3dft: Difference between revisions

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-[[Image:3dft.png|left|200px]]
-{{STRUCTURE_3dft|  PDB=3dft  |  SCENE=  }}
+==Phosphate ions in D33S mutant fructose-1,6-bisphosphate aldolase from rabbit muscle==
+<StructureSection load='3dft' size='340' side='right'caption='[[3dft]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3dft]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DFT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DFT FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.94&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dft OCA], [https://pdbe.org/3dft PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dft RCSB], [https://www.ebi.ac.uk/pdbsum/3dft PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dft ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ALDOA_RABIT ALDOA_RABIT] Plays a key role in glycolysis and gluconeogenesis. In addition, may also function as scaffolding protein.<ref>PMID:17329259</ref>
+== 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/df/3dft_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=3dft ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Fructose-1,6-bisphosphate muscle aldolase is an essential glycolytic enzyme that catalyzes reversible carbon-carbon bond formation by cleaving fructose 1,6-bisphosphate to yield dihydroxyacetone phosphate (DHAP) and d-glyceraldehyde phosphate. To elucidate the mechanistic role of conserved amino acid Asp-33, Asn-33 and Ser-33 mutants were examined by kinetic and structural analyses. The mutations significantly compromised enzymatic activity and carbanion oxidation in presence of DHAP. Detailed structural analysis demonstrated that, like native crystals, Asp-33 mutant crystals, soaked in DHAP solutions, trapped Schiff base-derived intermediates covalently attached to Lys-229. The mutant structures, however, exhibited an abridged conformational change with the helical region (34-65) flanking the active site as well as pK(a) reductions and increased side chain disorder by central lysine residues, Lys-107 and Lys-146. These changes directly affect their interaction with the C-terminal Tyr-363, consistent with the absence of active site binding by the C-terminal region in the presence of phosphate. Lys-146 pK(a) reduction and side chain disorder would further compromise charge stabilization during C-C bond cleavage and proton transfer during enamine formation. These mechanistic impediments explain diminished catalytic activity and a reduced level of carbanion oxidation and are consistent with rate-determining proton transfer observed in the Asn-33 mutant. Asp-33 reduces the entropic cost and augments the enthalpic gain during catalysis by rigidifying Lys-107 and Lys-146, stabilizing their protonated forms, and promoting a conformational change triggered by substrate or obligate product binding, which lower kinetic barriers in C-C bond cleavage and Schiff base-enamine interconversion.
-===Phosphate ions in D33S mutant fructose-1,6-bisphosphate aldolase from rabbit muscle===
+Charge Stabilization and Entropy Reduction of Central Lysine Residues in Fructose-Bisphosphate Aldolase.,St-Jean M, Blonski C, Sygusch J Biochemistry. 2009 Apr 22. PMID:19354220<ref>PMID:19354220</ref>
-{{ABSTRACT_PUBMED_19354220}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3dft" style="background-color:#fffaf0;"></div>
-[[3dft]] is a 4 chain structure of [[Aldolase]] with sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DFT OCA].
 ==See Also==
-*[[Aldolase|Aldolase]]
+*[[Aldolase 3D structures|Aldolase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019354220</ref><references group="xtra"/>
+__TOC__
-[[Category: Fructose-bisphosphate aldolase]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Oryctolagus cuniculus]]
-[[Category: St-Jean, M.]]
+[[Category: St-Jean M]]
-[[Category: Sygusch, J.]]
+[[Category: Sygusch J]]
-[[Category: Aldolase]]
-[[Category: Glycolysis]]
-[[Category: Ion]]
-[[Category: Lyase]]
-[[Category: Mutant]]
-[[Category: Phosphate]]
-[[Category: Phosphoprotein]]
-[[Category: Schiff base]]