SHV Lactamase Engineering Database: a reconciliation tool for SHV β-lactamases in public databases

Area of Science:

• Microbiology
• Structural Biology
• Bioinformatics

Background:

• SHV β-lactamases are enzymes conferring antibiotic resistance through accumulating mutations.
• The number of known SHV variants is rapidly increasing, with 117 variants in the SHV mutation table.
• Information on SHV β-lactamases is available in the NCBI protein database, but inconsistencies exist.

Purpose of the Study:

• To develop the SHV β-Lactamase Engineering Database (SHVED) for collecting and reconciling SHV β-lactamase sequence data.
• To provide a centralized resource for identifying new SHV variants and amino acid substitutions.
• To detect and resolve inconsistencies in existing databases.

Main Methods:

• Collected SHV β-lactamase sequences from the NCBI protein database and the SHV mutation table.
• Developed the SHVED to store 200 distinct protein entries and 20 crystal structures.
• Reconciled 27 protein entries with inconsistent SHV name identification using data from the SHV mutation table.

Main Results:

• The SHVED contains 200 distinct protein entries and 20 crystal structures.
• Identified 82 sequences unique to the NCBI protein database, including 22 unclassified full-length sequences.
• Resolved inconsistencies in SHV naming conventions by cross-referencing with the SHV mutation table.

Conclusions:

• The SHVED provides reconciled annotation for SHV variants, enhancing data accuracy.
• Facilitates the detection of inconsistencies within the NCBI protein database.
• Supports the identification of novel mutations and SHV variants, aiding in the study of sequence-function relationships.