3ttt: Difference between revisions

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 ==Structure of F413Y variant of E. coli KatE==
-<StructureSection load='3ttt' size='340' side='right' caption='[[3ttt]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
+<StructureSection load='3ttt' size='340' side='right'caption='[[3ttt]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ttt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TTT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TTT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ttt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TTT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TTT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.58&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ttu|3ttu]], [[3ttv|3ttv]], [[3ttw|3ttw]], [[3ttx|3ttx]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b1732, JW1721, katE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3ttt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ttt OCA], [https://pdbe.org/3ttt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ttt RCSB], [https://www.ebi.ac.uk/pdbsum/3ttt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ttt ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ttt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ttt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ttt RCSB], [http://www.ebi.ac.uk/pdbsum/3ttt PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CATE_ECOLI CATE_ECOLI]] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.
+[https://www.uniprot.org/uniprot/CATE_ECOLI CATE_ECOLI] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The monofunctional catalase KatE of Esherichia coli exhibits exceptional resistance to heat denaturation and proteolytic degradation. During an investigation of subtle conformation changes in Arg111 and Phe413 on the proximal side of the heme induced by H(2)O(2), variants at position R111, T115 and F413 were constructed. Because the residues are not situated in the distal side heme cavity where catalysis occurs, significant changes in reactivity were not expected and indeed, only small changes in the kinetic characteristics were observed in all of the variants. However, the F413Y variant was found to have undergone main chain cleavage whereas the R111A, T115A, F413E and F413K variants had not. Two sites of cleavage were identified in the crystal structure and by mass spectrometry at residues 111 and 115. In addition to main chain cleavage, modifications to the side chains of Tyr413, Thr115 and Arg111 were suggested by differences in the electron density maps compared to maps of the native and inactive variant H128N/F413Y. The inactive variant H128N/F413Y and the active variant T115A/F413Y both did not exhibit main chain cleavage and the R11A/F413Y variant exhibited less cleavage. In addition, the apparent modification of three side chains was largely absent in these variants. It is also significant that all three F413 single variants contained heme b suggesting that the fidelity of the phenyl group was important for mediating heme b oxidation to heme d. The reactions are attributed to the introduction of a new reactive center possibly involving a transient radical on Tyr413 formed during catalytic turn over.
-Mutation of Phe413 to Tyr in catalase KatE from Escherichia coli leads to side chain damage and main chain cleavage.,Jha V, Donald LJ, Loewen PC Arch Biochem Biophys. 2012 Sep 15;525(2):207-14. doi: 10.1016/j.abb.2011.11.022. , Epub 2011 Dec 8. PMID:22172685<ref>PMID:22172685</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Catalase|Catalase]]
+*[[Catalase 3D structures|Catalase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Catalase]]
 [[Category: Escherichia coli]]
-[[Category: Jha, V]]
+[[Category: Large Structures]]
-[[Category: Loewen, P C]]
+[[Category: Jha V]]
-[[Category: Heme orientation]]
+[[Category: Loewen PC]]
-[[Category: Oxidoreductase]]