1wnx: Difference between revisions

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-[[Image:1wnx.gif|left|200px]]
- {{Structure
+==D136E mutant of Heme Oxygenase from Corynebacterium diphtheriae (HmuO)==
-|PDB= 1wnx |SIZE=350|CAPTION= <scene name='initialview01'>1wnx</scene>, resolution 1.85&Aring;
+<StructureSection load='1wnx' size='340' side='right'caption='[[1wnx]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> and <scene name='pdbligand=HEM:PROTOPORPHYRIN IX CONTAINING FE'>HEM</scene>
+<table><tr><td colspan='2'>[[1wnx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WNX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WNX FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
-|GENE=
+<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=SO4:SULFATE+ION'>SO4</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=1wnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wnx OCA], [https://pdbe.org/1wnx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wnx RCSB], [https://www.ebi.ac.uk/pdbsum/1wnx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wnx ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HMUO_CORDI HMUO_CORDI] Allows the bacteria to use the host heme as an iron source. Involved in the oxidation of heme and subsequent release of iron from the heme moiety.
+== 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/wn/1wnx_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=1wnx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Heme oxygenases found in mammals, plants, and bacteria catalyze degradation of heme using the same mechanism. Roles of distal Asp (Asp-136) residue in HmuO, a heme oxygenase of Corynebacterium diphtheriae, have been investigated by site-directed mutagenesis, enzyme kinetics, resonance Raman spectroscopy, and x-ray crystallography. Replacements of the Asp-136 by Ala and Phe resulted in reduced heme degradation activity due to the formation of ferryl heme, showing that the distal Asp is critical in HmuO heme oxygenase activity. D136N HmuO catalyzed heme degradation at a similar efficiency to wild type and D136E HmuO, implying that the carboxylate moiety is not required for the heme catabolism by HmuO. Resonance Raman results suggest that the inactive ferryl heme formation in the HmuO mutants is induced by disruption of the interaction between a reactive Fe-OOH species and an adjacent distal pocket water molecule. Crystal structural analysis of the HmuO mutants confirms partial disappearance of this nearby water in D136A HmuO. Our results provide the first experimental evidence for the catalytic importance of the nearby water molecule that can be universally critical in heme oxygenase catalysis and propose that the distal Asp helps in positioning the key water molecule at a position suitable for efficient activation of the Fe-OOH species.
-'''D136E mutant of Heme Oxygenase from Corynebacterium diphtheriae (HmuO)'''
+Roles of distal Asp in heme oxygenase from Corynebacterium diphtheriae, HmuO: A water-driven oxygen activation mechanism.,Matsui T, Furukawa M, Unno M, Tomita T, Ikeda-Saito M J Biol Chem. 2005 Jan 28;280(4):2981-9. Epub 2004 Nov 4. PMID:15528205<ref>PMID:15528205</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1wnx" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Heme oxygenases found in mammals, plants, and bacteria catalyze degradation of heme using the same mechanism. Roles of distal Asp (Asp-136) residue in HmuO, a heme oxygenase of Corynebacterium diphtheriae, have been investigated by site-directed mutagenesis, enzyme kinetics, resonance Raman spectroscopy, and x-ray crystallography. Replacements of the Asp-136 by Ala and Phe resulted in reduced heme degradation activity due to the formation of ferryl heme, showing that the distal Asp is critical in HmuO heme oxygenase activity. D136N HmuO catalyzed heme degradation at a similar efficiency to wild type and D136E HmuO, implying that the carboxylate moiety is not required for the heme catabolism by HmuO. Resonance Raman results suggest that the inactive ferryl heme formation in the HmuO mutants is induced by disruption of the interaction between a reactive Fe-OOH species and an adjacent distal pocket water molecule. Crystal structural analysis of the HmuO mutants confirms partial disappearance of this nearby water in D136A HmuO. Our results provide the first experimental evidence for the catalytic importance of the nearby water molecule that can be universally critical in heme oxygenase catalysis and propose that the distal Asp helps in positioning the key water molecule at a position suitable for efficient activation of the Fe-OOH species.
+*[[Heme oxygenase 3D structures|Heme oxygenase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-WNX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WNX OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Roles of distal Asp in heme oxygenase from Corynebacterium diphtheriae, HmuO: A water-driven oxygen activation mechanism., Matsui T, Furukawa M, Unno M, Tomita T, Ikeda-Saito M, J Biol Chem. 2005 Jan 28;280(4):2981-9. Epub 2004 Nov 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15528205 15528205]
 [[Category: Corynebacterium diphtheriae]]
-[[Category: Heme oxygenase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Ikeda-Saito M]]
-[[Category: Ikeda-Saito, M.]]
+[[Category: Matsui T]]
-[[Category: Matsui, T.]]
+[[Category: Unno M]]
-[[Category: Unno, M.]]
-[[Category: HEM]]
-[[Category: NA]]
-[[Category: SO4]]
-[[Category: alpha-helix]]
-[[Category: heme]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:59:23 2008''