org/10.1128/AAC.00371‐20.
K. O'Hara, K. Ohmiya, and M. Kono, “Structure of Adenylylated Streptomycin Synthesized Enzymatically by Bacillus subtilis,” Antimicrobial Agents and Chemotherapy 32, no. 6 (June 1988): 949–950, https://doi.org/10.1128/AAC.32.6.949‐b.
C. Vonrhein, C. Flensburg, P. Keller, et al., “Data Processing and Analysis With the autoPROC Toolbox,” Acta Crystallographica. Section D, Biological Crystallography 67, no. Pt 4 (April 2011): 293–302, https://doi.org/10.1107/S0907444911007773.
P. Evans, “Scaling and Assessment of Data Quality,” Acta Crystallographica. Section D, Biological Crystallography 62, no. Pt 1 (January 2006): 72–82, https://doi.org/10.1107/S0907444905036693.
A. J. McCoy, R. W. Grosse‐Kunstleve, P. D. Adams, M. D. Winn, L. C. Storoni, and R. J. Read, “Phaser Crystallographic Software,” Journal of Applied Crystallography 40, no. Pt 4 (August 2007): 658–674, https://doi.org/10.1107/S0021889807021206.
J. Jumper, R. Evans, A. Pritzel, et al., “Highly Accurate Protein Structure Prediction With AlphaFold,” Nature 596, no. 7873 (August 2021): 583–589, https://doi.org/10.1038/s41586‐021‐03819‐2.
P. D. Adams, P. V. Afonine, G. Bunkoczi, et al., “PHENIX: A Comprehensive Python‐Based System for Macromolecular Structure Solution,” Acta Crystallographica. Section D, Biological Crystallography 66, no. Pt 2 (February 2010): 213–221, https://doi.org/10.1107/S0907444909052925.
P. Emsley, B. Lohkamp, W. G. Scott, and K. Cowtan, “Features and Development of Coot,” Acta Crystallographica. Section D, Biological Crystallography 66, no. Pt 4 (April 2010): 486–501, https://doi.org/10.1107/S0907444910007493.
C. Abril, I. Brodard, and V. Perreten, “Two Novel Antibiotic Resistance Genes, tet(44) and ant(6)‐Ib, Are Located Within a Transferable Pathogenicity Island in Campylobacter fetus Subsp. fetus,” Antimicrobial Agents and Chemotherapy 54, no. 7 (July 2010): 3052–3055, https://doi.org/10.1128/AAC.00304‐10.
R. H. Upson, R. P. Haugland, M. N. Malekzadeh, and R. P. Haugland, “A Spectrophotometric Method to Measure Enzymatic Activity in Reactions That Generate Inorganic Pyrophosphate,” Analytical Biochemistry 243, no. 1 (December 1996): 41–45, https://doi.org/10.1006/abio.1996.0479.
M. Morar, K. Bhullar, D. W. Hughes, M. Junop, and G. D. Wright, “Structure and Mechanism of the Lincosamide Antibiotic Adenylyltransferase LinB,” Structure 17, no. 12 (December 2009): 1649–1659, https://doi.org/10.1016/j.str.2009.10.013.
E. Krissinel and K. Henrick, “Inference of Macromolecular Assemblies From Crystalline State,” Journal of Molecular Biology 372, no. 3 (September 2007): 774–797, https://doi.org/10.1016/j.jmb.2007.05.022.
Y. Itoh, V. Singh, A. Khawaja, et al., “Structure of the Mitoribosomal Small Subunit With Streptomycin Reveals Fe‐S Clusters and Physiological Molecules,” eLife 11 (December 2022): e77460, https://doi.org/10.7554/eLife.77460.
L. Holm, A. Laiho, P. Toronen, and M. Salgado, “DALI Shines a Light on Remote Homologs: One Hundred Discoveries,” Protein Science 32, no. 1 (January 2023): e4519, https://doi.org/10.1002/pro.4519.
M. Latorre, P. Penalver, J. Revuelta, J. L. Asensio, E. Garcia‐Junceda, and A. Bastida, “Rescue of the Streptomycin Antibiotic Activity by Using Streptidine as a “Decoy Acceptor” for the Aminoglycoside‐Inactivating Enzyme Adenyl Transferase,” Chemical Communications (Cambridge) 27 (July 2007): 2829–2831, https://doi.org/10.1039/b704785a.
V. R. Porter, K. D. Green, O. E. Zolova, J. L. Houghton, and S. Garneau‐Tsodikova, “Dissecting the Cosubstrate Structure Requirements of the Staphylococcus aureus Aminoglycoside Resistance Enzyme ANT(4′),” Biochemical and Biophysical Research Communications 403, no. 1 (December 2010): 85–90, https://doi.org/10.1016/j.bbrc.2010.10.119.