1ppa: Difference between revisions

Revision as of 15:31, 21 February 2008

THE CRYSTAL STRUCTURE OF A LYSINE 49 PHOSPHOLIPASE A2 FROM THE VENOM OF THE COTTONMOUTH SNAKE AT 2.0 ANGSTROMS RESOLUTION

OverviewOverview

The crystal structure of a lysine 49 variant phospholipase A2 (K49 PLA2) has been determined at 2.0-A resolution. This particular phospholipase A2, purified from the venom of the eastern cottonmouth (Agkistrodon piscivorus piscivorus), a North American pit viper, differs significantly from others studied crystallographically because of replacement of the aspartate residue at position 49, whose side chain is important in calcium binding, by lysine. The crystallographic analysis of K49 PLA2 was undertaken to assess the structural ramifications of this substitution, particularly as they affect the binding mechanism of both the calcium cofactor and the phospholipid substrate. The protein crystals are tetragonal, space group P4(1)2(1)2, with unit cell dimensions of a = b = 71.7 (1) and c = 57.8 (3) A. Preliminary phases were obtained by molecular replacement techniques with a search model derived from the refined 2.5-A structure of a rattle-snake venom phospholipase A2 (Brunie, S., Bolin, J., Gewirth, D., and Sigler, P. B. (1985) J. Biol. Chem. 260, 9742-9749). The starting model gave an initial crystallographic RF of 0.526 (RF = sigma parallel to Fo /-/ Fc parallel to /sigma/Fo/). The structure was refined against all data to 2.0-A resolution. The final RF is 0.158. The final model includes 150 discrete water molecules. The K49 PLA2 model is composed primarily of alpha-helices joined by loops, some of which are quite extensive. Although dissimilarities are observed in the loop regions, the helical portions are very similar to those in other known phospholipase A2 structures. The proposed catalytic center (His48, Tyr73, and Asp99) is also structurally conserved. The region in K49 PLA2 corresponding to the calcium-binding site in other phospholipases A2 is occupied by the epsilon-amino group of lysine 49.

About this StructureAbout this Structure

1PPA is a Single protein structure of sequence from Agkistrodon piscivorus piscivorus with as ligand. Active as Phospholipase A(2), with EC number 3.1.1.4 Full crystallographic information is available from OCA.

ReferenceReference

The crystal structure of a lysine 49 phospholipase A2 from the venom of the cottonmouth snake at 2.0-A resolution., Holland DR, Clancy LL, Muchmore SW, Ryde TJ, Einspahr HM, Finzel BC, Heinrikson RL, Watenpaugh KD, J Biol Chem. 1990 Oct 15;265(29):17649-56. PMID:2120215

