1bk9: Difference between revisions

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.

1BK9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gloydius_halys Gloydius halys] with CA, PBP and BU1 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] Structure known Active Site: PBP. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BK9 OCA].  

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