1ppa

From Proteopedia

(Difference between revisions)

Current revision

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

Structural highlights

1ppa is a 1 chain structure with sequence from Agkistrodon piscivorus piscivorus. 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

PA2HB_AGKPI Snake venom phospholipase A2 (PLA2) that lacks enzymatic activity, but displays edema-inducing activities.^[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 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 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^[2]

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

References

↑ Scott DL, Achari A, Vidal JC, Sigler PB. Crystallographic and biochemical studies of the (inactive) Lys-49 phospholipase A2 from the venom of Agkistridon piscivorus piscivorus. J Biol Chem. 1992 Nov 5;267(31):22645-57. PMID:1429612
↑ Holland DR, Clancy LL, Muchmore SW, Ryde TJ, Einspahr HM, Finzel BC, Heinrikson RL, Watenpaugh KD. The crystal structure of a lysine 49 phospholipase A2 from the venom of the cottonmouth snake at 2.0-A resolution. J Biol Chem. 1990 Oct 15;265(29):17649-56. PMID:2120215

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ppa"

@@ Line 3: / Line 3: @@
 <StructureSection load='1ppa' size='340' side='right'caption='[[1ppa]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ppa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agkpi Agkpi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PPA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ppa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agkistrodon_piscivorus_piscivorus Agkistrodon piscivorus piscivorus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PPA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANL:ANILINE'>ANL</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANL:ANILINE'>ANL</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ppa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppa OCA], [https://pdbe.org/1ppa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ppa RCSB], [https://www.ebi.ac.uk/pdbsum/1ppa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppa ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/PA2HB_AGKPI PA2HB_AGKPI]] Snake venom phospholipase A2 (PLA2) that lacks enzymatic activity, but displays edema-inducing activities.<ref>PMID:1429612</ref>
+[https://www.uniprot.org/uniprot/PA2HB_AGKPI PA2HB_AGKPI] Snake venom phospholipase A2 (PLA2) that lacks enzymatic activity, but displays edema-inducing activities.<ref>PMID:1429612</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pp/1ppa_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 36: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Agkpi]]
+[[Category: Agkistrodon piscivorus piscivorus]]
 [[Category: Large Structures]]
-[[Category: Clancy, L L]]
+[[Category: Clancy LL]]
-[[Category: Einspahr, H M]]
+[[Category: Einspahr HM]]
-[[Category: Finzel, B C]]
+[[Category: Finzel BC]]
-[[Category: Heinrikson, R L]]
+[[Category: Heinrikson RL]]
-[[Category: Holland, D R]]
+[[Category: Holland DR]]
-[[Category: Muchmore, S W]]
+[[Category: Muchmore SW]]
-[[Category: Rydel, T J]]
+[[Category: Rydel TJ]]
-[[Category: Watenpaugh, K D]]
+[[Category: Watenpaugh KD]]

1ppa

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox