|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Melanocarpus albomyces laccase crystal soaked (4 sec) with 2,6-dimethoxyphenol== | | ==Melanocarpus albomyces laccase crystal soaked (4 sec) with 2,6-dimethoxyphenol== |
| - | <StructureSection load='3fu7' size='340' side='right' caption='[[3fu7]], [[Resolution|resolution]] 1.67Å' scene=''> | + | <StructureSection load='3fu7' size='340' side='right'caption='[[3fu7]], [[Resolution|resolution]] 1.67Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3fu7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_16460 Atcc 16460]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FU7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FU7 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3fu7]] 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=3FU7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FU7 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DM:2,6-DIMETHOXYPHENOL'>3DM</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=D2M:4-(2,6-DIMETHOXYPHENOXY)-2,6-DIMETHOXYPHENOL'>D2M</scene>, <scene name='pdbligand=KIA:2,6-DIMETHOXYCYCLOHEXA-2,5-DIENE-1,4-DIONE'>KIA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.67Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OHI:3-(2-OXO-2H-IMIDAZOL-4-YL)-L-ALANINE'>OHI</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DM:2,6-DIMETHOXYPHENOL'>3DM</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=D2M:4-(2,6-DIMETHOXYPHENOXY)-2,6-DIMETHOXYPHENOL'>D2M</scene>, <scene name='pdbligand=KIA:2,6-DIMETHOXYCYCLOHEXA-2,5-DIENE-1,4-DIONE'>KIA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OHI:3-(2-OXO-2H-IMIDAZOL-4-YL)-L-ALANINE'>OHI</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2q9o|2q9o]], [[3fu8|3fu8]], [[3fu9|3fu9]]</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=3fu7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fu7 OCA], [https://pdbe.org/3fu7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fu7 RCSB], [https://www.ebi.ac.uk/pdbsum/3fu7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fu7 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LAC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=204285 ATCC 16460])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fu7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fu7 OCA], [http://pdbe.org/3fu7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fu7 RCSB], [http://www.ebi.ac.uk/pdbsum/3fu7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fu7 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/LAC1_MELAO LAC1_MELAO]] Lignin degradation and detoxification of lignin-derived products (Probable).<ref>PMID:15474046</ref> | + | [https://www.uniprot.org/uniprot/LAC1_MELAO LAC1_MELAO] Lignin degradation and detoxification of lignin-derived products (Probable).<ref>PMID:15474046</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 32: |
Line 29: |
| | </div> | | </div> |
| | <div class="pdbe-citations 3fu7" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 3fu7" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Laccase 3D structures|Laccase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 16460]] | + | [[Category: Large Structures]] |
| - | [[Category: Laccase]] | + | [[Category: Melanocarpus albomyces]] |
| - | [[Category: Hakulinen, N]] | + | [[Category: Hakulinen N]] |
| - | [[Category: Kallio, J P]] | + | [[Category: Kallio JP]] |
| - | [[Category: Rouvinen, J]] | + | [[Category: Rouvinen J]] |
| - | [[Category: 6-dimethoxyphenol]]
| + | |
| - | [[Category: Complex structure]]
| + | |
| - | [[Category: Glycoprotein]]
| + | |
| - | [[Category: Lignin degradation]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Multicopper oxidase]]
| + | |
| - | [[Category: Oxidation of phenolic compound]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
3fu7 is a 2 chain structure with sequence from Melanocarpus albomyces. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.67Å |
| Ligands: | , , , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
LAC1_MELAO Lignin degradation and detoxification of lignin-derived products (Probable).[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Melanocarpus albomyces laccase crystals were soaked with 2,6-dimethoxyphenol, a common laccase substrate. Three complex structures from different soaking times were solved. Crystal structures revealed the binding of the original substrate and adducts formed by enzymatic oxidation of the substrate. The dimeric oxidation products were identified by mass spectrometry. In the crystals, a 2,6-dimethoxy-p-benzoquinone and a C-O dimer were observed, whereas a C-C dimer was the main product identified by mass spectrometry. Crystal structures demonstrated that the substrate and/or its oxidation products were bound in the pocket formed by residues Ala191, Pro192, Glu235, Leu363, Phe371, Trp373, Phe427, Leu429, Trp507 and His508. Substrate and adducts were hydrogen-bonded to His508, one of the ligands of type 1 copper. Therefore, this surface-exposed histidine most likely has a role in electron transfer by laccases. Based on our mutagenesis studies, the carboxylic acid residue Glu235 at the bottom of the binding site pocket is also crucial in the oxidation of phenolics. Glu235 may be responsible for the abstraction of a proton from the OH group of the substrate and His508 may extract an electron. In addition, crystal structures revealed a secondary binding site formed through weak dimerization in M. albomyces laccase molecules. This binding site most likely exists only in crystals, when the Phe427 residues are packed against each other.
Structure-function studies of a Melanocarpus albomyces laccase suggest a pathway for oxidation of phenolic compounds.,Kallio JP, Auer S, Janis J, Andberg M, Kruus K, Rouvinen J, Koivula A, Hakulinen N J Mol Biol. 2009 Oct 2;392(4):895-909. Epub 2009 Jun 27. PMID:19563811[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kiiskinen LL, Palonen H, Linder M, Viikari L, Kruus K. Laccase from Melanocarpus albomyces binds effectively to cellulose. FEBS Lett. 2004 Oct 8;576(1-2):251-5. PMID:15474046 doi:S0014579304010440
- ↑ Kallio JP, Auer S, Janis J, Andberg M, Kruus K, Rouvinen J, Koivula A, Hakulinen N. Structure-function studies of a Melanocarpus albomyces laccase suggest a pathway for oxidation of phenolic compounds. J Mol Biol. 2009 Oct 2;392(4):895-909. Epub 2009 Jun 27. PMID:19563811 doi:10.1016/j.jmb.2009.06.053
|
