1mf4: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1mf4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Naja_sagittifera Naja sagittifera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MF4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1mf4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Naja_sagittifera Naja sagittifera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MF4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.9&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1lff|1lff]], [[1ln8|1ln8]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mf4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mf4 OCA], [https://pdbe.org/1mf4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mf4 RCSB], [https://www.ebi.ac.uk/pdbsum/1mf4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mf4 ProSAT]</span></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=1mf4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mf4 OCA], [https://pdbe.org/1mf4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mf4 RCSB], [https://www.ebi.ac.uk/pdbsum/1mf4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mf4 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/PA2A3_NAJSG PA2A3_NAJSG]] PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.  
[https://www.uniprot.org/uniprot/PA2A3_NAJSG PA2A3_NAJSG] PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1mf4 ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1mf4 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Phospholipase A(2) (PLA(2)) (E. C. 3.1.1.4) is a common enzyme in the two-way cascade mechanism leading to the production of proinflammatory compounds known as eicosanoids. The binding of phospholipase A(2) to the membrane surface and hydrolysis of phospholipids are thought to involve the formation of a hydrophobic channel into which a single substrate molecule diffuses before its cleavage. To regulate the production of proinflammatory compounds, a specific peptide inhibitor Val-Ala-Phe-Arg-Ser (VAFRS) for the group I PLA(2) enzymes has been designed and synthesized. PLA(2) was isolated from Indian cobra (Naja naja sagittifera) venom and purified to homogeneity. The binding studies indicated the K(i) value of 1.02 +/- 0.10 x 10(-8) M. The purified PLA(2) samples and the designed inhibitor VAFRS were cocrystallized. The crystal structure of the complex was determined and refined to 1.9 A resolution. The peptide binds to PLA(2) at the active site and fills the hydrophobic channel completely. However, its placement with respect to the channel is in the opposite direction as compared to those observed in group II PLA(2)'s. Furthermore, the predominant intermolecular interactions involve strong electrostatic interactions between the side chains of peptide Arg and Asp 49 of PLA(2) together with a number of van der Waals interactions with other residues. A good number of observed interactions between the peptide and the protein indicate the significance of a structure-based drug design approach. The novel factor in the present sequence of the peptide is related to the introduction of a positively charged residue at the C-terminal part of the peptide.
Design of specific peptide inhibitors for group I phospholipase A2: structure of a complex formed between phospholipase A2 from Naja naja sagittifera (group I) and a designed peptide inhibitor Val-Ala-Phe-Arg-Ser (VAFRS) at 1.9 A resolution reveals unique features.,Singh RK, Vikram P, Makker J, Jabeen T, Sharma S, Dey S, Kaur P, Srinivasan A, Singh TP Biochemistry. 2003 Oct 14;42(40):11701-6. PMID:14529280<ref>PMID:14529280</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1mf4" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Naja sagittifera]]
[[Category: Naja sagittifera]]
[[Category: Dey, S]]
[[Category: Dey S]]
[[Category: Jabeen, T]]
[[Category: Jabeen T]]
[[Category: Kaur, P]]
[[Category: Kaur P]]
[[Category: Makker, J]]
[[Category: Makker J]]
[[Category: Paramsivam, M]]
[[Category: Paramsivam M]]
[[Category: Sharma, S]]
[[Category: Sharma S]]
[[Category: Singh, R K]]
[[Category: Singh RK]]
[[Category: Singh, T P]]
[[Category: Singh TP]]
[[Category: Srinivasan, A]]
[[Category: Srinivasan A]]
[[Category: Vikram, P]]
[[Category: Vikram P]]
[[Category: Designed inhibitor]]
[[Category: Hydrolase-hydrolase inhibitor complex]]
[[Category: Naja naja sagittifera]]
[[Category: Phospholipase a2]]

Latest revision as of 08:35, 10 April 2024

Structure-based design of potent and selective inhibitors of phospholipase A2: Crystal structure of the complex formed between phosholipase A2 from Naja Naja sagittifera and a designed peptide inhibitor at 1.9 A resolution

1mf4, resolution 1.90Å

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