Molecule of the Month: New Delhi Metallo-Beta-Lactamase
Antibiotics can save lives, but antibiotic-resistant strains of bacteria pose a dangerous threat
Exploring the Structure
NDM-1 and antibiotics (PDB entries 4eyf, 4eyl, 4rl0)
NDM-1 is particularly effective because it is not as specific as a typical enzyme. Most enzymes surround their substrates, so they recognize only their specific target molecules. NDM-1, on the other hand, recognizes the key reactive portion of the antibiotics using two zinc ions, but largely ignores the rest of the molecule. In that way, it can disable nearly all β-lactam antibiotics. The picture shown here shows the enzyme bound to the antibiotic ampicillin (PDB entry 3q6x ), seen after the enzyme has cleaved the small molecule. To look at this enzyme bound to penicillin, cephalosporin, and carbapenem antibiotics, click on the image for an interactive JSmol.
Topics for Further Discussion
- There are many stuctures related to β-lactam resistance in the PDB. You can explore some of these by using the Protein Feature View for TEM-1, KPC-2, or NDM-1.
- You can explore the structures of the antibiotics using the Ligand Summary page. For instance, take a look at the page for ampicillin.
Related PDB-101 Resources
- Browse Antimicrobial Resistance
- Browse Enzymes
- Browse Drug Action
- Browse Infectious Disease
- 4rl0: H. Feng, J. Ding, D. Zhu, C. Liu, X. Xu, Y. Zhang, S. Zang, D. C. Wang & W. Liu (2014) Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins. Journal of the American Chemical Society 136, 14694-14697.
- 3rxw: W. Ke, C. R. Bethel, K. M. Papp-Wallace, S. R. Pagadala, M. Nottingham, D. Fernandez, J. D. Buynak, R. A. Bonomo & F. van den Akker (2012) Crystal structures of KPC-2 β-lactamase in complex with 3-nitrophenyl boronic acid and the penam sulfone PSR-3-226. Antimicrobial Agents and Chemotherapy 56, 2713-2718.
- 4eyf, 4eyl: D. T. King, L. J. Worrall, R. Gruninger & N. C. Strynadka (2012) New Delhi metallo-β-lactamase: structural insights into β-lactam recognition and inhibition. Journal of the American Chemical Society 134, 11362- 11365.
- 3se7: V. M. D'Costa, C. E. King, L. Kalan, M. Morar, W. W. Sung, C. Schwarz, D. Froese, G. Zazula, F. Calmels, R. Debruyne, G. B. Golding, H. N. Poinar & G. D. Wright (2011) Antibiotic resistance is ancient. Nature 477, 457-461.
- 3q6x: H. Zhang & Q. Hao (2011) Crystal structure of NDM-1 reveals a common β-lactam hydrolysis mechanism. FASEB Journal 25, 2574-2582.
- 1e4e: D. I. Roper, T. Huyton, A. Vagin & G. Dodson (2000) The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate lyase (VanA). Proceedings of the National Academy of Science USA 97, 8921-8925.
July 2015, David Goodselldoi:10.2210/rcsb_pdb/mom_2015_7