1llp

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(New page: 200px<br /><applet load="1llp" size="450" color="white" frame="true" align="right" spinBox="true" caption="1llp, resolution 1.70&Aring;" /> '''LIGNIN PEROXIDASE (I...)
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[[Image:1llp.jpg|left|200px]]<br /><applet load="1llp" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1llp, resolution 1.70&Aring;" />
 
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'''LIGNIN PEROXIDASE (ISOZYME H2) PI 4.15'''<br />
 
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==Overview==
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==LIGNIN PEROXIDASE (ISOZYME H2) PI 4.15==
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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='1llp' size='340' side='right'caption='[[1llp]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1llp]] is a 1 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=1LLP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LLP 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]] 1.7&#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=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</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=1llp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1llp OCA], [https://pdbe.org/1llp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1llp RCSB], [https://www.ebi.ac.uk/pdbsum/1llp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1llp ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/LIG2_PHACH LIG2_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/ll/1llp_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=1llp 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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1LLP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Phanerochaete_chrysosporium Phanerochaete chrysosporium] with NAG, MAN, A2G, CA, HYD and HEM as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LLP OCA].
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*[[Lignin peroxidase|Lignin peroxidase]]
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__TOC__
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==Reference==
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</StructureSection>
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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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[[Category: Large Structures]]
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[[Category: Phanerochaete chrysosporium]]
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[[Category: Phanerodontia chrysosporium]]
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[[Category: Single protein]]
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[[Category: Choinowski TH]]
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[[Category: Choinowski, T.H.]]
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[[Category: Glumoff T]]
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[[Category: Glumoff, T.]]
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[[Category: Piontek K]]
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[[Category: Piontek, K.]]
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[[Category: A2G]]
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[[Category: CA]]
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[[Category: HEM]]
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[[Category: HYD]]
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[[Category: MAN]]
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[[Category: NAG]]
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[[Category: glyco protein]]
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[[Category: heme protein]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:39:37 2007''
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Current revision

LIGNIN PEROXIDASE (ISOZYME H2) PI 4.15

PDB ID 1llp

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