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| | ==Crystal structure of Glycine Oxidase G51S/A54R/H244A mutant in complex with inhibitor glycolate== | | ==Crystal structure of Glycine Oxidase G51S/A54R/H244A mutant in complex with inhibitor glycolate== |
| - | <StructureSection load='3if9' size='340' side='right' caption='[[3if9]], [[Resolution|resolution]] 2.60Å' scene=''> | + | <StructureSection load='3if9' size='340' side='right'caption='[[3if9]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3if9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IF9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IF9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3if9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IF9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IF9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOA:GLYCOLIC+ACID'>GOA</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]] 2.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ryi|1ryi]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOA:GLYCOLIC+ACID'>GOA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">goxB, yjbR, BSU11670 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=3if9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3if9 OCA], [https://pdbe.org/3if9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3if9 RCSB], [https://www.ebi.ac.uk/pdbsum/3if9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3if9 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_oxidase Glycine oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.19 1.4.3.19] </span></td></tr>
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| - | <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=3if9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3if9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3if9 RCSB], [http://www.ebi.ac.uk/pdbsum/3if9 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/GLYOX_BACSU GLYOX_BACSU] Catalyzes the FAD-dependent oxidative deamination of various amines and D-amino acids to yield the corresponding alpha-keto acids, ammonia/amine, and hydrogen peroxide. Oxidizes sarcosine (N-methylglycine), N-ethylglycine and glycine (PubMed:9827558, PubMed:11744710, PubMed:19864430). Can also oxidize the herbicide glyphosate (N-phosphonomethylglycine) (PubMed:19864430). Displays lower activities on D-alanine, D-valine, D-proline and D-methionine (PubMed:9827558, PubMed:11744710). Does not act on L-amino acids and other D-amino acids (PubMed:9827558). Is essential for thiamine biosynthesis since the oxidation of glycine catalyzed by ThiO generates the glycine imine intermediate (dehydroglycine) required for the biosynthesis of the thiazole ring of thiamine pyrophosphate (PubMed:12627963).<ref>PMID:11744710</ref> <ref>PMID:12627963</ref> <ref>PMID:19864430</ref> <ref>PMID:9827558</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/if/3if9_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/if/3if9_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </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/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </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=3if9 ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3if9" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Bacillus subtilis]] | | [[Category: Bacillus subtilis]] |
| - | [[Category: Glycine oxidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Molla, G]] | + | [[Category: Molla G]] |
| - | [[Category: Moschetti, T]] | + | [[Category: Moschetti T]] |
| - | [[Category: Pedotti, M]] | + | [[Category: Pedotti M]] |
| - | [[Category: Pollegioni, L]] | + | [[Category: Pollegioni L]] |
| - | [[Category: Rosini, E]] | + | [[Category: Rosini E]] |
| - | [[Category: Savino, C]] | + | [[Category: Savino C]] |
| - | [[Category: Vallone, B]] | + | [[Category: Vallone B]] |
| - | [[Category: Fad]]
| + | |
| - | [[Category: Flavoprotein]]
| + | |
| - | [[Category: G51s/a54r/h244a]]
| + | |
| - | [[Category: Glycolate]]
| + | |
| - | [[Category: Go structure]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
GLYOX_BACSU Catalyzes the FAD-dependent oxidative deamination of various amines and D-amino acids to yield the corresponding alpha-keto acids, ammonia/amine, and hydrogen peroxide. Oxidizes sarcosine (N-methylglycine), N-ethylglycine and glycine (PubMed:9827558, PubMed:11744710, PubMed:19864430). Can also oxidize the herbicide glyphosate (N-phosphonomethylglycine) (PubMed:19864430). Displays lower activities on D-alanine, D-valine, D-proline and D-methionine (PubMed:9827558, PubMed:11744710). Does not act on L-amino acids and other D-amino acids (PubMed:9827558). Is essential for thiamine biosynthesis since the oxidation of glycine catalyzed by ThiO generates the glycine imine intermediate (dehydroglycine) required for the biosynthesis of the thiazole ring of thiamine pyrophosphate (PubMed:12627963).[1] [2] [3] [4]
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
Glycine oxidase from Bacillus subtilis is a homotetrameric flavoprotein of great potential biotechnological use because it catalyzes the oxidative deamination of various amines and d-isomer of amino acids to yield the corresponding alpha-keto acids, ammonia/amine, and hydrogen peroxide. Glyphosate (N-phosphonomethylglycine), a broad spectrum herbicide, is an interesting synthetic amino acid: this compound inhibits 5-enolpyruvylshikimate-3-phosphate synthase in the shikimate pathway, which is essential for the biosynthesis of aromatic amino acids in plants and certain bacteria. In recent years, transgenic crops resistant to glyphosate were mainly generated by overproducing the plant enzyme or by introducing a 5-enolpyruvylshikimate-3-phosphate synthase insensitive to this herbicide. In this work, we propose that the enzymatic oxidation of glyphosate could be an effective alternative to this important biotechnological process. To reach this goal, we used a rational design approach (together with site saturation mutagenesis) to generate a glycine oxidase variant more active on glyphosate than on the physiological substrate glycine. The glycine oxidase containing three point mutations (G51S/A54R/H244A) reaches an up to a 210-fold increase in catalytic efficiency and a 15,000-fold increase in the specificity constant (the k(cat)/K(m) ratio between glyphosate and glycine) as compared with wild-type glycine oxidase. The inspection of its three-dimensional structure shows that the alpha2-alpha3 loop (comprising residues 50-60 and containing two of the mutated residues) assumes a novel conformation and that the newly introduced residue Arg(54) could be the key residue in stabilizing glyphosate binding and destabilizing glycine positioning in the binding site, thus increasing efficiency on the herbicide.
Glyphosate resistance by engineering the flavoenzyme glycine oxidase.,Pedotti M, Rosini E, Molla G, Moschetti T, Savino C, Vallone B, Pollegioni L J Biol Chem. 2009 Dec 25;284(52):36415-23. Epub 2009 Oct 28. PMID:19864430[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Job V, Marcone GL, Pilone MS, Pollegioni L. Glycine oxidase from Bacillus subtilis. Characterization of a new flavoprotein. J Biol Chem. 2002 Mar 1;277(9):6985-93. PMID:11744710 doi:10.1074/jbc.M111095200
- ↑ Settembre EC, Dorrestein PC, Park JH, Augustine AM, Begley TP, Ealick SE. Structural and mechanistic studies on ThiO, a glycine oxidase essential for thiamin biosynthesis in Bacillus subtilis. Biochemistry. 2003 Mar 18;42(10):2971-81. PMID:12627963 doi:10.1021/bi026916v
- ↑ Pedotti M, Rosini E, Molla G, Moschetti T, Savino C, Vallone B, Pollegioni L. Glyphosate resistance by engineering the flavoenzyme glycine oxidase. J Biol Chem. 2009 Dec 25;284(52):36415-23. Epub 2009 Oct 28. PMID:19864430 doi:http://dx.doi.org/10.1074/jbc.M109.051631
- ↑ Nishiya Y, Imanaka T. Purification and characterization of a novel glycine oxidase from Bacillus subtilis. FEBS Lett. 1998 Nov 6;438(3):263-6. PMID:9827558
- ↑ Pedotti M, Rosini E, Molla G, Moschetti T, Savino C, Vallone B, Pollegioni L. Glyphosate resistance by engineering the flavoenzyme glycine oxidase. J Biol Chem. 2009 Dec 25;284(52):36415-23. Epub 2009 Oct 28. PMID:19864430 doi:http://dx.doi.org/10.1074/jbc.M109.051631
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