1wdk: Difference between revisions

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-[[Image:1wdk.gif|left|200px]]
- {{Structure
+==fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form I (native2)==
-|PDB= 1wdk |SIZE=350|CAPTION= <scene name='initialview01'>1wdk</scene>, resolution 2.5&Aring;
+<StructureSection load='1wdk' size='340' side='right'caption='[[1wdk]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene> and <scene name='pdbligand=N8E:3,6,9,12,15-PENTAOXATRICOSAN-1-OL'>N8E</scene>
+<table><tr><td colspan='2'>[[1wdk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WDK FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Acetyl-CoA_C-acyltransferase Acetyl-CoA C-acyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.16 2.3.1.16]
+</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=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=N8E:3,6,9,12,15-PENTAOXATRICOSAN-1-OL'>N8E</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1wdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wdk OCA], [https://pdbe.org/1wdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wdk RCSB], [https://www.ebi.ac.uk/pdbsum/1wdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wdk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FADB_PSEFR FADB_PSEFR] Involved in the aerobic and anaerobic degradation of long-chain fatty acids via beta-oxidation cycle. Catalyzes the formation of 3-oxoacyl-CoA from enoyl-CoA via L-3-hydroxyacyl-CoA. It can also use D-3-hydroxyacyl-CoA and cis-3-enoyl-CoA as substrate.[HAMAP-Rule:MF_01621]
+== 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/wd/1wdk_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=1wdk ConSurf].
+<div style="clear:both"></div>
-'''fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form I (native2)'''
+==See Also==
+*[[Thiolase 3D structures|Thiolase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-The atomic view of the active site coupling termed channelling is a major subject in molecular biology. We have determined two distinct crystal structures of the bacterial multienzyme complex that catalyzes the last three sequential reactions in the fatty acid beta-oxidation cycle. The alpha2beta2 heterotetrameric structure shows the uneven ring architecture, where all the catalytic centers of 2-enoyl-CoA hydratase (ECH), L-3-hydroxyacyl-CoA dehydrogenase (HACD) and 3-ketoacyl-CoA thiolase (KACT) face a large inner solvent region. The substrate, anchored through the 3'-phosphate ADP moiety, allows the fatty acid tail to pivot from the ECH to HACD active sites, and finally to the KACT active site. Coupling with striking domain rearrangements, the incorporation of the tail into the KACT cavity and the relocation of 3'-phosphate ADP bring the reactive C2-C3 bond to the correct position for cleavage. The alpha-helical linker specific for the multienzyme contributes to the pivoting center formation and the substrate transfer through its deformation. This channelling mechanism could be applied to other beta-oxidation multienzymes, as revealed from the homology model of the human mitochondrial trifunctional enzyme complex.
+[[Category: Large Structures]]
-==About this Structure==
-WDK is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WDK OCA].
-==Reference==
-Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex., Ishikawa M, Tsuchiya D, Oyama T, Tsunaka Y, Morikawa K, EMBO J. 2004 Jul 21;23(14):2745-54. Epub 2004 Jul 1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15229654 15229654]
-[[Category: Acetyl-CoA C-acyltransferase]]
-[[Category: Protein complex]]
 [[Category: Pseudomonas fragi]]
-[[Category: Ishikawa, M.]]
+[[Category: Ishikawa M]]
-[[Category: Morikawa, K.]]
+[[Category: Morikawa K]]
-[[Category: Oyama, T.]]
+[[Category: Oyama T]]
-[[Category: Tsuchiya, D.]]
+[[Category: Tsuchiya D]]
-[[Category: Tsunaka, Y.]]
+[[Category: Tsunaka Y]]
-[[Category: ACO]]
-[[Category: HG]]
-[[Category: N8E]]
-[[Category: NAD]]
-[[Category: ZN]]
-[[Category: alpha2beta2 heterotetrameric complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:55:36 2008''