1u4j: Difference between revisions

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-{{Seed}}
-[[Image:1u4j.png|left|200px]]
-<!--
+==Crystal structure of a carbohydrate induced dimer of group I phospholipase A2 from Bungarus caeruleus at 2.1 A resolution==
-The line below this paragraph, containing "STRUCTURE_1u4j", creates the "Structure Box" on the page.
+<StructureSection load='1u4j' size='340' side='right'caption='[[1u4j]], [[Resolution|resolution]] 2.18&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'>[[1u4j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bungarus_caeruleus Bungarus caeruleus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U4J 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]] 2.18&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_1u4j|  PDB=1u4j  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1u4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u4j OCA], [https://pdbe.org/1u4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u4j RCSB], [https://www.ebi.ac.uk/pdbsum/1u4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u4j ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PA2B5_BUNCE PA2B5_BUNCE] Snake venom phospholipase A2 (PLA2) that shows anticoagulant and neurotoxic activities.  PLA2 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/u4/1u4j_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1u4j ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+This is the first crystal structure of a carbohydrate induced dimer of phospholipase A(2) (PLA(2)). This is an endogenous complex formed between two PLA(2) molecules and two mannoses. It was isolated from Krait venom (Bungarus caeruleus) and crystallized as such. The complete amino acid sequence of PLA(2) was determined using cDNA method. Three-dimensional structure of the complex has been solved with molecular replacement method and refined to a final R-factor of 0.192 for all the data in the resolution range 20.0-2.1A. The presence of mannose molecules in the protein crystals was confirmed using dinitrosalicylic acid test and the molecular weight of the dimer was verified with MALDI-TOF. As indicated by dynamic light scattering and analytical ultracentrifugation the dimer was also stable in solution. The good quality non-protein electron density at the interface of two PLA(2) molecules enabled us to model two mannoses. The mannoses are involved extensively in interactions with protein atoms of both PLA(2) molecules. Some of the critical amino acid residues such as Asp 49 and Tyr 31, which are part of the substrate-binding site, are found facing the interface and interacting with mannoses. The structure of the complex clearly shows that the dimerization is caused by mannoses and it results in the loss of enzymatic activity.
-===Crystal structure of a carbohydrate induced dimer of group I phospholipase A2 from Bungarus caeruleus at 2.1 A resolution===
+Crystal structure of a carbohydrate induced homodimer of phospholipase A2 from Bungarus caeruleus at 2.1A resolution.,Singh G, Gourinath S, Sarvanan K, Sharma S, Bhanumathi S, Betzel Ch, Yadav S, Srinivasan A, Singh TP J Struct Biol. 2005 Mar;149(3):264-72. PMID:15721580<ref>PMID:15721580</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1u4j" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15721580}}, 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 15721580 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15721580}}
+__TOC__
+</StructureSection>
-==About this Structure==
-U4J is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Bungarus_caeruleus Bungarus caeruleus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U4J OCA].
-==Reference==
-<ref group="xtra">PMID:15721580</ref><references group="xtra"/>
-[[Category: Bungarus caeruleus]]
-[[Category: Betzel, C.]]
-[[Category: Bhanumathi, S.]]
-[[Category: Gourinath, S.]]
-[[Category: Sharma, S.]]
-[[Category: Singh, G.]]
-[[Category: Singh, T P.]]
-[[Category: Srinivasan, A.]]
 [[Category: Bungarus caeruleus]]
-[[Category: Homodimer]]
+[[Category: Large Structures]]
-[[Category: Mannose]]
+[[Category: Betzel C]]
-[[Category: Phospholipase a2]]
+[[Category: Bhanumathi S]]
+[[Category: Gourinath S]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 09:50:19 2009''
+[[Category: Sharma S]]
+[[Category: Singh G]]
+[[Category: Singh TP]]
+[[Category: Srinivasan A]]