PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons

Related Articles
Design and Evolution: Molecular Sleuthing Reveals Drug Selectivity
June 2015
Families in Gene Neighborhoods
June 2015
Ryanodine Receptor
April 2015
CCR5 and HIV Infection
January 2015
Drug Targets: Bile Acids in Motion
September 2014
Drug Targets: S1R's Ligands and Partners
September 2014
P2Y Receptors and Blood Clotting
September 2014
Bacterial CDI Toxins
June 2014
Glucagon Receptor
April 2014
March 2014
Microbial Pathogenesis: Targeting Drug Resistance in Mycobacterium tuberculosis
February 2014
Design and Discovery: Virtual Drug Screening
January 2014
Cancer Networks: IFI16-mediated p53 Activation
November 2013
G Proteins and Cancer
November 2013
Drug Discovery: Antidepressant Potential of 6-NQ SERT Inhibitors
October 2013
Drug Discovery: Finding Druggable Targets
October 2013
Drug Discovery: Identifying Dynamic Networks by CONTACT
October 2013
Drug Discovery: Modeling NET Interactions
October 2013
Membrane Proteome: GPCR Substrate Recognition and Functional Selectivity
August 2013
Infectious Diseases: Determining the Essential Structome
May 2013
NDM-1 and Antibiotics
May 2013
Microbial Pathogenesis: Computational Epitope Prediction
January 2013
Microbial Pathogenesis: Influenza Inhibitor Screen
January 2013
Microbial Pathogenesis: Measles Virus Attachment
January 2013
Cytochrome Oxidase
November 2012
Membrane Proteome: The ABCs of Transport
November 2012
Bacterial Phosphotransferase System
October 2012
Regulatory insights
September 2012
Solute Channels
September 2012
Pocket changes
July 2012
Receptor bias
July 2012
Anthrax Stealth Siderophores
June 2012
G Protein-Coupled Receptors
May 2012
Substrate specificity sleuths
April 2012
Reading out regioselectivity
December 2011
Superbugs and Antibiotic Resistance
December 2011
Terminal activation
December 2011
A change to resistance
November 2011
Docking and rolling
October 2011
Breaking down the defenses
September 2011
A2A Adenosine Receptor
May 2011
Cell wall recycler
May 2011
Subtly different
March 2011
January 2011
Subtle shifts
January 2011
ABA receptor diversity
November 2010
COX inhibition: Naproxen by proxy
November 2010
Zinc Transporter ZntB
July 2010
Peptidoglycan binding: Calcium-free killing
June 2010
Treating sleeping sickness
May 2010
Bacterial spore kinase
April 2010
Antibiotics and Ribosome Function
March 2010
Safer Alzheimer's drugs?
March 2010
Anthrax evasion tactics
September 2009
GPCR subunits: Separate but not equal
September 2009
Antibiotic target
August 2009
Salicylic Acid Binding Protein 2
August 2009
July 2009
Tackling influenza
June 2009
Bacterial Leucine Transporter, LeuT
May 2009
Anthrax stealth molecule
March 2009
Drug targets to aim for
February 2009
High-energy storage system
February 2009
Transporter mechanism in sight
February 2009
Scavenger Decapping Enzyme DcpS
November 2008
Blocking AmtB
September 2008

Research Themes Drug discovery

NDM-1 and Antibiotics

SBKB [doi:10.3942/psi_sgkb/fm_2013_5]
Featured System - May 2013
Short description: With structural biology and computational analysis, PSI Biology researchers have revealed the catalytic pathway of an antibiotic-destroying enzyme.

Antibiotic resistance is a major threat to current medical practice, slowly eroding the life-saving progress we have made since the discovery of penicillin. A new class of bacteria, termed CRE (carbapenem-resistant enterobacteriaceae), have developed particularly powerful enzymes that destroy antibiotics, building on enzymes that have evolved over millennia of warfare between different microbes. In 2011, PSI researchers first revealed the structure of the most dangerous of these enzymes, the metallo-β-lactamase NDM-1 (as described in the Featured System article Superbugs and Antibiotic Resistance). NDM-1 is particularly effective because it is unusually promiscuous: it can destroy penicillin, ampicillin, cephalosporin, and every other β-lactam antibiotic.

The Down Side of Specificity

We normally admire enzymes for their remarkable specificity: they recognize specific molecules and perform a chemically exact reaction. NDM-1, on the other had, has a far more general task to perform: it needs to protect bacteria from an entire class of antibiotic molecules. Structures of NDM-1 with different antibiotics have revealed that it does this by recognizing only the common features between all these drugs. As seen above in the structure of NDM-1 with faropenem, solved by PSI Biology researchers at MCSG and MTBI (PDB entry 4hky), the enzyme has two metal ions (magenta) that bind to oxygen atoms in the distinctive β-lactam group. The rest of the active site is largely featureless and can accommodate antibiotics of many shapes and sizes.

Fighting Back

Of course, we are aggressively fighting back in this ongoing battle, searching for new antibiotics to fight infection by drug-resistant bacteria. The first success was found in L-captopril, a drug that is currently used to treat hypertension. As seen here in PDB entry 4exs, the drug binds to the metal ions in the active site of NDM-1 and blocks its action. Building on this structure, researchers are currently searching for more effective drugs.

NDM-1 Mechanism

A greater understanding of the mechanism of the enzyme will assist this search for new inhibitors. Soon after the first structures of NDM-1 were solved, several laboratories presented structures of the enzyme bound to the product of the reaction: hydrolyzed antibiotics. The earlier steps in the reaction, however, have been difficult to capture. PSI Biology researchers have revealed two of these steps by studying the enzyme with cadmium ions instead of the normal zinc ions. This slows the reaction, allowing the complex to be captured by crystallography. The faropenem structure shown above is one example, showing the binding of substrate, and they have also been able to capture an intermediate state of ampicillin, shown here from PDB entry 4hl1. Computational analysis of these structures underscored the importance of a hydroxide ion, shown here in turquoise, that is positioned by the metal ions. To explore these structures in detail, click on the image for an interactive Jmol.

The JSmol tab below displays an interactive JSmol

NDM-1 complexes (PDB entries 4hky, 4hl1, 4hl2 and 4exs)

This Jmol includes four structures showing different steps in the reaction. The first structure shows faropenem bound in the active site before reaction. The second structure captures an intermediate state of ampicillin that showed disordered electron density around the central ring. This was interpreted as a mixture of non-hydrolyzed and hydrolyzed forms, so several atoms of the central ring are missing. The third structure shows ampicillin after the reaction, with the β-lactam ring broken.


  1. Kim, Y., Cunningham, M. A., Mire, J., Tesar, C., Sacchettini, J. & Joachimiak, A. NDM-1, the ultimate promiscuous enzyme: substrate recognition and catalytic mechanism. FASEB J. 27, Epub ahead of print (2013).

  2. King, D. T., Worrall, L. J., Gruninger, R. & Strynadka, N. C. J. New Delhi metallo-β- lactamase: structural insights into β-lactam recognition and inhibition. JACS 134, 11362-11365 (2012).

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health