1gh4: Difference between revisions

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-{{Seed}}
-[[Image:1gh4.png|left|200px]]
-<!--
+==Structure of the triple mutant (K56M, K120M, K121M) of phospholipase A2==
-The line below this paragraph, containing "STRUCTURE_1gh4", creates the "Structure Box" on the page.
+<StructureSection load='1gh4' size='340' side='right'caption='[[1gh4]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1gh4]] is a 1 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=1GH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GH4 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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='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>
-{{STRUCTURE_1gh4|  PDB=1gh4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gh4 OCA], [https://pdbe.org/1gh4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gh4 RCSB], [https://www.ebi.ac.uk/pdbsum/1gh4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gh4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PA21B_BOVIN PA21B_BOVIN] PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gh/1gh4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1gh4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Phospholipase A(2) catalyses hydrolysis of the ester bond at the C2 position of 3-sn-phosphoglycerides. Here we report the 1.9A resolution crystal structure of the triple mutant K56,120,121M of bovine pancreatic phospholipase A(2). The structure was solved by molecular replacement method using the orthorhombic form of the recombinant phospholipase A(2). The final protein model contains all the 123 amino acid residues, two calcium ions, 125 water molecules and one 2-methyl-2-4-pentanediol molecule. The model has been refined to a crystallographic R-factor of 19.6% (R(free) of 25.9%) for all data between 14.2A and 1.9A. The residues 62-66, which are in a surface loop, are always disordered in the structures of bovine pancreatic phospholipase A(2) and its mutants. It is interesting to note that the residues 62-66 in the present structure is ordered and the conformation varies substantially from those in the previously published structures of this enzyme. An unexpected and interesting observation in the present structure is that, in addition to the functionally important calcium ion in the active site, one more calcium ion is found near the N terminus. Detailed structural analyses suggest that binding of the second calcium ion could be responsible for the conformational change and the ordering of the surface loop. Furthermore, the results suggest a structural reciprocity between the k(cat)(*) allosteric site and surface loop at the i-face, which represents a newly identified structural property of secreted phospholipase A(2).
-===Structure of the triple mutant (K56M, K120M, K121M) of phospholipase A2===
+Observation of additional calcium ion in the crystal structure of the triple mutant K56,120,121M of bovine pancreatic phospholipase A2.,Rajakannan V, Yogavel M, Poi MJ, Jeyaprakash AA, Jeyakanthan J, Velmurugan D, Tsai MD, Sekar K J Mol Biol. 2002 Dec 6;324(4):755-62. PMID:12460575<ref>PMID:12460575</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1gh4" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12460575}}, adds the Publication Abstract to the page
+*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12460575 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12460575}}
+__TOC__
+</StructureSection>
-==About this Structure==
-GH4 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=1GH4 OCA].
-==Reference==
-Observation of additional calcium ion in the crystal structure of the triple mutant K56,120,121M of bovine pancreatic phospholipase A2., Rajakannan V, Yogavel M, Poi MJ, Jeyaprakash AA, Jeyakanthan J, Velmurugan D, Tsai MD, Sekar K, J Mol Biol. 2002 Dec 6;324(4):755-62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12460575 12460575]
 [[Category: Bos taurus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Sekar, K.]]
+[[Category: Sekar K]]
-[[Category: Tsai, M D.]]
+[[Category: Tsai MD]]
-[[Category: Velmurugan, D.]]
+[[Category: Velmurugan D]]
-[[Category: Alpha helix]]
-[[Category: Beta sheet]]
-[[Category: Triple mutant]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 05:16:41 2008''