Insight into stereochemistry of a new IMP allelic variant (IMP-55) metallo-β-lactamase identified in a clinical strain of Acinetobacter baumannii.
Metallo-β-lactamases (MBLs) such as IMPs are broad-spectrum β-lactamases that inactivate virtually all β-lactam antibiotics including carbapenems. In this study, we investigated the hydrolytic activity, phylogenetic relationship, three dimensional (3D) structure including zinc binding motif of a new IMP variant (IMP-55) identified in a clinical strain of Acinetobacter baumannii (AB). AB strain 56 was isolated from an adult ICU of a teaching hospital in Kerman, Iran. It exhibited MIC 32μg/ml to imipenem and showed MBL activity. Hydrolytic property of the MBL enzyme was measured phenotypically. Presence of blaIMPgene encoded by class 1 integrons was detected by PCR-sequencing. Phylogenetic tree of IMP protein was constructed using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and 3D model including zinc binding motif was predicted by bioinformatics softwares. Analysis of IMP sequence led to the identification of a novel IMP-type designated as IMP-55 (GenBank: KU299753.1; UniprotKB: A0A0S2MTX2). Impact in term of hydrolytic activity compared to the closest variants suggested efficient imipenem hydrolysis by this enzyme. Evolutionary distance matrix assessment indicated that IMP-55 protein is not closely related to other A. baumannii IMPs, however, shared 98% homology with Escherichia coli IMP-30 (UniprotKB: A0A0C5PJR0) and Pseudomonas aeruginosa IMP-1 (UniprotKB: Q19KT1). It consisted of five α-helices, ten β-sheets and six loops. A monovalent zinc ion attached to core of enzyme via His95, His97, His157 and Cys176. Multiple amino acid sequence alignments and mutational trajectory with reported IMPs showed 4 amino acid substitutions at positions 12(Phe→Ile), 31(Asp→Glu), 172(Leu→Phe) and 185(Asn→Lys). We suggest that the pleiotropic effect of mutations due to frequent administration of imipenem is responsible for emergence of new IMP variant in our hospitals.
Department of Microbiology and Virology, Kerman University of Medical Sciences, Kerman, Iran; Infection Diseases and Tropical Medicine Research Center, Kerman University of Medical Sciences, Kerman, Iran. Electronic address: mr_shakibaei@kmu.ac.ir.
Mohammad Reza
MR
Shakibaie
Department of Microbiology and Virology, Kerman University of Medical Sciences, Kerman, Iran.
Omid
O
Azizi
Department of Bacteriology, Microbiology Center, Pasteur Institute of Iran, Tehran, Iran.
Fereshteh
F
Shahcheraghi
D000151:Acinetobacter Infections / Q000188:drug therapy / Q000382:microbiology; D040981:Acinetobacter baumannii / Q000145:classification / Q000187:drug effects / Q000201:enzymology* / Q000302:isolation & purification; D000483:Alleles; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000627:therapeutic use; D001665:Binding Sites; D015870:Gene Expression; D006801:Humans; D015378:Imipenem / Q000737:chemistry* / Q000627:therapeutic use; D007527:Isoenzymes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008826:Microbial Sensitivity Tests; D008958:Models, Molecular; D010802:Phylogeny; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity; D015032:Zinc / Q000737:chemistry* / Q000378:metabolism; D001618:beta-Lactamases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
D000900:Anti-Bacterial Agents; D007527:Isoenzymes; D015378:Imipenem; D001618:beta-Lactamases; D015032:Zinc
Acinetobacter baumannii; Metallo-β-lactamase; Mutation; PCR; Protein modeling