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1qpa

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[[Image:1qpa.gif|left|200px]]<br />
 
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<applet load="1qpa" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1qpa, resolution 1.80&Aring;" />
 
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'''LIGNIN PEROXIDASE ISOZYME LIP4.65 (PI 4.65)'''<br />
 
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==Overview==
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==LIGNIN PEROXIDASE ISOZYME LIP4.65 (PI 4.65)==
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The crystal structure of lignin peroxidase (LiP) from the white rot fungus, Phanerochaete chrysosporium was refined to an R-factor of 16.2 % utilizing, synchrotron data in the resolution range from 10 to 1.7 A. The final model, comprises all 343 amino acid residues, 370 water molecules, the heme, four, carbohydrates, and two calcium ions. Lignin peroxidase shows the typical, peroxidase fold and the heme has a close environment as found in other, peroxidases. During refinement of the LiP model an unprecedented, modification of an amino acid was recognized. The surface residue, tryptophan 171 in LiP is stereospecifically hydroxylated at the Cbeta atom, due to an autocatalytic process. We propose that during the catalytic, cycle of LiP a transient radical at Trp171 occurs that is different from, those previously assumed for this type of peroxidase. Recently, the, existence of a second substrate-binding site centered at Trp171 has been, reported, by us which is different from the "classical heme edge" site, found in other peroxidases. Here, we report evidence for a radical, formation at Trp171 using spin trapping, which supports the concept of, Trp171 being a redox active amino acid and being involved in the oxidation, of veratryl alcohol. On the basis of our current model, an electron, pathway from Trp171 to the heme is envisaged, relevant for the oxidation, of veratryl alcohol and possibly lignin. Beside the opening leading to the, heme edge, which can accommodate small aromatic substrate molecules, a, smaller channel giving access to the distal heme pocket was identified, that is large enough for molecules such as hydrogen peroxide. Furthermore, it was found that in LiP the bond between the heme iron and the Nepsilon2, atom of the proximal histidine residue is significantly longer than in, cytochrome c peroxidase (CcP). The weaker Fe-N bond in LiP renders the, heme more electron deficient and destabilizes high oxidation states, which, could explain the higher redox potential of LiP as compared to CcP.
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<StructureSection load='1qpa' size='340' side='right'caption='[[1qpa]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1qpa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Phanerodontia_chrysosporium Phanerodontia chrysosporium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QPA 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HTR:BETA-HYDROXYTRYPTOPHANE'>HTR</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1qpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qpa OCA], [https://pdbe.org/1qpa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qpa RCSB], [https://www.ebi.ac.uk/pdbsum/1qpa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qpa ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/LIG4_PHACH LIG4_PHACH] Depolymerization of lignin. Catalyzes the C(alpha)-C(beta) cleavage of the propyl side chains of lignin.
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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/qp/1qpa_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=1qpa 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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1QPA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Basidiomycete_phanerochaete_chrysosporium Basidiomycete phanerochaete chrysosporium] with NAG, MAN, CA and HEM as [http://en.wikipedia.org/wiki/ligands ligands]. Structure known Active Site: HE3. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QPA OCA].
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*[[Beta-N-acetylhexosaminidase 3D structures|Beta-N-acetylhexosaminidase 3D structures]]
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*[[Lignin peroxidase|Lignin peroxidase]]
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==Reference==
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__TOC__
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The crystal structure of lignin peroxidase at 1.70 A resolution reveals a hydroxy group on the cbeta of tryptophan 171: a novel radical site formed during the redox cycle., Choinowski T, Blodig W, Winterhalter KH, Piontek K, J Mol Biol. 1999 Feb 26;286(3):809-27. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10024453 10024453]
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</StructureSection>
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[[Category: Basidiomycete phanerochaete chrysosporium]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Phanerodontia chrysosporium]]
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[[Category: Choinowski, T.H.]]
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[[Category: Choinowski TH]]
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[[Category: Piontek, K.]]
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[[Category: Piontek K]]
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[[Category: CA]]
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[[Category: HEM]]
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[[Category: MAN]]
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[[Category: NAG]]
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[[Category: glycoprotein]]
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[[Category: heme]]
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[[Category: lignin degradation]]
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[[Category: oxidoreductase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 12:53:40 2007''
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Current revision

LIGNIN PEROXIDASE ISOZYME LIP4.65 (PI 4.65)

PDB ID 1qpa

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