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

Fedaa Attana¹, Soobin Kim¹, James Spencer²

¹UCL School of Pharmacy, University College London, London, United Kingdom.

Antimicrobial Agents and Chemotherapy

|May 27, 2025

Summary

This summary is machine-generated.

Class D β-lactamases cause antibiotic resistance. A new standardized naming system (SAND) unifies residue and secondary structure annotations for class D β-lactamases, improving data comparison and accelerating research.

Keywords:

OXA SAND class D secondary structure annotation structure-based sequence alignment β-lactamases

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Last Updated: Sep 20, 2025

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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

Biochemistry
Structural Biology
Microbiology

Background:

Class D β-lactamases are crucial enzymes conferring antibiotic resistance by degrading β-lactam antibiotics.
Previous research has advanced understanding of their mechanisms and specificity through molecular biology and structural analysis.
Inconsistent residue numbering and secondary structure annotations hinder data comparison and interpretation across studies.

Purpose of the Study:

To introduce SAND (Standardized ANnotation system for beta-lactamase Domains), a novel naming system for residues and secondary structures.
To establish a unified framework for class D β-lactamase data, facilitating cross-study comparisons and interpretation.
To enable efficient data mining using AI-driven natural language processing (NLP) for accelerated research.

Main Methods:

Comprehensive structural alignment of all documented class D β-lactamase sequences.
Inclusion of experimentally obtained crystal structures for accurate annotation.
Development of a standardized naming convention for residues and secondary structure elements.

Main Results:

A proposed standardized naming system (SAND) for class D β-lactamase residues and secondary structures.
A unified framework that addresses inconsistencies in current annotation practices.
Facilitation of direct comparison and enhanced interpretation of diverse β-lactamase data.

Conclusions:

The SAND system provides a crucial tool for standardizing class D β-lactamase research.
This standardization will streamline data integration and interpretation, accelerating the discovery of new insights.
The framework is expected to enhance AI-driven analysis of scientific literature, speeding up advancements in antibiotic resistance research.