Abstract
BackgroundThe number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using only structural similarity.ResultsHere we present the PDB-UF database, a web-accessible collection of predictions of enzymatic properties using structure-function relationship. The assignments were conducted for three-dimensional protein structures of unknown function that come from structural genomics initiatives. We show that 4 hypothetical proteins (with PDB accession codes: 1VH0, 1NS5, 1O6D, and 1TO0), for which standard BLAST tools such as PSI-BLAST or RPS-BLAST failed to assign any function, are probably methyltransferase enzymes.ConclusionWe suggest that the structure-based prediction of an EC number should be conducted having the different similarity score cutoff for different protein folds. Moreover, performing the annotation using two different algorithms can reduce the rate of false positive assignments. We believe, that the presented web-based repository will help to decrease the number of protein structures that have functions marked as "unknown" in the PDB file.Availability and
Highlights
The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB)
The "youngest" annotated in PDBSprotEC or SCOPEC protein was released by PDB in lFPperSivgoIe-utBlerL(ilenAowS1Teitrhscrdoigirhfefteocrhfeatnhrte)emnzoysmt seimfuinlacrtipornotaetinthwe i1thst,e2fnudn(cutpiopenrvreigrhstucshPaSrIt-)B, L3ArdS(Tlowsceorreleoftfcthaertm),oasntdsi4mthilaErC PSI-BLAST score of the most similar protein with the same enzyme function versus PSI-BLAST score of the most similar protein with different enzyme function at the 1st, 2nd, 3rd, and 4th Enzymatic Classification (EC) level
If assignments were fully consistent, we indicated it with an 'n' in the fourth EC level (e.g. 2.3.4.n) which means that exact activity of this enzyme was predicted, but a sequence number has not been yet assigned by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)
Summary
We present the PDB-UF database, a web-accessible collection of predictions of enzymatic properties using structure-function relationship. The assignments were conducted for three-dimensional protein structures of unknown function that come from structural genomics initiatives. We show that 4 hypothetical proteins (with PDB accession codes: 1VH0, 1NS5, 1O6D, and 1TO0), for which standard BLAST tools such as PSI-BLAST or RPS-BLAST failed to assign any function, are probably methyltransferase enzymes
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