Related Experiment Video
Updated: May 27, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
BYKdb: the Bacterial protein tYrosine Kinase database
Fanny Jadeau1, Christophe Grangeasse, Lei Shi
1Unité Bases Moléculaires et Structurales des Systèmes Infectieux, UMR 5086 CNRS - Université Claude Bernard Lyon 1, IBCP FR 3302 - 7, Passage du Vercors, 69367 Lyon CEDEX 07, France.
Nucleic Acids Research
|November 15, 2011
Summary
Bacterial protein tyrosine-kinases (BY-kinases) have a unique signature, but database annotations are incomplete. We created BYKdb, a specialized database for comprehensive BY-kinase sequence annotation and analysis.
Area of Science:
- Biochemistry
- Molecular Biology
- Bioinformatics
Background:
- Bacterial tyrosine-kinases, termed BY-kinases, are distinct from eukaryotic counterparts and regulate bacterial cell functions.
- Recent studies have elucidated a common signature for BY-kinases through biochemical and structural analyses.
- Existing primary databases have incomplete annotations for BY-kinase sequences.
Purpose of the Study:
- To develop a specialized, computer-annotated database for bacterial protein tyrosine-kinase sequences.
- To address the limitations of incomplete BY-kinase annotations in public databases.
- To provide a centralized resource for studying bacterial tyrosine-kinases.
Main Methods:
- Identification of BY-kinase sequences using a previously established workflow.
- Annotation of UniProtKB entries through a secondary computational workflow.
- Development of a web interface for database access, querying, and integrated sequence analysis.
Main Results:
- Creation of the Bacterial protein tyrosine-kinase database (BYKdb).
- Comprehensive annotation of BY-kinase sequences.
- A user-friendly web interface enabling static and dynamic queries.
- Integration of sequence analysis tools within the database.
Conclusions:
- BYKdb provides a valuable, annotated resource for bacterial tyrosine-kinases.
- The database facilitates deeper understanding of BY-kinase functions and evolution.
- BYKdb is accessible online at http://bykdb.ibcp.fr for the research community.
Related Concept Videos
01:26Receptor Tyrosine Kinases
Receptor tyrosine kinases or RTKs are membrane-bound receptors that phosphorylate specific tyrosine on protein substrates. RTKs regulate cellular growth, differentiation, survival, and migration. They contain an extracellular ligand binding domain, a transmembrane domain, and a cytosolic tail with intrinsic kinase activity. Several extracellular signaling molecules activate RTKs in one or more ways and relay the signal downstream. Ligands such as platelet-derived growth factor (PDGF) or...
01:00Enzyme-linked Receptors
Enzyme-linked receptors are proteins that act as both receptor and enzyme, activating multiple intracellular signals. This is a large group of receptors that include the receptor tyrosine kinase (RTK) family. Many growth factors and hormones bind to and activate the RTKs.
Neurotrophin (NT) receptors are a family of RTKs, including trkA, trkB, and trkC (tropomyosin-related kinase) receptors. TrkA is specific for nerve growth factor (NGF), neurotrophin-6, and neurotrophin-7. TrkB binds...
Neurotrophin (NT) receptors are a family of RTKs, including trkA, trkB, and trkC (tropomyosin-related kinase) receptors. TrkA is specific for nerve growth factor (NGF), neurotrophin-6, and neurotrophin-7. TrkB binds...
01:27Transducer Mechanism: Enzyme-Linked Receptors
Enzyme-linked receptors are cell-surface receptors acting as an enzyme or associating with an enzyme intracellularly. They make excellent drug targets. Drugs can bind to the extracellular ligand-binding domain or directly affect their enzymatic domain and alter their activity.
Major types that are helpful drug targets include:
Major types that are helpful drug targets include:
02:54Protein Kinases and Phosphatases
Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
02:54Protein Kinases and Phosphatases
Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
01:26Bacterial Protein Maturation
Bacterial protein maturation is a tightly regulated process that ensures newly synthesized polypeptides achieve correct functional conformations. This maturation involves a series of modifications, folding events, and quality control steps, often assisted by specialized chaperone proteins.N-Terminal ModificationsThe maturation of bacterial polypeptides begins cotranslationally as the polypeptide exits the ribosome. The first amino acid, N-formylmethionine (fMet), is typically modified at the...