1o9i

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[[Image:1o9i.gif|left|200px]]
 
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{{Structure
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==Crystal structure of the Y42F mutant of manganese catalase from Lactobacillus plantarum at 1.33A resolution==
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|PDB= 1o9i |SIZE=350|CAPTION= <scene name='initialview01'>1o9i</scene>, resolution 1.33&Aring;
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<StructureSection load='1o9i' size='340' side='right'caption='[[1o9i]], [[Resolution|resolution]] 1.33&Aring;' scene=''>
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|SITE= <scene name='pdbsite=BND:Mes+Binding+Site+For+Chain+F'>BND</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=MN3:MANGANESE+(III)+ION'>MN3</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene> and <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC ACID'>MES</scene>
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<table><tr><td colspan='2'>[[1o9i]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactiplantibacillus_plantarum Lactiplantibacillus plantarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O9I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1O9I FirstGlance]. <br>
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|ACTIVITY= [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]
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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]] 1.33&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MN3:MANGANESE+(III)+ION'>MN3</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene></td></tr>
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}}
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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=1o9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o9i OCA], [https://pdbe.org/1o9i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1o9i RCSB], [https://www.ebi.ac.uk/pdbsum/1o9i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o9i ProSAT]</span></td></tr>
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</table>
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'''CRYSTAL STRUCTURE OF THE Y42F MUTANT OF MANGANESE CATALASE FROM LACTOBACILLUS PLANTARUM AT 1.33A RESOLUTION'''
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== Function ==
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[https://www.uniprot.org/uniprot/MCAT_LACPN MCAT_LACPN]
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== Evolutionary Conservation ==
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==Overview==
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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/o9/1o9i_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=1o9i ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
X-ray crystallography of the nonheme manganese catalase from Lactobacillus plantarum (LPC) [Barynin, V.V., Whittaker, M.M., Antonyuk, S.V., Lamzin, V.S., Harrison, P.M., Artymiuk, P.J. &amp; Whittaker, J.W. (2001) Structure9, 725-738] has revealed the structure of the dimanganese redox cluster together with its protein environment. The oxidized [Mn(III)Mn(III)] cluster is bridged by two solvent molecules (oxo and hydroxo, respectively) together with a micro 1,3 bridging glutamate carboxylate and is embedded in a web of hydrogen bonds involving an outer sphere tyrosine residue (Tyr42). A novel homologous expression system has been developed for production of active recombinant LPC and Tyr42 has been replaced by phenylalanine using site-directed mutagenesis. Spectroscopic and structural studies indicate that disruption of the hydrogen-bonded web significantly perturbs the active site in Y42F LPC, breaking one of the solvent bridges and generating an 'open' form of the dimanganese cluster. Two of the metal ligands adopt alternate conformations in the crystal structure, both conformers having a broken solvent bridge in the dimanganese core. The oxidized Y42F LPC exhibits strong optical absorption characteristic of high spin Mn(III) in low symmetry and lower coordination number. MCD and EPR measurements provide complementary information defining a ferromagnetically coupled electronic ground state for a cluster containing a single solvent bridge, in contrast to the diamagnetic ground state found for the native cluster containing a pair of solvent bridges. Y42F LPC has less than 5% of the catalase activity and much higher Km for H2O2 ( approximately 1.4 m) at neutral pH than WT LPC, although the activity is slightly restored at high pH where the cluster is converted to a diamagnetic form. These studies provide new insight into the contribution of the outer sphere tyrosine to the stability of the dimanganese cluster and the role of the solvent bridges in catalysis by dimanganese catalases.
X-ray crystallography of the nonheme manganese catalase from Lactobacillus plantarum (LPC) [Barynin, V.V., Whittaker, M.M., Antonyuk, S.V., Lamzin, V.S., Harrison, P.M., Artymiuk, P.J. &amp; Whittaker, J.W. (2001) Structure9, 725-738] has revealed the structure of the dimanganese redox cluster together with its protein environment. The oxidized [Mn(III)Mn(III)] cluster is bridged by two solvent molecules (oxo and hydroxo, respectively) together with a micro 1,3 bridging glutamate carboxylate and is embedded in a web of hydrogen bonds involving an outer sphere tyrosine residue (Tyr42). A novel homologous expression system has been developed for production of active recombinant LPC and Tyr42 has been replaced by phenylalanine using site-directed mutagenesis. Spectroscopic and structural studies indicate that disruption of the hydrogen-bonded web significantly perturbs the active site in Y42F LPC, breaking one of the solvent bridges and generating an 'open' form of the dimanganese cluster. Two of the metal ligands adopt alternate conformations in the crystal structure, both conformers having a broken solvent bridge in the dimanganese core. The oxidized Y42F LPC exhibits strong optical absorption characteristic of high spin Mn(III) in low symmetry and lower coordination number. MCD and EPR measurements provide complementary information defining a ferromagnetically coupled electronic ground state for a cluster containing a single solvent bridge, in contrast to the diamagnetic ground state found for the native cluster containing a pair of solvent bridges. Y42F LPC has less than 5% of the catalase activity and much higher Km for H2O2 ( approximately 1.4 m) at neutral pH than WT LPC, although the activity is slightly restored at high pH where the cluster is converted to a diamagnetic form. These studies provide new insight into the contribution of the outer sphere tyrosine to the stability of the dimanganese cluster and the role of the solvent bridges in catalysis by dimanganese catalases.
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==About this Structure==
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Outer sphere mutagenesis of Lactobacillus plantarum manganese catalase disrupts the cluster core. Mechanistic implications.,Whittaker MM, Barynin VV, Igarashi T, Whittaker JW Eur J Biochem. 2003 Mar;270(6):1102-16. PMID:12631270<ref>PMID:12631270</ref>
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1O9I is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_plantarum Lactobacillus plantarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O9I OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Outer sphere mutagenesis of Lactobacillus plantarum manganese catalase disrupts the cluster core. Mechanistic implications., Whittaker MM, Barynin VV, Igarashi T, Whittaker JW, Eur J Biochem. 2003 Mar;270(6):1102-16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12631270 12631270]
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</div>
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[[Category: Catalase]]
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<div class="pdbe-citations 1o9i" style="background-color:#fffaf0;"></div>
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[[Category: Lactobacillus plantarum]]
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[[Category: Single protein]]
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[[Category: Barynin, V V.]]
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[[Category: Whittaker, J W.]]
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[[Category: Whittaker, M M.]]
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[[Category: CA]]
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[[Category: MES]]
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[[Category: MN3]]
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[[Category: NA]]
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[[Category: O]]
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[[Category: dimanganese catalase]]
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[[Category: hexamer]]
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[[Category: metalloenzyme]]
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[[Category: oxidoreductase]]
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[[Category: preoxidase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:07:46 2008''
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==See Also==
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*[[Catalase 3D structures|Catalase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Lactiplantibacillus plantarum]]
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[[Category: Large Structures]]
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[[Category: Barynin VV]]
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[[Category: Whittaker JW]]
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[[Category: Whittaker MM]]

Current revision

Crystal structure of the Y42F mutant of manganese catalase from Lactobacillus plantarum at 1.33A resolution

PDB ID 1o9i

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