5ACS: Y233A-Investigation of the impact from residues W228 and Y233 in the metallo-beta-lactamase GIM-1

Metallo-beta-lactamases (MBLs) hydrolyze virtually all beta-lactam antibiotics, including penicillins, cephalosporins, and carbapenems. The worldwide emergence of antibiotic-resistant bacteria harboring MBLs poses an increasing clinical threat. The MBL German imipenemase-1 (GIM-1) possesses an active site that is narrower and more hydrophobic than the active sites of other MBLs. The GIM-1 active-site groove is shaped by the presence of the aromatic side chains of tryptophan at residue 228 and tyrosine at residue 233, positions where other MBLs harbor hydrophilic residues. To investigate the importance of these two residues, eight site-directed mutants of GIM-1, W228R/A/Y/S and Y233N/A/I/S, were generated and characterized using enzyme kinetics, thermostability assays, and determination of the MICs of representative beta-lactams. The structures of selected mutants were obtained by X-ray crystallography, and their interactions with beta-lactam substrates were modeled in silico. Steady-state kinetics revealed that both positions are important to GIM-1 activity but that the effects of individual mutations vary depending on the beta-lactam substrate. Activity against type 1 substrates bearing electron-donating C-3/C-4 substituents (cefoxitin, meropenem) could be enhanced by mutations at position 228, whereas hydrolysis of type 2 substrates (benzylpenicillin, ampicillin, ceftazidime, imipenem) with methyl or positively charged substituents was favored by mutations at position 233. The crystal structures showed that mutations at position 228 or the Y233A variant alters the conformation of GIM-1 loop L1 rather than that of loop L3, on which the mutations are located. Taken together, these data show that point mutations at both positions 228 and 233 can influence the catalytic properties and the structure of GIM-1.
PDB ID: 5ACSDownload
MMDB ID: 135025
PDB Deposition Date: 2015/8/17
Updated in MMDB: 2015/12
Experimental Method:
x-ray diffraction
Resolution: 1.459  Å
Source Organism:
Similar Structures:
Biological Unit for 5ACS: dimeric; determined by author and by software (PISA)
Molecular Components in 5ACS
Label Count Molecule
Proteins (2 molecules)
Gim-1 Protein
Molecule annotation
Chemicals (4 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB