1bk9

PHOSPHOLIPASE A2 MODIFIED BY PBPBPHOSPHOLIPASE A2 MODIFIED BY PBPB

Structural highlights

1bk9 is a 1 chain structure with sequence from Gloydius halys. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PA2A_GLOHA Snake venom phospholipase A2 (PLA2) that acts in vivo as an anti-thrombotic agent. Inhibits platelet aggregation induced by ADP, arachidonic acid, and thrombin. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The crystal structure of acidic phospholipase A2 (APLA2) from Agkistrodon halys pallas covalently modified by p-bromo-phenacyl-bromide (pBPB) was determined to a resolution of 2.0 A by an isomorphous difference Fourier method with the native APLA2 structure as an initial model and refined to a crystallographic R factor of 15.3%. The modified APLA2 structure is remarkably similar to that of the native one. Least-squares superposition of C alpha atoms of native and modified APLA2 results in a root-mean-square coordinate deviation of 0.243 A. The p-bromo-phenacyl group near the active site occupies a position similar to that in pBPB modified bovine pancreatic PLA2. The inhibitor covalently bound to the NDI atom of His48 fits well in the hydrophobic channel, forming extensive hydrophobic interactions with the surrounding residues, especially with the side chains of Phe5 and Cys45 and the main chain of Gly30. However, the inhibitor does not change the conformation of these residues except that Trp31 at the entrance of the hydrophobic channel moves slightly toward the inhibitor. Compared with native APLA2, the Ca2+-binding loop shows a little conformational change and a cation, probably Na+, occupies in the position of Ca2+. The binding of pBPB to APLA2 induce no other significant conformational changes in the enzyme molecule elsewhere.

Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide.,Zhao H, Tang L, Wang X, Zhou Y, Lin Z Toxicon. 1998 Jun;36(6):875-86. PMID:9663694^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wang Y, Cui G, Zhao M, Yang J, Wang C, Giese RW, Peng S. Bioassay-directed purification of an acidic phospholipase A(2) from Agkistrodon halys pallas venom. Toxicon. 2008 Jun 1;51(7):1131-9. doi: 10.1016/j.toxicon.2008.01.003. Epub 2008, Jan 17. PMID:18456297 doi:http://dx.doi.org/10.1016/j.toxicon.2008.01.003
↑ Zhao H, Tang L, Wang X, Zhou Y, Lin Z. Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide. Toxicon. 1998 Jun;36(6):875-86. PMID:9663694

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OCA

[1] Wang Y, Cui G, Zhao M, Yang J, Wang C, Giese RW, Peng S. Bioassay-directed purification of an acidic phospholipase A(2) from Agkistrodon halys pallas venom. Toxicon. 2008 Jun 1;51(7):1131-9. doi: 10.1016/j.toxicon.2008.01.003. Epub 2008, Jan 17. PMID:18456297 doi:http://dx.doi.org/10.1016/j.toxicon.2008.01.003

[2] Zhao H, Tang L, Wang X, Zhou Y, Lin Z. Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide. Toxicon. 1998 Jun;36(6):875-86. PMID:9663694

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