Fig 1.
Alignment of DIM-1 with Selected Subclass B1 Metallo-β-Lactamases.
Invariant residues are highlighted on a red background; conservative substitutions are colored red. Residue numbers according to the Class B β-Lactamase (BBL) standard numbering scheme are positioned above the sequences; individual residues discussed in the text are numbered below the sequences. This Figure was prepared using ESPript [15].
Table 1.
Data Collection and Refinement Statistics.
Fig 2.
A. Overall fold of the enzyme. Protein backbone is color-ramped from blue (N-) to red (C-terminus). Active site residues are rendered as sticks (carbon atoms in green, other atom colors as standard). Zinc ions (gray) and water molecules (red) are shown as spheres. B. Superposition of B1 MBL structures: DIM-1 (green); BcII (pdb accession 1BC2 ([43], blue); IMP-1 (1DDK [23], teal); VIM-2 (1KO3 [44], magenta); BlaB (1M2X [45], dark green); CcrA (1ZNB [46], yellow); NDM-1 (3Q6X [41], cyan); IND-7 (3L6N [47], red) and GIM-1 (2YNT [48], orange). This Figure was generated using Pymol (www.pymol.org).
Fig 3.
L3 Loop Conformations in Subclass B1 Metallo-β-Lactamases.
A. DIM-1 (green); B. IMP-1 (1DDK [23], teal); C. VIM-2 (1KO3 [44], magenta); D. NDM-1 (3Q6X [41], cyan). This Figure was generated using Pymol.
Fig 4.
Comparison of DIM-1 Active Site with L-Captopril-bound Complexes of Subclass B1 Metallo-β-Lactamases.
A. DIM-1 (green); B. IMP-1 (4C1F, teal); C. VIM-2 (4C1D, magenta); D. NDM-1 (4EXS [17], cyan). This Figure was generated using Pymol.
Fig 5.
Active Site Grooves of B1 Metallo-β-Lactamases.
Figure shows surfaces of A. DIM-1; B. GIM-1 (pdb accession 2YNT [48]) C. IMP-1 (1DDK [23]) and D. NDM-1 (3Q6X [41]) colored according to electrostatic potential from red (- 0.5 V) to blue (+ 0.5 V). Hydrolyzed ampicillin bound to NDM-1 is shown as sticks (carbon atoms green, other atom colors as standard). This Figure was generated using CCP4MG [50].
Fig 6.
DIM-1 Active Site and Comparison with Selected B1 Metallo-β-Lactamases.
A. Stereogram of DIM-1 active site (dataset 1 structure). Carbon atoms are colored green, zinc ions gray, water molecules red, other atom colors as standard. Electron density map shown is 2|Fo|-|Fc|.ϕcalc, contoured at 1.0 σ. B. Overlay of DIM-1 active sites for the four independently refined molecules. Structures from dataset 1 are in darker, and dataset 2 in lighter, shades. Dashed lines show metal:ligand interactions in chain A of dataset 1. Note presence of additional water molecule (Wat-3; dataset 1 chain B) or chloride ions (dataset 2 structures) bound to Zn2 ion, and bridging chloride ion in dataset 2 chain A structure. C. Active site of IND-7 (3L6N [47]). Note five- and four-fold co-ordination of Zn1 and Zn2, respectively. D. Active site of VIM-2 (1KO3 [44]). Not five-fold co-ordination of both Zn2+ ions. E. Active site of NDM-1 (3PSU [54]) Note four- and five-fold co-ordination of Zn1 and Zn2, respectively. This Figure was generated using Pymol.
Table 2.
Metal:ligand distances (Å).
Fig 7.
Overlay of B1 Metallo-β-Lactamase Active Sites Showing Hydrolyzed β-Lactam Binding.
Figure shows DIM-1, IMP-1 (1DDK [23], carbon, zinc and waters teal); VIM-2 (1KO3 [44], carbon, zinc and waters magenta) and NDM-1:ampicillin complex (3Q6X [41], carbon, zinc and waters cyan). Interactions of hydrolyzed ampicillin with NDM-1 are shown as dashed lines. Note differing positions of Arg-161 (224) (DIM-1), Lys-224 (IMP-1, NDM-1) and Arg-228 (VIM-2). This Figure was generated using Pymol.