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| | <StructureSection load='4cag' size='340' side='right'caption='[[4cag]], [[Resolution|resolution]] 2.50Å' scene=''> | | <StructureSection load='4cag' size='340' side='right'caption='[[4cag]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4cag]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"clostridium_licheniforme"_weigmann_1898 "clostridium licheniforme" weigmann 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CAG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CAG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4cag]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CAG FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.498Å</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=4cag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cag OCA], [http://pdbe.org/4cag PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4cag RCSB], [http://www.ebi.ac.uk/pdbsum/4cag PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4cag ProSAT]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=4cag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cag OCA], [https://pdbe.org/4cag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cag RCSB], [https://www.ebi.ac.uk/pdbsum/4cag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cag ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q65KY4_BACLD Q65KY4_BACLD] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Clostridium licheniforme weigmann 1898]] | + | [[Category: Bacillus licheniformis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Jers, C]] | + | [[Category: Jers C]] |
| - | [[Category: Larsen, D M]] | + | [[Category: Larsen DM]] |
| - | [[Category: Larsen, S]] | + | [[Category: Larsen S]] |
| - | [[Category: Mikkelsen, J D]] | + | [[Category: Mikkelsen JD]] |
| - | [[Category: Nyffenegger, C]] | + | [[Category: Nyffenegger C]] |
| - | [[Category: Otten, H]] | + | [[Category: Otten H]] |
| - | [[Category: Silva, I I.C Rodrigues da]] | + | [[Category: Rodrigues da Silva IIC]] |
| - | [[Category: Beta-propeller]]
| + | |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
Function
Q65KY4_BACLD
Publication Abstract from PubMed
Rhamnogalacturonan I lyases (RGI lyases) (EC 4.2.2.-) catalyze cleavage of alpha-1,4 bonds between rhamnose and galacturonic acid in the backbone of pectins by beta-elimination. In the present study, targeted improvement of the thermostability of a PL family 11 RGI lyase from Bacillus licheniformis (DSM 13/ATCC14580) was examined by using a combinatorial protein engineering approach exploring additive effects of single amino acid substitutions. These were selected by using a consensus approach together with assessing protein stability changes (PoPMuSiC) and B-factor iterative test (B-FIT). The second-generation mutants involved combinations of two to seven individually favorable single mutations. Thermal stability was examined as half-life at 60 degrees C and by recording of thermal transitions by circular dichroism. Surprisingly, the biggest increment in thermal stability was achieved by producing the wild-type RGI lyase in Bacillus subtilis as opposed to in Pichia pastoris; this effect is suggested to be a negative result of glycosylation of the P. pastoris expressed enzyme. A ~ twofold improvement in thermal stability at 60 degrees C, accompanied by less significant increases in T m of the enzyme mutants, were obtained due to additive stabilizing effects of single amino acid mutations (E434L, G55V, and G326E) compared to the wild type. The crystal structure of the B. licheniformis wild-type RGI lyase was also determined; the structural analysis corroborated that especially mutation of charged amino acids to hydrophobic ones in surface-exposed loops produced favorable thermal stability effects.
Design of thermostable rhamnogalacturonan lyase mutants from Bacillus licheniformis by combination of targeted single point mutations.,Silva IR, Jers C, Otten H, Nyffenegger C, Larsen DM, Derkx PM, Meyer AS, Mikkelsen JD, Larsen S Appl Microbiol Biotechnol. 2014 May;98(10):4521-31. doi:, 10.1007/s00253-013-5483-8. Epub 2014 Jan 14. PMID:24419797[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Silva IR, Jers C, Otten H, Nyffenegger C, Larsen DM, Derkx PM, Meyer AS, Mikkelsen JD, Larsen S. Design of thermostable rhamnogalacturonan lyase mutants from Bacillus licheniformis by combination of targeted single point mutations. Appl Microbiol Biotechnol. 2014 May;98(10):4521-31. doi:, 10.1007/s00253-013-5483-8. Epub 2014 Jan 14. PMID:24419797 doi:http://dx.doi.org/10.1007/s00253-013-5483-8
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