2ih9

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(New page: 200px<br /><applet load="2ih9" size="450" color="white" frame="true" align="right" spinBox="true" caption="2ih9, resolution 2.000&Aring;" /> '''A high-dose crystal...)
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[[Image:2ih9.gif|left|200px]]<br /><applet load="2ih9" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2ih9, resolution 2.000&Aring;" />
 
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'''A high-dose crystal structure of a recombinant Melanocarbus albomyces laccase'''<br />
 
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==Overview==
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==A high-dose crystal structure of a recombinant Melanocarbus albomyces laccase==
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Laccases (p-diphenol dioxygen oxidoreductases) belong to the family of, blue multicopper oxidases, which catalyse the four-electron reduction of, dioxygen to water concomitantly through the oxidation of substrate, molecules. Blue multicopper oxidases have four coppers, a copper (T1), forming a mononuclear site and a cluster of three coppers (T2, T3, and, T3') forming a trinuclear site. Because X-rays are known to liberate, electrons during data collection and may thus affect the oxidation state, of metals, we have investigated the effect of X-ray radiation upon the, crystal structure of a recombinant laccase from Melanocarpus albomyces, through the use of crystallography and crystal absorption spectroscopy., Two data sets with different strategies, a low and a high-dose data set, were collected at synchrotron. We have observed earlier that the, trinuclear site had an elongated electron density amidst coppers, suggesting dioxygen binding. The low-dose synchrotron structure showed, similar elongated electron density, but the high-dose X-ray radiation, removed the bulk of this density. Therefore, X-ray radiation could alter, the active site of laccase from M. albomyces. Absorption spectra of the, crystals (320, 420, and 590nm) during X-ray radiation were measured at a, home laboratory. Spectra clearly showed how that the band at 590nm had, vanished, resulting from the T1 copper being reduced, during the long, X-ray measurements. The crystal colour changed from blue to colourless., Absorptions at 320 and 420nm seemed to be rather permanent. The absorption, at 320nm is due to the T3 coppers and it is proposed that absorption at, 420nm is due to the T2 copper when dioxygen or a reaction intermediate is, close to this copper.
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<StructureSection load='2ih9' size='340' side='right'caption='[[2ih9]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2ih9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Melanocarpus_albomyces Melanocarpus albomyces]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IH9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IH9 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]] 2&#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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2ih9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ih9 OCA], [https://pdbe.org/2ih9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ih9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ih9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ih9 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/LAC1_MELAO LAC1_MELAO] Lignin degradation and detoxification of lignin-derived products (Probable).<ref>PMID:15474046</ref>
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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/ih/2ih9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2ih9 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 ==
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Laccases (p-diphenol dioxygen oxidoreductases) belong to the family of blue multicopper oxidases, which catalyse the four-electron reduction of dioxygen to water concomitantly through the oxidation of substrate molecules. Blue multicopper oxidases have four coppers, a copper (T1) forming a mononuclear site and a cluster of three coppers (T2, T3, and T3') forming a trinuclear site. Because X-rays are known to liberate electrons during data collection and may thus affect the oxidation state of metals, we have investigated the effect of X-ray radiation upon the crystal structure of a recombinant laccase from Melanocarpus albomyces through the use of crystallography and crystal absorption spectroscopy. Two data sets with different strategies, a low and a high-dose data set, were collected at synchrotron. We have observed earlier that the trinuclear site had an elongated electron density amidst coppers, suggesting dioxygen binding. The low-dose synchrotron structure showed similar elongated electron density, but the high-dose X-ray radiation removed the bulk of this density. Therefore, X-ray radiation could alter the active site of laccase from M. albomyces. Absorption spectra of the crystals (320, 420, and 590nm) during X-ray radiation were measured at a home laboratory. Spectra clearly showed how that the band at 590nm had vanished, resulting from the T1 copper being reduced, during the long X-ray measurements. The crystal colour changed from blue to colourless. Absorptions at 320 and 420nm seemed to be rather permanent. The absorption at 320nm is due to the T3 coppers and it is proposed that absorption at 420nm is due to the T2 copper when dioxygen or a reaction intermediate is close to this copper.
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==About this Structure==
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A crystallographic and spectroscopic study on the effect of X-ray radiation on the crystal structure of Melanocarpus albomyces laccase.,Hakulinen N, Kruus K, Koivula A, Rouvinen J Biochem Biophys Res Commun. 2006 Dec 1;350(4):929-34. Epub 2006 Oct 5. PMID:17045575<ref>PMID:17045575</ref>
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2IH9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Melanocarpus_albomyces Melanocarpus albomyces] with NAG, CU, CL, SO4 and 5AX as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Laccase Laccase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.2 1.10.3.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2IH9 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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A crystallographic and spectroscopic study on the effect of X-ray radiation on the crystal structure of Melanocarpus albomyces laccase., Hakulinen N, Kruus K, Koivula A, Rouvinen J, Biochem Biophys Res Commun. 2006 Dec 1;350(4):929-34. Epub 2006 Oct 5. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17045575 17045575]
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</div>
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[[Category: Laccase]]
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<div class="pdbe-citations 2ih9" style="background-color:#fffaf0;"></div>
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[[Category: Melanocarpus albomyces]]
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[[Category: Single protein]]
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[[Category: Hakulinen, N.]]
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[[Category: Rouvinen, J.]]
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[[Category: 5AX]]
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[[Category: CL]]
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[[Category: CU]]
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[[Category: NAG]]
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[[Category: SO4]]
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[[Category: laccase]]
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[[Category: multicopper oxidase]]
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[[Category: redox enzyme]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 12:19:02 2007''
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==See Also==
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*[[Laccase 3D structures|Laccase 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: Large Structures]]
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[[Category: Melanocarpus albomyces]]
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[[Category: Hakulinen N]]
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[[Category: Rouvinen J]]

Current revision

A high-dose crystal structure of a recombinant Melanocarbus albomyces laccase

PDB ID 2ih9

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