1j4e: Difference between revisions

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-[[Image:1j4e.png|left|200px]]
-<!--
+==FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE COVALENTLY BOUND TO THE SUBSTRATE DIHYDROXYACETONE PHOSPHATE==
-The line below this paragraph, containing "STRUCTURE_1j4e", creates the "Structure Box" on the page.
+<StructureSection load='1j4e' size='340' side='right'caption='[[1j4e]], [[Resolution|resolution]] 2.65&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'>[[1j4e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. The February 2004 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''The Glycolytic Enzymes''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2004_2 10.2210/rcsb_pdb/mom_2004_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J4E 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]] 2.65&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene></td></tr>
-{{STRUCTURE_1j4e|  PDB=1j4e  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1j4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j4e OCA], [https://pdbe.org/1j4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j4e RCSB], [https://www.ebi.ac.uk/pdbsum/1j4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j4e 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/j4/1j4e_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=1j4e ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Fructose-1,6-bis(phosphate) aldolase is an essential glycolytic enzyme found in all vertebrates and higher plants that catalyzes the cleavage of fructose 1,6-bis(phosphate) (Fru-1,6-P(2)) to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). Mutations in the aldolase genes in humans cause hemolytic anemia and hereditary fructose intolerance. The structure of the aldolase-DHAP Schiff base has been determined by X-ray crystallography to 2.6 A resolution (R(cryst) = 0.213, R(free) = 0.249) by trapping the catalytic intermediate with NaBH(4) in the presence of Fru-1,6-P(2). This is the first structure of a trapped covalent intermediate for this essential glycolytic enzyme. The structure allows the elucidation of a comprehensive catalytic mechanism and identification of a conserved chemical motif in Schiff-base aldolases. The position of the bound DHAP relative to Asp33 is consistent with a role for Asp33 in deprotonation of the C4-hydroxyl leading to C-C bond cleavage. The methyl side chain of Ala31 is positioned directly opposite the C3-hydroxyl, sterically favoring the S-configuration of the substrate at this carbon. The "trigger" residue Arg303, which binds the substrate C6-phosphate group, is a ligand to the phosphate group of DHAP. The observed movement of the ligand between substrate and product phosphates may provide a structural link between the substrate cleavage and the conformational change in the C-terminus associated with product release. The position of Glu187 in relation to the DHAP Schiff base is consistent with a role for the residue in protonation of the hydroxyl group of the carbinolamine in the dehydration step, catalyzing Schiff-base formation. The overlay of the aldolase-DHAP structure with that of the covalent enzyme-dihydroxyacetone structure of the mechanistically similar transaldolase and KDPG aldolase allows the identification of a conserved Lys-Glu dyad involved in Schiff-base formation and breakdown. The overlay highlights the fact that Lys146 in aldolase is replaced in transaldolase with Asn35. The substitution in transaldolase stabilizes the enamine intermediate required for the attack of the second aldose substrate, changing the chemistry from aldolase to transaldolase.
-'''FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE COVALENTLY BOUND TO THE SUBSTRATE DIHYDROXYACETONE PHOSPHATE'''
+Snapshots of catalysis: the structure of fructose-1,6-(bis)phosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate.,Choi KH, Shi J, Hopkins CE, Tolan DR, Allen KN Biochemistry. 2001 Nov 20;40(46):13868-75. PMID:11705376<ref>PMID:11705376</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1j4e" style="background-color:#fffaf0;"></div>
-{{ABSTRACT_11705376}}
+==See Also==
+*[[Aldolase 3D structures|Aldolase 3D structures]]
-==About this Structure==
+== References ==
-J4E is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. The following page contains interesting information on the relation of 1J4E with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb50_1.html The Glycolytic Enzymes]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J4E OCA].
+<references/>
-[[Category: Fructose-bisphosphate aldolase]]
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Oryctolagus cuniculus]]
-[[Category: Single protein]]
+[[Category: RCSB PDB Molecule of the Month]]
 [[Category: The Glycolytic Enzymes]]
-[[Category: Allen, K N.]]
+[[Category: Allen KN]]
-[[Category: Choi, K H.]]
+[[Category: Choi KH]]
-[[Category: Hopkins, C E.]]
+[[Category: Hopkins CE]]
-[[Category: Shi, J.]]
+[[Category: Shi J]]
-[[Category: Tolan, D R.]]
+[[Category: Tolan DR]]
-[[Category: Aldolase]]
-[[Category: Glycolysis]]
-[[Category: Lyase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 26 17:34:39 2008''