2vfl: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:2vfl.jpg|left|200px]]
-<!--
+==AKAP18 delta central domain - CMP==
-The line below this paragraph, containing "STRUCTURE_2vfl", creates the "Structure Box" on the page.
+<StructureSection load='2vfl' size='340' side='right'caption='[[2vfl]], [[Resolution|resolution]] 2.25&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'>[[2vfl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VFL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VFL 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]] 2.25&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene></td></tr>
-{{STRUCTURE_2vfl|  PDB=2vfl  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vfl OCA], [https://pdbe.org/2vfl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vfl RCSB], [https://www.ebi.ac.uk/pdbsum/2vfl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vfl ProSAT]</span></td></tr>
+</table>
+== 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/vf/2vfl_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=2vfl ConSurf].
+<div style="clear:both"></div>
-'''AKAP18 DELTA CENTRAL DOMAIN- CMP'''
+==See Also==
+*[[A-kinase anchor protein 3D structures|A-kinase anchor protein 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-Protein kinase A anchoring proteins (AKAPs), defined by their capacity to target the cAMP-dependent protein kinase to distinct subcellular locations, function as molecular scaffolds mediating the assembly of multicomponent complexes to integrate and organise multiple signalling events. Despite their central importance in regulating cellular processes, little is known regarding their diverse structures and molecular mechanisms. Here, using bioinformatics and X-ray crystallography, we define a central domain of AKAP18 delta (AKAP18(CD)) as a member of the 2H phosphoesterase family. The domain features two conserved His-x-Thr motifs positioned at the base of a groove located between two lobes related by pseudo 2-fold symmetry. Nucleotide co-crystallisation screening revealed that this groove binds specifically to adenosine 5'-monophosphate (5'AMP) and cytosine 5'-monophosphate (5'CMP), with the affinity constant for AMP in the physiological concentration range. This is the first example of an AKAP capable of binding a small molecule. Our data generate two functional hypotheses for the AKAP18 central domain. It may act as a phosphoesterase, although we did not identify a substrate, or as an AMP sensor with the potential to couple intracellular AMP levels to PKA signalling events.
-==About this Structure==
-VFL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VFL OCA].
-==Reference==
-AKAP18 contains a phosphoesterase domain that binds AMP., Gold MG, Smith FD, Scott JD, Barford D, J Mol Biol. 2008 Feb 1;375(5):1329-43. Epub 2007 Nov 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18082768 18082768]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Barford, D.]]
+[[Category: Barford D]]
-[[Category: Gold, M G.]]
+[[Category: Gold MG]]
-[[Category: Scott, J D.]]
+[[Category: Scott JD]]
-[[Category: Smith, F D.]]
+[[Category: Smith FD]]
-[[Category: Akap]]
-[[Category: Apo]]
-[[Category: Camp]]
-[[Category: Cmp]]
-[[Category: Hydrolase]]
-[[Category: Phosphoesterase]]
-[[Category: Pka]]
-[[Category: Scaffold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May  7 08:44:22 2008''