Dataset Information

An Integrative Database of ?-Lactamase Enzymes: Sequences, Structures, Functions, and Phylogenetic Trees.

ABSTRACT: ?-Lactamase enzymes have attracted substential medical attention from researchers and clinicians because of their clinical, ecological, and evolutionary interest. Here, we present a comprehensive online database of ?-lactamase enzymes. The current database is manually curated and incorporates the primary amino acid sequences, closest structural information in an external structure database (the Protein Data Bank [PDB]) and the functional profiles and phylogenetic trees of the four molecular classes (A, B, C, and D) of ?-lactamases. The functional profiles are presented according to the MICs and kinetic parameters that make them more useful for the investigators. Here, a total of 1,147 ?-lactam resistance genes are analyzed and described in the database. The database is implemented in MySQL and the related website is developed with Zend Framework 2 on an Apache server, supporting all major web browsers. Users can easily retrieve and visualize biologically important information using a set of efficient queries from a graphical interface. This database is freely accessible at http://ifr48.timone.univ-mrs.fr/beta-lactamase/public/.

SUBMITTER: Keshri V

PROVIDER: S-EPMC6496087 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Publications

An Integrative Database of β-Lactamase Enzymes: Sequences, Structures, Functions, and Phylogenetic Trees.

Keshri Vivek V Diene Seydina M SM Estienne Adrien A Dardaillon Justine J Chabrol Olivier O Tichit Laurent L Rolain Jean-Marc JM Raoult Didier D Pontarotti Pierre P

Antimicrobial agents and chemotherapy 20190425 5

β-Lactamase enzymes have attracted substential medical attention from researchers and clinicians because of their clinical, ecological, and evolutionary interest. Here, we present a comprehensive online database of β-lactamase enzymes. The current database is manually curated and incorporates the primary amino acid sequences, closest structural information in an external structure database (the Protein Data Bank [PDB]) and the functional profiles and phylogenetic trees of the four molecular clas ...[more]

PMID: 30783007

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Project description:BACKGROUND: TEM beta-lactamases are the main cause for resistance against beta-lactam antibiotics. Sequence information about TEM beta-lactamases is mainly found in the NCBI peptide database and TEM mutation table at http://www.lahey.org/Studies/temtable.asp. While the TEM mutation table is manually curated by experts in the lactamase field, who guarantee reliable and consistent information, the rapidly growing sequence and annotation information from the NCBI peptide database is sometimes inconsistent. Therefore, the Lactamase Engineering Database has been developed to collect the TEM beta-lactamase sequences from the NCBI peptide database and the TEM mutation table, systematically compare sequence information and naming, identify inconsistencies, and thus provide a versatile tool for reconciliation of data and for an investigation of the sequence-function relationship. DESCRIPTION: The LacED currently provides 2399 sequence entries and 37 structure entries. Sequence information on 150 different TEM beta-lactamases was derived from the TEM mutation table which provides a unique number to each protein classified as TEM beta-lactamase. 293 TEM-like proteins were found in the NCBI protein database, but only 113 TEM beta-lactamase were common to both data sets. The 180 TEM beta-lactamases from the NCBI protein database which have not yet been assigned to a TEM number fall in three classes: (1) 89 proteins from microbial organisms and 35 proteins from cloning or expression vectors had a new mutation profile; (2) 55 proteins had inconsistent annotation in terms of TEM assignment or reported mutation profile; (3) 39 proteins are fragments. The LacED is web accessible at http://www.LacED.uni-stuttgart.de and contains multisequence alignments, structure information and reconciled annotation of TEM beta-lactamases. The LacED is weekly updated and supplies all data for download. CONCLUSION: The Lactamase Engineering Database enables a systematic analysis of TEM beta-lactamase sequence and annotation data from different data sources, and thus provides a valuable tool to identify inconsistencies in sequences from the NCBI peptide database, to detect TEM beta-lactamases with a novel mutation profile, and to identify new amino acid positions at which mutations can occur.

Dataset Information

An Integrative Database of ?-Lactamase Enzymes: Sequences, Structures, Functions, and Phylogenetic Trees.

Publications

An Integrative Database of β-Lactamase Enzymes: Sequences, Structures, Functions, and Phylogenetic Trees.

Similar Datasets

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