The metal-independent lipase from Streptomyces albidoflavus NA297 (SaPLA1) is a phospholipase A1 as it preferentially hydrolyzes the sn-1 acyl ester in glycerophospholipids, yielding a fatty acid and 2-acyllysophospholipid. The molecular mechanism underlying the substrate binding by SaPLA(1) is currently unknown. In this study, the crystal structure of SaPLA(1) was determined at 1.75 angstrom resolutions by molecular replacement. A structural similarity search indicated the highest structural similarity to an esterase from Streptomyces scabies, followed by GDSL family enzymes. The SaPLA(1) active site is composed of a Ser-His dyad (Ser11 and His218), whereby stabilization of the imidazole is provided by the main-chain carbonyl oxygen of Ser216, a common variation of the catalytic triad in many serine hydrolases, where this carbonyl maintains the orientation of the active site histidine residue. The hydrophobic pocket and cleft for lipid binding are adjacent to the active site, and are approximately 13-15 angstrom deep and 14-16 angstrom long. A partial polyethylene glycol structure was found in this hydrophobic pocket. (c) 2013 Elsevier Inc. All rights reserved.