SFR Database (formerly called ACT) Structure-Function Relationships of Proteins

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SFR (formerly called ACT) is a database describing the structure-function relationships of proteins. SFR represents the interactions of a subset of PDB (Protein Data Bank) proteins with their substrates, cofactors, and binding partners at a high level of structural and functional detail.

The PDB contains a vast amount of information about protein structures, but the integration of its data with functional information has not previously been fully automated. SFR makes it possible for automated analysis of large numbers protein structure-function relationships to be performed in just the same way as if each structure were analyzed by hand. A typical SFR entry for a protein (or complex) will describe

• Residues making up functional sites on the protein
• Chemical role played by functional residues (e.g. binding, recognition, catalysis, allosteric binding, etc.)
• Substrate(s) and substrate type(s) (e.g. DNA, protein, metal, etc.)
• Cofactor(s) and types of cofactor(s)
• Presence in a complex structure of the substrate or an analog of the substrate ("analog" meaning, e.g., a phosphate ion bound in a DNA-binding site); ditto for cofactors.
• Type of chemical interaction between protein & its substrates & cofactors (e.g. hydrolase, kinase, binding, etc.) and E.C. (Enzyme Commission) numbers.

Special attention has been paid to the spatial (homo-oligomeric and/or crystallographic) symmetries of the protein molecules. SFR represents each functional site as it would exist in the biological oligomer, not just as it appears in the raw PDB file (asymmetric unit). Symmetry operations are built into SFR format, and are cross-referenced to PDB coordinate files. Another unique feature of SFR is its use of sub-classifications for both catalytic and non-catalytic interactions (e.g. protein-binding, allosteric binding, etc.)

Most of the information in the database is derived directly from the literature for each protein (see photo below); thus, much of the data can only be found in machine-readable format from SFR.

The SFR database was designed by Frank K. Pettit in the lab of James U. Bowie, which is located in the NIH-Molecular Biology Institute at UCLA.

The SFR (ACT) Project Undergrads

We are indebted to the undergrads who contributed to this work, and who are shown here with a small fraction of the many journal articles they read in full to create entries in SFR. From right to left: Albert Tsai, Emiko Bare, Ani Manukyan and Stacey Hom.

* The graphic at the top of this page is a structure of glutamine synthetase in complex with glutamine, PDB code 2LGS, by S.-H. Liaw & D. Eisenberg.