4HYQ

Crystal structure of phospholipase A1 from Streptomyces albidoflavus NA297

Summary for 4HYQ

• Entry DOI: 10.2210/pdb4hyq/pdb
• Descriptor: phospholipase A1, PENTAETHYLENE GLYCOL (3 entities in total)
• Functional Keywords: lipase, glycerophospholipid, hydrolase
• Biological source: Streptomyces albidoflavus
• Total number of polymer chains: 1
• Total formula weight: 24438.09

Authors

Murayama, K.,Sugimori, D. (deposition date: 2012-11-14, release date: 2013-05-29, Last modification date: 2024-11-06)

Primary citation

Murayama, K.,Kano, K.,Matsumoto, Y.,Sugimori, D.
Crystal structure of phospholipase A1 from Streptomyces albidoflavus NA297
J.Struct.Biol., 182:192-196, 2013

PubMed Abstract: 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-acyl-lysophospholipid. The molecular mechanism underlying the substrate binding by SaPLA1 is currently unknown. In this study, the crystal structure of SaPLA1 was determined at 1.75Å 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 SaPLA1 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 13-15Å deep and 14-16Å long. A partial polyethylene glycol structure was found in this hydrophobic pocket.

PubMed: 23416196
DOI: 10.1016/j.jsb.2013.02.003

Experimental method

X-RAY DIFFRACTION (1.75 Å)