Patterns of Ligands Coordinated to Metallocofactors Extracted from the Protein Data Bank

A new
R tool is described that rapidly identifies, ranks, and clusters
sequence patterns coordinated to metallocofactors. This tool, PdPDB,
fills a void because, unlike currently available tools, PdPDB searches
through sequences with metal coordination as the primary determinant
and can identify patterns consisting of amino acids, nucleotides,
and small molecule ligands at once. PdPDB was tested by analyzing
structures that coordinate Fe2+/3+, [2Fe-2S], [4Fe-4S],
Zn2+, and Mg2+ cofactors. PdPDB confirmed previously
identified sequence motifs and revealed which residues are enriched
(e.g., glycine) and are under-represented (e.g., glutamine) near ligands
to metal centers. The data show the similarities and differences between
different metal-binding sites. The patterns that coordinate metallocofactors
vary, depending upon whether the metal ions play a structural or catalytic
role, with catalytic metal centers exhibiting partial coordination
by small molecule ligands. PdPDB 2.0.1 is freely available as a CRAN
package.