Crystal structure of NDM‐1 reveals a common β‐lactam hydrolysis mechanism

Zhang, HongMin; Hao, Quan

doi:10.1096/fj.11-184036

Cited by 227 publications

(382 citation statements)

References 50 publications

Supporting

Mentioning

352

Contrasting

Order By: Relevance

“…At this point it may be necessary to briefly discuss the connection between the tighter and weaker metal ion binding sites (characterised by K d1 and K d2 ) and the two available binding sites in the catalytic centre, labelled Zn1 and Zn2 (Figure 4). In B1-and B3-type MBLs Zn1 is likely to be associated with K d1 , supported, for instance, by crystallographic data that indicate a higher metal ion occupancy for this site than Zn2 [35] [36] [46] [59] [64]. An exception appears to be the B3-type MBL GOB from Elizabethkingia meningoseptica, where H116 in the Zn1 position (Figure 4) is replaced by a glutamine; a combination of kinetic and spectroscopic data indicate that this enzyme operates in mononuclear form with the metal ion bound to Zn2 (i.e.…”

Section: Interactions Between Mbls and Metal Ionsmentioning

confidence: 88%

Metallo-β-Lactamases: A Major Threat to Human Health

Phelan¹,

Miraula²,

Selleck³

et al. 2014

AJMB

View full text Add to dashboard Cite

Antibiotic resistance is one of the most significant challenges facing global healthcare. Since the 1940s, antibiotics have been used to fight infections, initially with penicillin and subsequently with various derivatives including cephalosporins, carbapenams and monobactams. A common characteristic of these antibiotics is the four-membered β-lactam ring. Alarmingly, in recent years an increasing number of bacteria have become resistant to these antibiotics. A major strategy employed by these pathogens is to use Zn(II)-dependent enzymes, the metallo-β-lactamases (MBLs), which hydrolyse the β-lactam ring. Clinically useful MBL inhibitors are not yet available. Consequently, MBLs remain a major threat to human health. In this review biochemical properties of MBLs are discussed, focusing in particular on the interactions between the enzymes and the functionally essential metal ions. The precise role(s) of these metal ions is still debated and may differ between different MBLs. However, since they are required for catalysis, their binding site may present an alternative target for inhibitor design.

show abstract

Section: Interactions Between Mbls and Metal Ionsmentioning

confidence: 88%

Metallo-β-Lactamases: A Major Threat to Human Health

Phelan¹,

Miraula²,

Selleck³

et al. 2014

AJMB

View full text Add to dashboard Cite

show abstract

“…These hydrogen bonds and interactions are absent in VIM-7 and VIM-4 due to the presence of histidine at this position (16,20). Residue 224 is a conserved lysine in many B1 family MBLs and was found to be critical for binding the carboxyl group on the C-3/C-4 atom of the substrate (21,32,33). Here we created a H224Y mutant to investigate the role of residue 224 in the structure, enzymatic activity, and thermostability of VIM-7 and the importance of potential additional hydrogen bonds.…”

mentioning

confidence: 99%

His224 Alters the R2 Drug Binding Site and Phe218 Influences the Catalytic Efficiency of the Metallo-β-Lactamase VIM-7

Leiros

Skagseth

Edvardsen

et al. 2014

Antimicrob Agents Chemother

View full text Add to dashboard Cite

b Metallo-␤-lactamases (MBLs) are the causative mechanism for resistance to ␤-lactams, including carbapenems, in many Gramnegative pathogenic bacteria. One important family of MBLs is the Verona integron-encoded MBLs (VIM). In this study, the importance of residues Asp120, Phe218, and His224 in the most divergent VIM variant, VIM-7, was investigated to better understand the roles of these residues in VIM enzymes through mutations, enzyme kinetics, crystal structures, thermostability, and docking experiments. The tVIM-7-D120A mutant with a tobacco etch virus (TEV) cleavage site was enzymatically inactive, and its structure showed the presence of only the Zn1 ion. The mutant was less thermostable, with a melting temperature (T m ) of 48.5°C, compared to 55.3°C for the wild-type tVIM-7. In the F218Y mutant, a hydrogen bonding cluster was established involving residues Asn70, Asp84, and Arg121. The tVIM-7-F218Y mutant had enhanced activity compared to wild-type tVIM-7, and a slightly higher T m (57.1°C) was observed, most likely due to the hydrogen bonding cluster. Furthermore, the introduction of two additional hydrogen bonds adjacent to the active site in the tVIM-7-H224Y mutant gave a higher thermostability (T m , 62.9°C) and increased enzymatic activity compared to those of the wild-type tVIM-7. Docking of ceftazidime in to the active site of tVIM-7, tVIM-7-H224Y, and VIM-7-F218Y revealed that the side-chain conformations of residue 224 and Arg228 in the L3 loop and Tyr67 in the L1 loop all influence possible substrate binding conformations. In conclusion, the residue composition of the L3 loop, as shown with the single H224Y mutation, is important for activity particularly toward the positively charged cephalosporins like cefepime and ceftazidime.

show abstract

“…It is not yet known which position(s) plays a critical role in the enzymatic activities. The crystal structure of NDM-1 revealed that the active site of NDM-1 is located at the bottom of a shallow groove enclosed by 2 important loops, L3 and L10 (21,22,23,24). Residues 88 and 130, however, were not lo- cated in these loops.…”

mentioning

confidence: 99%