1dji: Difference between revisions

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-[[Image:1dji.jpg|left|200px]]
- {{Structure
+==PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH CALCIUM==
-|PDB= 1dji |SIZE=350|CAPTION= <scene name='initialview01'>1dji</scene>, resolution 2.5&Aring;
+<StructureSection load='1dji' size='340' side='right'caption='[[1dji]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>
+<table><tr><td colspan='2'>[[1dji]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DJI FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoinositide_phospholipase_C Phosphoinositide phospholipase C], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.11 3.1.4.11] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-|GENE= CDNA FRAGMENT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dji OCA], [https://pdbe.org/1dji PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dji RCSB], [https://www.ebi.ac.uk/pdbsum/1dji PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dji ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dji OCA], [http://www.ebi.ac.uk/pdbsum/1dji PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dji RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/PLCD1_RAT PLCD1_RAT] The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. Essential for trophoblast and placental development.
+== 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/dj/1dji_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=1dji ConSurf].
+<div style="clear:both"></div>
-'''PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH CALCIUM'''
+==See Also==
+*[[Phospholipase C|Phospholipase C]]
+__TOC__
-==Overview==
+</StructureSection>
-We have determined the crystal structures of complexes of phosphoinositide-specific phospholipase C-delta1 from rat with calcium, barium, and lanthanum at 2.5-2.6 A resolution. Binding of these metal ions is observed in the active site of the catalytic TIM barrel and in the calcium binding region (CBR) of the C2 domain. The C2 domain of PLC-delta1 is a circularly permuted topological variant (P-variant) of the synaptotagmin I C2A domain (S-variant). On the basis of sequence analysis, we propose that both the S-variant and P-variant topologies are present among other C2 domains. Multiple adjacent binding sites in the C2 domain were observed for calcium and the other metal/enzyme complexes. The maximum number of binding sites observed was for the calcium analogue lanthanum. This complex shows an array-like binding of three lanthanum ions (sites I-III) in a crevice on one end of the C2 beta-sandwich. Residues involved in metal binding are contained in three loops, CBR1, CBR2, and CBR3. Sites I and II are maintained in the calcium and barium complexes, whereas sites II and III coincide with a binary calcium binding site in the C2A domain of synaptotagmin I. Several conformers for CBR1 are observed. The conformation of CBR1 does not appear to be strictly dependent on metal binding; however, metal binding may stabilize certain conformers. No significant structural changes are observed for CBR2 or CBR3. The surface of this ternary binding site provides a cluster of freely accessible liganding positions for putative phospholipid ligands of the C2 domain. It may be that the ternary metal binding site is also a feature of calcium-dependent phospholipid binding in solution. A ternary metal binding site might be a conserved feature among C2 domains that contain the critical calcium ligands in their CBR's. The high cooperativity of calcium-mediated lipid binding by C2 domains described previously is explained by this novel type of calcium binding site.
+[[Category: Large Structures]]
-==About this Structure==
-DJI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJI OCA].
-==Reference==
-A ternary metal binding site in the C2 domain of phosphoinositide-specific phospholipase C-delta1., Essen LO, Perisic O, Lynch DE, Katan M, Williams RL, Biochemistry. 1997 Mar 11;36(10):2753-62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9062102 9062102]
-[[Category: Phosphoinositide phospholipase C]]
 [[Category: Rattus norvegicus]]
-[[Category: Single protein]]
+[[Category: Essen L-O]]
-[[Category: Essen, L O.]]
+[[Category: Perisic O]]
-[[Category: Perisic, O.]]
+[[Category: Williams RL]]
-[[Category: Williams, R L.]]
-[[Category: calcium-binding]]
-[[Category: hydrolase]]
-[[Category: lipid degradation]]
-[[Category: phosphoinositide-specific]]
-[[Category: phospholipase c]]
-[[Category: phosphoric diester hydrolase]]
-[[Category: transducer]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:42:42 2008''