2bd1

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[[Image:2bd1.gif|left|200px]]
 
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{{Structure
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==A possible role of the second calcium ion in interfacial binding: Atomic and medium resolution crystal structures of the quadruple mutant of phospholipase A2==
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|PDB= 2bd1 |SIZE=350|CAPTION= <scene name='initialview01'>2bd1</scene>, resolution 1.90&Aring;
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<StructureSection load='2bd1' size='340' side='right'caption='[[2bd1]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>
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<table><tr><td colspan='2'>[[2bd1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BD1 FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[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] </span>
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</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>
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|GENE= PLA2G1B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 Bos taurus])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bd1 OCA], [https://pdbe.org/2bd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bd1 RCSB], [https://www.ebi.ac.uk/pdbsum/2bd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bd1 ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1une|1UNE]], [[1mkt|1MKT]], [[1vl9|1VL9]], [[2bch|2BCH]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bd1 OCA], [http://www.ebi.ac.uk/pdbsum/2bd1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2bd1 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/PA21B_BOVIN PA21B_BOVIN] PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bd/2bd1_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2bd1 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structures of the monoclinic and trigonal forms of the quadruple mutant K53,56,120,121M of recombinant bovine pancreatic phospholipase A2 (PLA2) have been solved and refined at 1.9 and 1.1 A resolution, respectively. Interestingly, the monoclinic form reveals the presence of the second calcium ion. Furthermore, the surface-loop residues are ordered and the conformation of residues 62-66 is similar to that observed in other structures containing the second calcium ion. On the other hand, in the trigonal form the surface loop is disordered and the second calcium is absent. Docking studies suggest that the second calcium and residues Lys62 and Asp66 from the surface loop could be involved in the interaction with the polar head group of the membrane phospholipid. It is hypothesized that the two structures of the quadruple mutant, monoclinic and trigonal, represent the conformations of PLA2 at the lipid interface and in solution, respectively. A docked structure with a phospholipid molecule and with a transition-state analogue bound, one at the active site coordinating to the catalytic calcium and the other at the second calcium site, but both at the i-face, is presented.
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'''A possible role of the second calcium ion in interfacial binding: Atomic and medium resolution crystal structures of the quadruple mutant of phospholipase A2'''
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Suggestive evidence for the involvement of the second calcium and surface loop in interfacial binding: monoclinic and trigonal crystal structures of a quadruple mutant of phospholipase A2.,Sekar K, Yogavel M, Kanaujia SP, Sharma A, Velmurugan D, Poi MJ, Dauter Z, Tsai MD Acta Crystallogr D Biol Crystallogr. 2006 Jul;62(Pt 7):717-24. Epub 2006, Jun 20. PMID:16790927<ref>PMID:16790927</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2bd1" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The crystal structures of the monoclinic and trigonal forms of the quadruple mutant K53,56,120,121M of recombinant bovine pancreatic phospholipase A2 (PLA2) have been solved and refined at 1.9 and 1.1 A resolution, respectively. Interestingly, the monoclinic form reveals the presence of the second calcium ion. Furthermore, the surface-loop residues are ordered and the conformation of residues 62-66 is similar to that observed in other structures containing the second calcium ion. On the other hand, in the trigonal form the surface loop is disordered and the second calcium is absent. Docking studies suggest that the second calcium and residues Lys62 and Asp66 from the surface loop could be involved in the interaction with the polar head group of the membrane phospholipid. It is hypothesized that the two structures of the quadruple mutant, monoclinic and trigonal, represent the conformations of PLA2 at the lipid interface and in solution, respectively. A docked structure with a phospholipid molecule and with a transition-state analogue bound, one at the active site coordinating to the catalytic calcium and the other at the second calcium site, but both at the i-face, is presented.
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*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2BD1 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BD1 OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Suggestive evidence for the involvement of the second calcium and surface loop in interfacial binding: monoclinic and trigonal crystal structures of a quadruple mutant of phospholipase A2., Sekar K, Yogavel M, Kanaujia SP, Sharma A, Velmurugan D, Poi MJ, Dauter Z, Tsai MD, Acta Crystallogr D Biol Crystallogr. 2006 Jul;62(Pt 7):717-24. Epub 2006, Jun 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16790927 16790927]
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[[Category: Bos taurus]]
[[Category: Bos taurus]]
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[[Category: Phospholipase A(2)]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Sekar K]]
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[[Category: Sekar, K.]]
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[[Category: Tsai MD]]
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[[Category: Tsai, M D.]]
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[[Category: Velmurugan D]]
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[[Category: Velmurugan, D.]]
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[[Category: alpha helix]]
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[[Category: beta sheet]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:04:34 2008''
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Current revision

A possible role of the second calcium ion in interfacial binding: Atomic and medium resolution crystal structures of the quadruple mutant of phospholipase A2

PDB ID 2bd1

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