2q9o: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2q9o.jpg|left|200px]]
- {{Structure
+==Near-atomic resolution structure of a Melanocarpus albomyces laccase==
-|PDB= 2q9o |SIZE=350|CAPTION= <scene name='initialview01'>2q9o</scene>, resolution 1.30&Aring;
+<StructureSection load='2q9o' size='340' side='right'caption='[[2q9o]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Nag+Binding+Site+For+Residue+A+1001'>AC1</scene>, <scene name='pdbsite=AC2:Nag+Binding+Site+For+Residue+C+11'>AC2</scene>, <scene name='pdbsite=AC3:Nag+Binding+Site+For+Residue+C+12'>AC3</scene>, <scene name='pdbsite=AC4:Nag+Binding+Site+For+Residue+D+21'>AC4</scene>, <scene name='pdbsite=AC5:Nag+Binding+Site+For+Residue+D+22'>AC5</scene>, <scene name='pdbsite=AC6:Nag+Binding+Site+For+Residue+E+31'>AC6</scene>, <scene name='pdbsite=AC7:Nag+Binding+Site+For+Residue+E+32'>AC7</scene>, <scene name='pdbsite=AC8:Man+Binding+Site+For+Residue+E+33'>AC8</scene>, <scene name='pdbsite=AC9:Nag+Binding+Site+For+Residue+A+1002'>AC9</scene>, <scene name='pdbsite=BC1:Nag+Binding+Site+For+Residue+A+1003'>BC1</scene>, <scene name='pdbsite=BC2:Nag+Binding+Site+For+Residue+A+1051'>BC2</scene>, <scene name='pdbsite=BC3:Nag+Binding+Site+For+Residue+G+61'>BC3</scene>, <scene name='pdbsite=BC4:Nag+Binding+Site+For+Residue+G+62'>BC4</scene>, <scene name='pdbsite=BC5:Man+Binding+Site+For+Residue+G+63'>BC5</scene>, <scene name='pdbsite=BC6:Man+Binding+Site+For+Residue+G+64'>BC6</scene>, <scene name='pdbsite=BC7:Man+Binding+Site+For+Residue+G+65'>BC7</scene>, <scene name='pdbsite=BC8:Nag+Binding+Site+For+Residue+A+1071'>BC8</scene>, <scene name='pdbsite=BC9:Nag+Binding+Site+For+Residue+B+1001'>BC9</scene>, <scene name='pdbsite=CC1:Nag+Binding+Site+For+Residue+H+1011'>CC1</scene>, <scene name='pdbsite=CC2:Nag+Binding+Site+For+Residue+H+1012'>CC2</scene>, <scene name='pdbsite=CC3:Man+Binding+Site+For+Residue+H+1013'>CC3</scene>, <scene name='pdbsite=CC4:Nag+Binding+Site+For+Residue+I+1021'>CC4</scene>, <scene name='pdbsite=CC5:Nag+Binding+Site+For+Residue+I+1022'>CC5</scene>, <scene name='pdbsite=CC6:Nag+Binding+Site+For+Residue+J+1031'>CC6</scene>, <scene name='pdbsite=CC7:Nag+Binding+Site+For+Residue+J+1032'>CC7</scene>, <scene name='pdbsite=CC8:Nag+Binding+Site+For+Residue+K+1041'>CC8</scene>, <scene name='pdbsite=CC9:Nag+Binding+Site+For+Residue+K+1042'>CC9</scene>, <scene name='pdbsite=DC1:Nag+Binding+Site+For+Residue+B+1051'>DC1</scene>, <scene name='pdbsite=DC2:Nag+Binding+Site+For+Residue+L+1061'>DC2</scene>, <scene name='pdbsite=DC3:Nag+Binding+Site+For+Residue+L+1062'>DC3</scene>, <scene name='pdbsite=DC4:Man+Binding+Site+For+Residue+L+1063'>DC4</scene>, <scene name='pdbsite=DC5:Man+Binding+Site+For+Residue+L+1064'>DC5</scene>, <scene name='pdbsite=DC6:Man+Binding+Site+For+Residue+L+1065'>DC6</scene>, <scene name='pdbsite=DC7:Cu+Binding+Site+For+Residue+A+2001'>DC7</scene>, <scene name='pdbsite=DC8:Cu+Binding+Site+For+Residue+A+2002'>DC8</scene>, <scene name='pdbsite=DC9:Cu+Binding+Site+For+Residue+A+2003'>DC9</scene>, <scene name='pdbsite=EC1:Cu+Binding+Site+For+Residue+A+2004'>EC1</scene>, <scene name='pdbsite=EC2:Cl+Binding+Site+For+Residue+A+2010'>EC2</scene>, <scene name='pdbsite=EC3:Cu+Binding+Site+For+Residue+B+2001'>EC3</scene>, <scene name='pdbsite=EC4:Cu+Binding+Site+For+Residue+B+2002'>EC4</scene>, <scene name='pdbsite=EC5:Cu+Binding+Site+For+Residue+B+2003'>EC5</scene>, <scene name='pdbsite=EC6:Cu+Binding+Site+For+Residue+B+2004'>EC6</scene>, <scene name='pdbsite=EC7:Cl+Binding+Site+For+Residue+B+2010'>EC7</scene>, <scene name='pdbsite=EC8:So4+Binding+Site+For+Residue+A+4001'>EC8</scene>, <scene name='pdbsite=EC9:So4+Binding+Site+For+Residue+B+4002'>EC9</scene>, <scene name='pdbsite=FC1:So4+Binding+Site+For+Residue+A+4003'>FC1</scene>, <scene name='pdbsite=FC2:So4+Binding+Site+For+Residue+B+4004'>FC2</scene>, <scene name='pdbsite=FC3:So4+Binding+Site+For+Residue+A+4005'>FC3</scene>, <scene name='pdbsite=FC4:Oxy+Binding+Site+For+Residue+A+4006'>FC4</scene>, <scene name='pdbsite=FC5:Oxy+Binding+Site+For+Residue+B+4005'>FC5</scene>, <scene name='pdbsite=FC6:Gol+Binding+Site+For+Residue+A+3001'>FC6</scene> and <scene name='pdbsite=FC7:Gol+Binding+Site+For+Residue+B+3002'>FC7</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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>
+<table><tr><td colspan='2'>[[2q9o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_16460 Atcc 16460]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q9O FirstGlance]. <br>
-|ACTIVITY= <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
-|GENE= LAC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=204285 Melanocarpus albomyces])
+<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>
