Crystal Structure of a Class XIB Phospholipase A2 (PLA2)

Abstract

Phospholipase A 2 catalyzes the specific hydrolysis of the sn-2 acyl bond of various glycerophospholipids, producing fatty acids and lysophospholipids. Phospholipase A 2 s (PLA 2 s) constitute a large superfamily of enzymes whose products are important for a multitude of signal transduction processes, lipid mediator release, lipid metabolism, development, plant stress responses, and host defense. The crystal structure of rice (Oryza sativa) isoform 2 phospholipase A 2 has been determined to 2.0 Å resolution using sulfur SAD phasing, and shows that the class XIb phospholipases have a unique structure compared with other secreted PLA 2 s. The N-terminal half of the chain contains mainly loop structure, including the conserved Ca 2؉ -binding loop, but starts with a short 3 10 -helix and also includes two short anti-parallel ␤-strands. The C-terminal half is folded into three anti-parallel ␣-helices, of which the two first are also present in other secreted PLA 2 s and contain the conserved catalytic histidine and calcium liganding aspartate residues. The structure is stabilized by six disulfide bonds. The water structure around the calcium ion binding site suggests the involvement of a second water molecule in the mechanism for hydrolysis, the water-assisted calcium-coordinate oxyanion mechanism. The octanoate molecule in the complex structure is bound in a hydrophobic pocket, which extends to the likely membrane interface and is proposed to model the binding of the product fatty acid. Due to the differences in structure, the suggested surface for binding to the membrane has a different morphology in the rice PLA 2 compared with other phospholipases.Phospholipase A 2 (PLA 2 ) 3 catalyzes the specific hydrolysis of the sn-2 acyl bond of various glycerophospholipids, producing fatty acids and lysophospholipids. PLA 2 s are widely distributed in nature and constitute a large superfamily of enzymes whose products are important for a multitude of signal transduction processes, lipid mediator release, lipid metabolism, and host defense (1). In plants they are implicated in plant growth, development, stress responses, and defense signaling (2-7). Translocation, secretion, and catalytic activation by many different stimuli control the activities of PLA 2 s. Based on sequence, and specific characteristics, 15 distinct groups of PLA 2 s are defined, and these are divided into 5 main clades within the superfamily: secreted sPLA 2 s, cytosolic cPLA 2 s, calcium-independent iPLA 2 s, platelet-activating factor acetylhydrolases, and the lysosomal PLA 2 s (8). The sPLA 2 s are small secreted proteins of 14 -18 kDa that usually contain 5-8 disulfide bonds and an active site His/Asp dyad and are dependent on binding of Ca 2ϩ ions for activity (1). The sPLA 2 s display different tissue distribution patterns and distinct physiological functions. The sPLA 2 s contain PLA 2 groups I-III, V, and IX-XIV, including the snake venoms PLA 2 s (9) and the mammalian pancreatic PLA 2 s (10). Members of this family were first studied nearly 100 ...

Phospholipase A2 Enzymes: Physical Structure, Biological Function, Disease Implication, Chemical Inhibition, and Therapeutic Intervention

“…The plant GXIB sPLA 2 has been shown to lack β-wings. 28 The prokaryotic GXIV sPLA 2 shows a different, all α-helical, protein folding. 29 …”

Biology and Biochemistry of Plant Phospholipases

“…The mature plant sPLA 2 proteins contain 12 cysteine residues that form six disulfide bonds, which are important for protein stability and enzymatic activity (Ryu, 2004). Recently, the crystal structure of rice isoform 2 sPLA 2 (AJ238117) was determined, and appears to be quite different from its animal counterparts (Guy et al, 2009). For instance, although the N-terminal half of the chain contains mainly a Downloaded by [Stanford University Libraries] at 07:34 19 October 2012 loop structure, including the conserved Ca 2+ -binding loop, it starts with a short 3 10 -helix and also includes two short antiparallel β-strands.…”

Molecular details of secretory phospholipase A2 from flax (Linum usitatissimum L.) provide insight into its structure and function

“…Although three-dimensional structures of plant sPLA 2 s 18 have been predicted, structural data for flax is unavailable. The homology modelled structures of LusPLA 2 I (Fig.…”

“…Among plants, the structure of arabidopsis ( Arabidopsis thaliana ) sPLA 2 isoform α and soybean ( Glycine max ) sPLA 2 isoform II has been elucidated by homology modelling. Currently, tertiary structure of sPLA 2 isoform II from rice (OssPLA 2 II) is available and is the only testimony (PDB entry 2WG7A) 18 of sPLA 2 s from plants. However, three-dimensional structures of flax sPLA 2 s are hitherto not available in any database.…”