Mechanistic and spectroscopic studies of metallo-β-lactamase NDM-1

Biochemistry. 2012 May 8;51(18):3839-47. doi: 10.1021/bi300056y. Epub 2012 Apr 25.

Abstract

In an effort to biochemically characterize metallo-β-lactamase NDM-1, we cloned, overexpressed, purified, and characterized several maltose binding protein (MBP)-NDM-1 fusion proteins with different N-termini (full-length, Δ6, Δ21, and Δ36). All MBP-NDM-1 fusion proteins were soluble; however, only one, MBP-NDM-1Δ36, exhibited high activity and bound 2 equiv of Zn(II). Thrombin cleavage of this fusion protein resulted in the truncated NDM-1Δ36 variant, which exhibited a k(cat) of 16 s(-1) and a K(m) of 1.1 μM when using nitrocefin as a substrate, bound 2 equiv of Zn(II), and was monomeric in solution. Extended X-ray absorption fine structure studies of the NDM-1Δ36 variant indicate the average metal binding site for Zn(II) in this variant consists of four N/O donors (two of which are histidines) and 0.5 sulfur donor per zinc, with a Zn-Zn distance of 3.38 Å. This metal binding site is very similar to those of other metallo-β-lactamases that belong to the B1 subclass. Pre-steady-state kinetic studies using nitrocefin and chromacef and the NDM-1Δ36 variant indicate that the enzyme utilizes a kinetic mechanism similar to that used by metallo-β-lactamases L1 and CcrA, in which a reactive nitrogen anion is stabilized and its protonation is rate-limiting. While they are very different in terms of amino acid sequence, these studies demonstrate that NDM-1 is structurally and mechanistically very similar to metallo-β-lactamase CcrA.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / metabolism
  • Binding Sites
  • Catalytic Domain
  • Cephalosporins / metabolism
  • Kinetics
  • Light
  • Recombinant Fusion Proteins / metabolism
  • Scattering, Radiation
  • Thrombin / metabolism
  • X-Ray Absorption Spectroscopy
  • Zinc / chemistry
  • Zinc / metabolism*
  • beta-Lactamases / chemistry
  • beta-Lactamases / metabolism*

Substances

  • Bacterial Proteins
  • Cephalosporins
  • Recombinant Fusion Proteins
  • Thrombin
  • beta-Lactamases
  • beta-lactamase NDM-1
  • carbapenemase
  • nitrocefin
  • Zinc