3RKJ: Crystal Structure Of New Delhi Metallo-Beta-Lactamase-1 From Klebsiella Pnueumoniae

The New Delhi Metallo-beta-lactamase (NDM-1) gene makes multiple pathogenic microorganisms resistant to all known beta-lactam antibiotics. The rapid emergence of NDM-1 has been linked to mobile plasmids that move between different strains resulting in world-wide dissemination. Biochemical studies revealed that NDM-1 is capable of efficiently hydrolyzing a wide range of beta-lactams, including many carbapenems considered as "last resort" antibiotics. The crystal structures of metal-free apo- and monozinc forms of NDM-1 presented here revealed an enlarged and flexible active site of class B1 metallo-beta-lactamase. This site is capable of accommodating many beta-lactam substrates by having many of the catalytic residues on flexible loops, which explains the observed extended spectrum activity of this zinc dependent beta-lactamase. Indeed, five loops contribute "keg" residues in the active site including side chains involved in metal binding. Loop 1 in particular, shows conformational flexibility, apparently related to the acceptance and positioning of substrates for cleavage by a zinc-activated water molecule.
PDB ID: 3RKJDownload
MMDB ID: 90664
PDB Deposition Date: 2011/4/18
Updated in MMDB: 2011/09
Experimental Method:
x-ray diffraction
Resolution: 2  Å
Source Organism:
Similar Structures:
Biological Unit for 3RKJ: monomeric; determined by author and by software (PISA)
Molecular Components in 3RKJ
Label Count Molecule
Protein (1 molecule)
Beta-lactamase Ndm-1(Gene symbol: PNDMMAR_p010)
Molecule annotation
Chemicals (3 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB