3wxo: Difference between revisions

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 <StructureSection load='3wxo' size='340' side='right'caption='[[3wxo]], [[Resolution|resolution]] 2.12&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3wxo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Anacystis_nidulans_r2 Anacystis nidulans r2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WXO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WXO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3wxo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_elongatus_PCC_7942_=_FACHB-805 Synechococcus elongatus PCC 7942 = FACHB-805]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WXO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WXO FirstGlance]. <br>
-</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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NIZ:PYRIDINE-4-CARBOHYDRAZIDE'>NIZ</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]] 2.12&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">katG, Synpcc7942_1656 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1140 Anacystis nidulans R2])</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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NIZ:PYRIDINE-4-CARBOHYDRAZIDE'>NIZ</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Catalase_peroxidase Catalase peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.21 1.11.1.21] </span></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=3wxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wxo OCA], [https://pdbe.org/3wxo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wxo RCSB], [https://www.ebi.ac.uk/pdbsum/3wxo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wxo ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/KATG_SYNE7 KATG_SYNE7]] Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity.[HAMAP-Rule:MF_01961]
+[https://www.uniprot.org/uniprot/KATG_SYNE7 KATG_SYNE7] Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity.[HAMAP-Rule:MF_01961]
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Isoniazid (INH) is one of the most effective antibiotics against tuberculosis. INH is a prodrug that is activated by KatG. Although extensive studies have been performed in order to understand the mechanism of KatG, even the binding site of INH in KatG remains controversial. In this study, we determined the crystal structure of KatG from Synechococcus elongatus PCC7942 (SeKatG) in a complex with INH at 2.12-A resolution. Three INH molecules were bound to the molecular surface. One INH molecule was bound at the entrance to the epsilon-edge side of heme (designated site 1), another was bound at the entrance to the gamma-edge side of heme (site 2), and another was bound to the loop structures in front of the heme propionate side chain (site 3). All of the interactions between KatG and the bound INH seemed to be weak, being mediated mainly by van der Waals contacts. Structural comparisons revealed that the identity and configuration of the residues in site 1 were very similar among SeKatG, Burkholderia pseudomallei KatG, and Mycobacterium tuberculosis KatG. In contrast, sites 2 and 3 were structurally diverse among the three proteins. Thus, site 1 is probably the common KatG INH-binding site. A static enzymatic analysis and thermal shift assay suggested that the INH-activating reaction does not proceed in site 1, but rather that this site may function as an initial trapping site for the INH molecule. DATABASE: The atomic coordinates and structure factors have been deposited in the Protein Data Bank under the accession number 3WXO.
-The crystal structure of isoniazid-bound KatG catalase-peroxidase from Synechococcus elongatus PCC7942.,Kamachi S, Hirabayashi K, Tamoi M, Shigeoka S, Tada T, Wada K FEBS J. 2015 Jan;282(1):54-64. doi: 10.1111/febs.13102. Epub 2014 Oct 30. PMID:25303560<ref>PMID:25303560</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3wxo" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Catalase 3D structures|Catalase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Anacystis nidulans r2]]
-[[Category: Catalase peroxidase]]
 [[Category: Large Structures]]
-[[Category: Kamachi, S]]
+[[Category: Synechococcus elongatus PCC 7942 = FACHB-805]]
-[[Category: Tada, T]]
+[[Category: Kamachi S]]
-[[Category: Wada, K]]
+[[Category: Tada T]]
-[[Category: Catalase subfamily]]
+[[Category: Wada K]]
-[[Category: Covalent trp-tyr-met adduct]]
-[[Category: Cross-link]]
-[[Category: Heme b fe]]
-[[Category: Oxidoreductase]]
-[[Category: Oxidoreductase peroxidase]]
-[[Category: Peroxidase]]
-[[Category: Peroxidase family]]