1afw

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[[Image:1afw.gif|left|200px]]<br />
 
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<applet load="1afw" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1afw, resolution 1.8&Aring;" />
 
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'''THE 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE DIMERIC PEROXISOMAL THIOLASE OF SACCHAROMYCES CEREVISIAE'''<br />
 
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==Overview==
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==THE 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE DIMERIC PEROXISOMAL THIOLASE OF SACCHAROMYCES CEREVISIAE==
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The dimeric, peroxisomal 3-ketoacyl-CoA thiolase catalyses the conversion, of 3-ketoacyl-CoA into acyl-CoA, which is shorter by two carbon atoms., This reaction is the last step of the beta-oxidation pathway. The crystal, structure of unliganded peroxisomal thiolase of the yeast Saccharomyces, cerevisiae has been refined at 1.8 A resolution. An unusual feature of, this structure is the presence of two helices, completely buried in the, dimer and sandwiched between two beta-sheets. The analysis of the, structure shows that the sequences of these helices are not hydrophobic, but generate two amphipathic helices. The helix in the N-terminal domain, exposes the polar side-chains to a cavity at the dimer interface, filled, with structured water molecules. The central helix in the C-terminal, domain exposes its polar residues to an interior polar pocket. The refined, structure has also been used to predict the mode of binding of the, substrate molecule acetoacetyl-CoA, as well as the reaction mechanism., From previous studies it is known that Cys125, His375 and Cys403 are, important catalytic residues. In the proposed model the acetoacetyl group, fits near the two catalytic cysteine residues, such that the oxygen atoms, point towards the protein interior. The distance between SG(Cys125) and, C3(acetoacetyl-CoA) is 3.7 A. The O2 atom of the docked acetoacetyl group, makes a hydrogen bond to N(Gly405), which would favour the formation of, the covalent bond between SG(Cys125) and C3(acetoacetyl-CoA) of the, intermediate complex of the two-step reaction. The CoA moiety is proposed, to bind in a groove on the surface of the protein molecule. Most of the, interactions of the CoA molecule are with atoms of the loop domain. The, three phosphate groups of the CoA moiety are predicted to interact with, side-chains of lysine and arginine residues, which are conserved in the, dimeric thiolases.
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<StructureSection load='1afw' size='340' side='right'caption='[[1afw]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1afw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AFW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AFW FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1afw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1afw OCA], [https://pdbe.org/1afw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1afw RCSB], [https://www.ebi.ac.uk/pdbsum/1afw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1afw ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/THIK_YEAST THIK_YEAST]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/af/1afw_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1afw ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1AFW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with MRD as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Structure known Active Sites: AVA and AVB. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1AFW OCA].
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*[[Thiolase 3D structures|Thiolase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism., Mathieu M, Modis Y, Zeelen JP, Engel CK, Abagyan RA, Ahlberg A, Rasmussen B, Lamzin VS, Kunau WH, Wierenga RK, J Mol Biol. 1997 Oct 31;273(3):714-28. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9402066 9402066]
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[[Category: Large Structures]]
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[[Category: Acetyl-CoA C-acyltransferase]]
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[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Single protein]]
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[[Category: Mathieu M]]
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[[Category: Mathieu, M.]]
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[[Category: Wierenga RK]]
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[[Category: Wierenga, R.K.]]
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[[Category: MRD]]
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[[Category: fatty acid metabolism]]
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[[Category: thiolase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 15:17:41 2007''
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Current revision

THE 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE DIMERIC PEROXISOMAL THIOLASE OF SACCHAROMYCES CEREVISIAE

PDB ID 1afw

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