Computational analysis of pathogen-borne metallo β-lactamases reveals discriminating structural features between B1 types

被引：15

作者：

Eithon Cadag

Elizabeth Vitalis

Kristin P Lennox

Carol L Ecale Zhou

Adam T Zemla

机构：

[1] Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore

[2] Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore

[3] National Security Engineering Division, Lawrence Livermore National Laboratory, Livermore

来源：

BMC Research Notes | / 5卷 / 1期

关键词：

Protein Data Bank; Linker Region; Structural Alignment; Active Cavity; Zinc Binding Site;

D O I：

10.1186/1756-0500-5-96

中图分类号：

学科分类号：

摘要：

Background: Genes conferring antibiotic resistance to groups of bacterial pathogens are cause for considerable concern, as many once-reliable antibiotics continue to see a reduction in efficacy. The recent discovery of the metallo β-lactamase blaNDM-1 gene, which appears to grant antibiotic resistance to a variety of Enterobacteriaceae via a mobile plasmid, is one example of this distressing trend. The following work describes a computational analysis of pathogen-borne MBLs that focuses on the structural aspects of characterized proteins. Results: Using both sequence and structural analyses, we examine residues and structural features specific to various pathogen-borne MBL types. This analysis identifies a linker region within MBL-like folds that may act as a discriminating structural feature between these proteins, and specifically resistance-associated acquirable MBLs. Recently released crystal structures of the newly emerged NDM-1 protein were aligned against related MBL structures using a variety of global and local structural alignment methods, and the overall fold conformation is examined for structural conservation. Conservation appears to be present in most areas of the protein, yet is strikingly absent within a linker region, making NDM-1 unique with respect to a linker-based classification scheme. Variability analysis of the NDM-1 crystal structure highlights unique residues in key regions as well as identifying several characteristics shared with other transferable MBLs. Conclusions: A discriminating linker region identified in MBL proteins is highlighted and examined in the context of NDM-1 and primarily three other MBL types: IMP-1, VIM-2 and ccrA. The presence of an unusual linker region variant and uncommon amino acid composition at specific structurally important sites may help to explain the unusually broad kinetic profile of NDM-1 and may aid in directing research attention to areas of this protein, and possibly other MBLs, that may be targeted for inactivation or attenuation of enzymatic activity. © 2012 Cadag et al; licensee BioMed Central Ltd.

引用

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