Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2009 Dec 22;48(50):11840-7.
doi: 10.1021/bi901690r.

The 1.4 A crystal structure of the class D beta-lactamase OXA-1 complexed with doripenem

Kyle D Schneider  1 , Mary E Karpen, Robert A Bonomo, David A Leonard, Rachel A Powers
Affiliations
Comparative Study

The 1.4 A crystal structure of the class D beta-lactamase OXA-1 complexed with doripenem

Kyle D Schneider et al. Biochemistry. .

Abstract

The clinical efficacy of carbapenem antibiotics depends on their resistance to the hydrolytic action of beta-lactamase enzymes. The structure of the class D beta-lactamase OXA-1 as an acyl complex with the carbapenem doripenem was determined to 1.4 A resolution. Unlike most class A and class C carbapenem complexes, the acyl carbonyl oxygen in the OXA-1-doripenem complex is bound in the oxyanion hole. Interestingly, no water molecules were observed in the vicinity of the acyl linkage, providing an explanation for why carbapenems inhibit OXA-1. The side chain amine of K70 remains fully carboxylated in the acyl structure, and the resulting carbamate group forms a hydrogen bond to the alcohol of the 6alpha-hydroxyethyl moiety of doripenem. The carboxylate attached to the beta-lactam ring of doripenem is stabilized by a salt bridge to K212 and a hydrogen bond with T213, in lieu of the interaction with an arginine side chain found in most other beta-lactamase-beta-lactam complexes (e.g., R244 in the class A member TEM-1). This novel set of interactions with the carboxylate results in a major shift of the carbapenem's pyrroline ring compared to the structure of the same ring in meropenem bound to OXA-13. Additionally, bond angles of the pyrroline ring suggest that after acylation, doripenem adopts the Delta(1) tautomer. These findings provide important insights into the role that carbapenems may have in the inactivation process of class D beta-lactamases.

PubMed Disclaimer

Figures

Figure 1
Figure 1
(A) The structure of doripenem. (B) Conversion of the Δ2 doripenem tautomer to the Δ1 form after acylation.
Figure 2
Figure 2
Stereoview of the overall structure of OXA-1 bound to doripenem. This and all subsequent figures were created with PyMOL (29).
Figure 3
Figure 3
Stereoview of the 2Fo-Fc electron density maps contoured at 1.0 σ surrounding doripenem and active site residues S67, KCX70, K212 and T213. Atoms are colored as follows: carbon atoms of OXA-1 are light blue, carbon atoms of doripenem green, nitrogens blue, oxygens red and sulfurs yellow. (B) Hydrogen bonding interactions (red dashes) between OXA-1 and doripenem. (C) Overlay of imipenem (salmon) in the active site of TEM-1 (PDB entry 1BT5) (3) and doripenem (green) in OXA-1, showing the different orientations of the carbonyl oxygen with respect to the oxyanion hole (right side). Residue numbers are for OXA-1.
Figure 4
Figure 4
Superposition of the structures of OXA-13/meropenem (cyan) (5) with OXA-1/doripenem (green). (A) Overall structural similarity of the main-chains. (B) Comparison of the mode by which OXA-1 and OXA-13 stabilize the carbapenem carboxylate.
Figure 5
Figure 5
Comparison of the carbapenem hydroxyethyl moiety for (A) doripenem and V117 of OXA-1 and (B), imipenem and N132 of TEM-1 (3).
Figure 6
Figure 6
The geometry of carbon C3 of doripenem bound to OXA-1. (A) Electron density showing that the location of the sulfur atom (S31) is above the plane of the pyrroline ring. (B) Overlay showing the different positions assumed by the sulfur in OXA-1/doripenem (R configuration; green), TEM-1/imipenem (planar; salmon) (3) and BlaC/meropenem (S configuration; brown) (9).
See this image and copyright information in PMC

References

    1. Pillar CM, Torres MK, Brown NP, Shah D, Sahm DF. In vitro activity of doripenem, a carbapenem for the treatment of challenging infections caused by gram-negative bacteria, against recent clinical isolates from the United States. Antimicrob. Agents Chemother. 2008;52:4388–4399. - PMC - PubMed
    1. Beadle BM, Shoichet BK. Structural basis for imipenem inhibition of class C β-lactamases. Antimicrob. Agents Chemother. 2002;46:3978–3980. - PMC - PubMed
    1. Maveyraud L, Mourey L, Kotra LP, Pedelacq J-D, Guillet V, Mobashery S, Samama J-P. Structural basis for clinical longevity of carbapenem antibiotics in the face of challenge by the common class A β-lactamases from the antibiotic-resistant bacteria. J. Am. Chem. Soc. 1998;120:9748–9752.
    1. Fisher JF, Meroueh SO, Mobashery S. Bacterial resistance to β-lactam antibiotics: compelling opportunism, compelling opportunity. Chem. Rev. 2005;105:395–424. - PubMed
    1. Pernot L, Frenois F, Rybkine T, L'Hermite G, Petrella S, Delettre J, Jarlier V, Collatz E, Sougakoff W. Crystal structures of the class D β-lactamase OXA-13 in the native form and in complex with meropenem. J. Mol. Biol. 2001;310:859–874. - PubMed

Publication types

Associated data