3dkh: Difference between revisions

← Older edit

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

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3dkh.png|left|200px]]
-<!--
+==L559A mutant of Melanocarpus albomyces laccase==
-The line below this paragraph, containing "STRUCTURE_3dkh", creates the "Structure Box" on the page.
+<StructureSection load='3dkh' size='340' side='right'caption='[[3dkh]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3dkh]] 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=3DKH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DKH FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
--->
+<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=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=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3dkh|  PDB=3dkh  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dkh OCA], [https://pdbe.org/3dkh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dkh RCSB], [https://www.ebi.ac.uk/pdbsum/3dkh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dkh 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/dk/3dkh_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=3dkh ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The C-terminus of the fungal laccase from Melanocarpus albomyces (MaL) is processed during secretion at a processing site conserved among the ascomycete laccases. The three-dimensional structure of MaL has been solved as one of the first complete laccase structures. According to the crystal structure of MaL, the four C-terminal amino acids of the mature protein penetrate into a tunnel leading towards the trinuclear site. The C-terminal carboxylate group forms a hydrogen bond with a side chain of His140, which also coordinates to the type 3 copper. In order to analyze the role of the processed C-terminus, site-directed mutagenesis of the MaL cDNA was performed, and the mutated proteins were expressed in Trichoderma reesei and Saccharomyces cerevisiae. Changes in the C-terminus of MaL caused major defects in protein production in both expression hosts. The deletion of the last four amino acids dramatically affected the activity of the enzyme, as the deletion mutant delDSGL(559) was practically inactive. Detailed characterization of the purified L559A mutant expressed in S. cerevisiae showed the importance of the C-terminal plug for laccase activity, stability, and kinetics. Moreover, the crystal structure of the L559A mutant expressed in S. cerevisiae showed that the C-terminal mutation had clearly affected the trinuclear site geometry. The results in this study clearly confirm the critical role of the last amino acids in the C-terminus of MaL.
-===L559A mutant of Melanocarpus albomyces laccase===
+Essential role of the C-terminus in Melanocarpus albomyces laccase for enzyme production, catalytic properties and structure.,Andberg M, Hakulinen N, Auer S, Saloheimo M, Koivula A, Rouvinen J, Kruus K FEBS J. 2009 Nov;276(21):6285-300. Epub 2009 Sep 24. PMID:19780817<ref>PMID:19780817</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3dkh" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19780817}}, adds the Publication Abstract to the page
+*[[Laccase 3D structures|Laccase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19780817 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19780817}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-DKH is a 2 chains structure with sequences 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=3DKH OCA].
-==Reference==
-<ref group="xtra">PMID:19780817</ref><references group="xtra"/>
-[[Category: Laccase]]
 [[Category: Melanocarpus albomyces]]
-[[Category: Hakulinen, N.]]
+[[Category: Hakulinen N]]
-[[Category: Rouvinen, J.]]
+[[Category: Rouvinen J]]
-[[Category: Ascomycete]]
-[[Category: C-terminal mutant]]
-[[Category: Glycoprotein]]
-[[Category: Laccase]]
-[[Category: Lignin degradation]]
-[[Category: Metal-binding]]
-[[Category: Multicopper oxidase]]
-[[Category: Oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec  8 11:13:44 2010''