PDB ID or protein name

1vap » Snake phospholipase A2, group II

1vap » Snake phospholipase A2, group II
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Topology in Secreted
Topologyout side
in side
1vap » Snake phospholipase A2, group II
Depth 5.1 ± 0.6 Å
Tilt Angle 88 ± 5°
ΔGtransfer -10.3 kcal/mol
Links to 1vap PDB Sum, PDB, SCOP, MSD, OCA, MMDB
Topology out
Resolution 1.6 Å
Other PDB entries representing this structure none
Number of subunits 1
Experimental Verification for 1vap » Snake phospholipase A2, group II
The following residues are buried in the membrane core: F3, M18, V19, W30, M61, I63, and W109. According to flourescence data (Lathrop et al. 2001), W20, W30, and W109 interact with lipids (value of Fmax for W30+ mutant in Table 1 from Lathrop et al. indicates that W30 contributes to the protein-lipid interactions). W20 occupies interfacial region in the calculated orientation of phospholipase (residue numbering corresponds to UniProt and PDB). Maximal membrane binding affinity is -10.6 kcal/mol (Stahelin and Cho 2001) or -5.2 kcal/mol (Tatulian 2002).
4 references
Diraviyam K, Murray D. 2006. Computational analysis of the membrane association of group IIA secreted phospholipases A2: a differential role for electrostatics. Biochemistry. 45:2584-98. PubMed
Lathrop B, Gadd M, Biltonen RL, Rule GS. 2001. Changes in Ca2+ affinity upon activation of Agkistrodon piscivorus piscivorus phospholipase A2. Biochemistry. 40:3264-72. PubMed
Stahelin, R.V., and Cho, W. 2001. Differential roles of ionic, aliphatic, and aromatic residues in membrane-protein interactions: a surface plasmon resonance study on phospholipases A2. Biochemistry. 40:4672-4678. PubMed
Tatulian SA. 2002. Quantitative characterization of membrane binding of peripheral proteins by spin-label EPR spectroscopy. J. Phys. Chem. B106: 8870-8877.
Comments on 1vap » Snake phospholipase A2, group II
This orientation is similar to one suggested by Diraviyam and Murray (2006). However, phospholipase penetrates by ~10 A deeper in the membrane according to our results (nonpolar residues are inserted in the hydrocarbon core, not in the head group region).