SAND: a comprehensive annotation of class D β-lactamases using structural alignment-based numbering

Abstract

Class D β-lactamases are a diverse group of enzymes that contribute to antibiotic resistance by inactivating β-lactam antibiotics. Examination of class D β-lactamases has evolved significantly over the years, with advancements in molecular biology and structural analysis providing deeper insights into their mechanisms of action and variation in specificity. However, one of the challenges in the field is the inconsistent residue numbering and secondary structure annotation across different studies, which complicates the comparison and interpretation of data. To address this, we propose SAND-a standardized naming system for both residues and secondary structure elements, based on a comprehensive structural alignment of all documented sequences and experimentally obtained crystal structures of class D β-lactamases. This unified framework will streamline cross-study comparisons and enhance data interpretation. Moreover, the standardized framework will enable AI-driven natural language processing (NLP) techniques to efficiently mine and compile relevant data from scientific literature, speeding up the discovery process and contributing to more rapid advancements in β-lactamase research.

Keywords: OXA; SAND; class D; secondary structure annotation; structure-based sequence alignment; β-lactamases.

Fig 1

Example of SAND assigned to a query sequence. Sequence alignment of OXA-1, OXA-10, OXA-23, OXA-143, and OXA-181 to OXA-48 (the reference sequence). Signal peptide, which is removed post-translationally during export to the bacterial periplasm, is assigned using Deepsig (5) and colored in gray. Loops framing the active site are mapped above the corresponding residue numbers. Residues involved in catalytic activity are highlighted in red. Positions identified to be highly conserved, based on alignment of the latest set of DBLs listed on bldb.eu, are highlighted with an asterisk on top.

Fig 2

Secondary structure assignment for class D β-lactamases. (A) Flat diagram with consensus annotation of secondary structure elements of class D β-lactamases. Putative variable elements (shown in light gray) represent assignments that are transient or not conserved across the majority of the class D β-lactamase family. (B) Secondary structure annotation mapped onto the 3D structure of OXA-48 (PDB ID: 5DTK (22). (C) Table with residues bordering major secondary structure elements of OXA-48 as assigned according to the DSSP algorithm. An illustration of the secondary structural alignment of representative DBLs can be found in Fig. S2.