Page seeded by OCA on Thu Feb 21 14:31:04 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1ppa.gif|left|200px]]<br /><applet load="1ppa" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1ppa.gif|left|200px]]<br /><applet load="1ppa" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1ppa, resolution 2.0&Aring;" />
 '''THE CRYSTAL STRUCTURE OF A LYSINE 49 PHOSPHOLIPASE A2 FROM THE VENOM OF THE COTTONMOUTH SNAKE AT 2.0 ANGSTROMS RESOLUTION'''<br />
 ==Overview==
-The crystal structure of a lysine 49 variant phospholipase A2 (K49 PLA2), has been determined at 2.0-A resolution. This particular phospholipase A2, purified from the venom of the eastern cottonmouth (Agkistrodon piscivorus, piscivorus), a North American pit viper, differs significantly from others, studied crystallographically because of replacement of the aspartate, residue at position 49, whose side chain is important in calcium binding, by lysine. The crystallographic analysis of K49 PLA2 was undertaken to, assess the structural ramifications of this substitution, particularly as, they affect the binding mechanism of both the calcium cofactor and the, phospholipid substrate. The protein crystals are tetragonal, space group, P4(1)2(1)2, with unit cell dimensions of a = b = 71.7 (1) and c = 57.8 (3), A. Preliminary phases were obtained by molecular replacement techniques, with a search model derived from the refined 2.5-A structure of a, rattle-snake venom phospholipase A2 (Brunie, S., Bolin, J., Gewirth, D., and Sigler, P. B. (1985) J. Biol. Chem. 260, 9742-9749). The starting, model gave an initial crystallographic RF of 0.526 (RF = sigma parallel to, Fo /-/ Fc parallel to /sigma/Fo/). The structure was refined against all, data to 2.0-A resolution. The final RF is 0.158. The final model includes, 150 discrete water molecules. The K49 PLA2 model is composed primarily of, alpha-helices joined by loops, some of which are quite extensive. Although, dissimilarities are observed in the loop regions, the helical portions are, very similar to those in other known phospholipase A2 structures. The, proposed catalytic center (His48, Tyr73, and Asp99) is also structurally, conserved. The region in K49 PLA2 corresponding to the calcium-binding, site in other phospholipases A2 is occupied by the epsilon-amino group of, lysine 49.
+The crystal structure of a lysine 49 variant phospholipase A2 (K49 PLA2) has been determined at 2.0-A resolution. This particular phospholipase A2, purified from the venom of the eastern cottonmouth (Agkistrodon piscivorus piscivorus), a North American pit viper, differs significantly from others studied crystallographically because of replacement of the aspartate residue at position 49, whose side chain is important in calcium binding, by lysine. The crystallographic analysis of K49 PLA2 was undertaken to assess the structural ramifications of this substitution, particularly as they affect the binding mechanism of both the calcium cofactor and the phospholipid substrate. The protein crystals are tetragonal, space group P4(1)2(1)2, with unit cell dimensions of a = b = 71.7 (1) and c = 57.8 (3) A. Preliminary phases were obtained by molecular replacement techniques with a search model derived from the refined 2.5-A structure of a rattle-snake venom phospholipase A2 (Brunie, S., Bolin, J., Gewirth, D., and Sigler, P. B. (1985) J. Biol. Chem. 260, 9742-9749). The starting model gave an initial crystallographic RF of 0.526 (RF = sigma parallel to Fo /-/ Fc parallel to /sigma/Fo/). The structure was refined against all data to 2.0-A resolution. The final RF is 0.158. The final model includes 150 discrete water molecules. The K49 PLA2 model is composed primarily of alpha-helices joined by loops, some of which are quite extensive. Although dissimilarities are observed in the loop regions, the helical portions are very similar to those in other known phospholipase A2 structures. The proposed catalytic center (His48, Tyr73, and Asp99) is also structurally conserved. The region in K49 PLA2 corresponding to the calcium-binding site in other phospholipases A2 is occupied by the epsilon-amino group of lysine 49.
 ==About this Structure==
-PPA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Agkistrodon_piscivorus_piscivorus Agkistrodon piscivorus piscivorus] with ANL as [http://en.wikipedia.org/wiki/ligand ligand]. 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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PPA OCA].
+PPA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Agkistrodon_piscivorus_piscivorus Agkistrodon piscivorus piscivorus] with <scene name='pdbligand=ANL:'>ANL</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPA OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Phospholipase A(2)]]
 [[Category: Single protein]]
-[[Category: Clancy, L.L.]]
+[[Category: Clancy, L L.]]
-[[Category: Einspahr, H.M.]]
+[[Category: Einspahr, H M.]]
-[[Category: Finzel, B.C.]]
+[[Category: Finzel, B C.]]
-[[Category: Heinrikson, R.L.]]
+[[Category: Heinrikson, R L.]]
-[[Category: Holland, D.R.]]
+[[Category: Holland, D R.]]
-[[Category: Muchmore, S.W.]]
+[[Category: Muchmore, S W.]]
-[[Category: Rydel, T.J.]]
+[[Category: Rydel, T J.]]
-[[Category: Watenpaugh, K.D.]]
+[[Category: Watenpaugh, K D.]]
 [[Category: ANL]]
 [[Category: hydrolase(carboxylic esterase)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:59:37 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:31:04 2008''