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brenda-database

Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.

Author

@K-Dense-AI

Category

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BRENDA Enzyme Database Skill

Skill Overview

BRENDA is the world’s most comprehensive enzyme information system. Through its official SOAP API it provides kinetic parameters (Km, kcat) for over 45,000 enzymes, reaction equations, substrate specificity, organism information, and optimal conditions data, supporting biochemical research, metabolic engineering, and enzyme discovery.

Use Cases

  • Enzyme kinetic parameter queries

    • When researchers need to find specific enzyme kinetic constants such as Km, kcat, or Vmax, they can perform precise searches using EC numbers, substrate names, or organisms to obtain experimental data from the literature.

  • Metabolic engineering and enzyme modification

    • When designing biosynthetic pathways or optimizing enzyme performance, compare properties of isoenzymes from different species to find thermostable or acid- and alkali-resistant enzyme variants, providing data support for enzyme engineering.

  • Metabolic pathway reconstruction

    • Start from a product and search backwards for enzymes that catalyze the required reactions, build complete enzymatic pathways, evaluate pathway feasibility, and obtain reaction conditions and kinetic parameters for each step.

    Core Features

  • Kinetic parameter retrieval

    • Query Km, kcat, Vmax, and other parameters by EC number, substrate, or organism; support filtering by experimental conditions such as pH and temperature; provide structured data for downstream analysis and modeling.

  • Cross-species enzyme property comparison

    • Compare optimal pH, temperature ranges, and kinetic constants for the same enzyme across different organisms to identify enzyme variants suitable for industrial applications in extreme environments.

  • Enzyme discovery and pathway construction

    • Search for enzymes based on substrates or products, obtain reaction equations and catalytic conditions, and assist in de novo design and feasibility assessment of metabolic pathways.

    Frequently Asked Questions

    Does the BRENDA database require payment?

    BRENDA offers free academic accounts; users need to register on the official website to obtain login credentials. After registering, you can access the SOAP API using your email and password. This skill supports configuring authentication via environment variables or a .env file.

    How do I find the corresponding enzyme by substrate?

    You can use the search_enzymes_by_substrate() function and input the substrate name (e.g., "glucose"). The system will return a list of all enzymes that catalyze that substrate, including EC numbers, enzyme names, and reaction information. You can also search by product or filter by reaction mode (e.g., "oxidation").

    Are there request limits for the BRENDA API?

    Yes, the BRENDA API has moderate rate limits. It is recommended not to exceed 1 request per second and not more than 5 requests within 10 seconds. For bulk queries, add delays between requests and cache commonly used data to reduce repeated calls.