-|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00394 Cu-oxidase], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam07732 Cu-oxidase_3], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam07731 Cu-oxidase_2]</span>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1gw0|1gw0]], [[2ih8|2ih8]], [[2ih9|2ih9]]</div></td></tr>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q9o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9o OCA], [http://www.ebi.ac.uk/pdbsum/2q9o PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2q9o RCSB]</span>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LAC1 ([https://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'>[https://en.wikipedia.org/wiki/Laccase Laccase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=2q9o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9o OCA], [https://pdbe.org/2q9o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q9o RCSB], [https://www.ebi.ac.uk/pdbsum/2q9o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q9o ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/LAC1_MELAO LAC1_MELAO]] Lignin degradation and detoxification of lignin-derived products (Probable).<ref>PMID:15474046</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q9/2q9o_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2q9o ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have solved a crystal structure from Melanocarpus albomyces laccase expressed in the filamentous fungus Trichoderma reesei (rMaL) at 1.3A resolution by using synchrotron radiation at 100K. At the moment, this is the highest resolution that has been attained for any multicopper oxidase. The present structure confirmed our earlier proposal regarding the dynamic behaviour of the copper cluster. Thermal ellipsoids of copper atoms indicated movements of trinuclear site coppers. The direction of the type-3 copper motion was perpendicular to the type-2 copper. In addition, the structure at 1.3A resolution allowed us to describe important solvent cavities of the enzyme and the structure is also compared with other known multicopper oxidases. T2 and T3 solvent cavities, and a putative SDS-gate, formed by Ser142, Ser510 and the C-terminal Asp556 of rMaL, are described. We also observed a 2-oxohistidine, an oxidized histidine, possibly caused by a metal-catalysed oxidation by the trinuclear site coppers. To our knowledge, this is the first time that 2-oxohistidine has been observed in a protein crystal structure.
-'''Near-atomic resolution structure of a Melanocarpus albomyces laccase'''
+A near atomic resolution structure of a Melanocarpus albomyces laccase.,Hakulinen N, Andberg M, Kallio J, Koivula A, Kruus K, Rouvinen J J Struct Biol. 2008 Apr;162(1):29-39. Epub 2007 Dec 28. PMID:18249560<ref>PMID:18249560</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2q9o" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-We have solved a crystal structure from Melanocarpus albomyces laccase expressed in the filamentous fungus Trichoderma reesei (rMaL) at 1.3A resolution by using synchrotron radiation at 100K. At the moment, this is the highest resolution that has been attained for any multicopper oxidase. The present structure confirmed our earlier proposal regarding the dynamic behaviour of the copper cluster. Thermal ellipsoids of copper atoms indicated movements of trinuclear site coppers. The direction of the type-3 copper motion was perpendicular to the type-2 copper. In addition, the structure at 1.3A resolution allowed us to describe important solvent cavities of the enzyme and the structure is also compared with other known multicopper oxidases. T2 and T3 solvent cavities, and a putative SDS-gate, formed by Ser142, Ser510 and the C-terminal Asp556 of rMaL, are described. We also observed a 2-oxohistidine, an oxidized histidine, possibly caused by a metal-catalysed oxidation by the trinuclear site coppers. To our knowledge, this is the first time that 2-oxohistidine has been observed in a protein crystal structure.
+*[[Laccase 3D structures|Laccase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-Q9O is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Melanocarpus_albomyces Melanocarpus albomyces]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9O OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Atcc 16460]]
-A near atomic resolution structure of a Melanocarpus albomyces laccase., Hakulinen N, Andberg M, Kallio J, Koivula A, Kruus K, Rouvinen J, J Struct Biol. 2007 Dec 28;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18249560 18249560]
 [[Category: Laccase]]
-[[Category: Melanocarpus albomyces]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Hakulinen, N]]
-[[Category: Hakulinen, N.]]
+[[Category: Rouvinen, J]]
-[[Category: Rouvinen, J.]]
 [[Category: 2-oxohistidine]]
-[[Category: laccase]]
+[[Category: Melanocarpus albomyce]]
-[[Category: melanocarpus albomyce]]
+[[Category: Multicopper oxidase]]
-[[Category: multicopper oxidase]]
+[[Category: Oxidoreductase]]
-[[Category: oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 09:52:35 2008''