3if9 - Revision history

OCA at 15:57, 1 November 2023

OCA — Wed, 01 Nov 2023 15:57:47 GMT

←Older revision		Revision as of 15:57, 1 November 2023
Line 3:		Line 3:
	<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 [https://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. 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>	+	<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" id="~~ligandDat~~">~~<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"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1ryi\|1ryi]]</div>~~</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 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1423~~ "~~Vibrio subtilis~~" ~~Ehrenberg 1835])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Glycine_oxidase Glycine oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.19 1.4.3.19]~~ </~~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=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='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>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~GLOX_BACSU GLOX_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. Can also oxidize the herbicide glyphosate (N-phosphonomethylglycine). Displays lower activities on D-alanine, D-valine, D-proline and D-methionine. Does not act on L-amino acids and other D-amino acids. 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.<ref>PMID:~~9827558~~</ref> <ref>PMID:12627963</ref>	+	[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]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835]]~~	+	[[Category: Bacillus subtilis]]
-	~~[[Category: Glycine oxidase~~]]	+
	[[Category: Large Structures]]		[[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~~]]	+

OCA at 07:47, 10 November 2021

OCA — Wed, 10 Nov 2021 07:47:09 GMT

←Older revision		Revision as of 07:47, 10 November 2021
Line 1:		Line 1:

	==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/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. 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/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. 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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ryi\|1ryi]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ryi\|1ryi]]</div></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 "Vibrio subtilis" Ehrenberg 1835])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">goxB, yjbR, BSU11670 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glycine_oxidase Glycine oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.19 1.4.3.19] </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=3if9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3if9 OCA], [~~http~~://pdbe.org/3if9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3if9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3if9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3if9 ProSAT]</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=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>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GLOX_BACSU GLOX_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. Can also oxidize the herbicide glyphosate (N-phosphonomethylglycine). Displays lower activities on D-alanine, D-valine, D-proline and D-methionine. Does not act on L-amino acids and other D-amino acids. 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.<ref>PMID:9827558</ref> <ref>PMID:12627963</ref>	+	[[https://www.uniprot.org/uniprot/GLOX_BACSU GLOX_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. Can also oxidize the herbicide glyphosate (N-phosphonomethylglycine). Displays lower activities on D-alanine, D-valine, D-proline and D-methionine. Does not act on L-amino acids and other D-amino acids. 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.<ref>PMID:9827558</ref> <ref>PMID:12627963</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 37:
	[[Category: Vibrio subtilis ehrenberg 1835]]		[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: Glycine oxidase]]		[[Category: Glycine oxidase]]
		+	[[Category: Large Structures]]
	[[Category: Molla, G]]		[[Category: Molla, G]]
	[[Category: Moschetti, T]]		[[Category: Moschetti, T]]

OCA at 09:35, 19 December 2018

OCA — Wed, 19 Dec 2018 09:35:31 GMT

←Older revision		Revision as of 09:35, 19 December 2018
Line 1:		Line 1:
		+
	==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_globigii~~"~~_migula_1900~~ "~~bacillus globigii~~" ~~migula 1900~~]. 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 [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. 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>
	</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='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>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ryi\|1ryi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ryi\|1ryi]]</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 globigii~~" ~~Migula 1900~~])</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 "Vibrio subtilis" Ehrenberg 1835])</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>		<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>
-	<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://pdbe.org/3if9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3if9 RCSB], [http://www.ebi.ac.uk/pdbsum/3if9 PDBsum]</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=3if9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3if9 OCA], [http://pdbe.org/3if9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3if9 RCSB], [http://www.ebi.ac.uk/pdbsum/3if9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3if9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	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>
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus globigii migula 1900~~]]	+	[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: Glycine oxidase]]		[[Category: Glycine oxidase]]
	[[Category: Molla, G]]		[[Category: Molla, G]]

OCA at 23:37, 9 February 2016

OCA — Tue, 09 Feb 2016 23:37:14 GMT

←Older revision		Revision as of 23:37, 9 February 2016
Line 2:		Line 2:
	<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 [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. 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>
	</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='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>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ryi\|1ryi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ryi\|1ryi]]</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='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 globigii" Migula 1900])</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>		<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>
-	<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>	+	<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://pdbe.org/3if9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3if9 RCSB], [http://www.ebi.ac.uk/pdbsum/3if9 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<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;">
Line 29:		Line 29:
	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/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Glycine oxidase]]		[[Category: Glycine oxidase]]
	[[Category: Molla, G]]		[[Category: Molla, G]]

OCA at 10:17, 25 December 2014

OCA — Thu, 25 Dec 2014 10:17:42 GMT

←Older revision		Revision as of 10:17, 25 December 2014
Line 9:		Line 9:
	<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>		<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 ==
		+	[[http://www.uniprot.org/uniprot/GLOX_BACSU GLOX_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. Can also oxidize the herbicide glyphosate (N-phosphonomethylglycine). Displays lower activities on D-alanine, D-valine, D-proline and D-methionine. Does not act on L-amino acids and other D-amino acids. 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.<ref>PMID:9827558</ref> <ref>PMID:12627963</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:02, 8 December 2014

OCA — Mon, 08 Dec 2014 09:02:09 GMT

←Older revision		Revision as of 09:02, 8 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3if9.~~png~~\|~~left~~\|200px]]	+	==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=''>
		+	== 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>
		+	</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>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ryi\|1ryi]]</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='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>
		+	<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>
		+	== 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/if/3if9_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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== 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.

-	~~{{STRUCTURE_3if9\| PDB=3if9 \| SCENE= }}~~	+	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<ref>PMID:19864430</ref>

-	~~===Crystal structure~~ of ~~Glycine Oxidase G51S~~/~~A54R/H244A mutant in complex with inhibitor glycolate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19864430}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[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].~~	+	</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Glycine oxidase]]		[[Category: Glycine oxidase]]
-	[[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: Fad]]
	[[Category: Flavoprotein]]		[[Category: Flavoprotein]]

OCA: Protected "3if9" [edit=sysop:move=sysop]

OCA — Wed, 02 Jan 2013 08:03:09 GMT

Protected "3if9" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:03, 2 January 2013

OCA at 08:03, 2 January 2013

OCA — Wed, 02 Jan 2013 08:03:07 GMT

←Older revision		Revision as of 08:03, 2 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3if9.png\|left\|200px]]		[[Image:3if9.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3if9", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3if9\| PDB=3if9 \| SCENE= }}		{{STRUCTURE_3if9\| PDB=3if9 \| SCENE= }}

	===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===

		+	{{ABSTRACT_PUBMED_19864430}}

	==About this Structure==		==About this Structure==
-	~~3IF9~~ is a 4 ~~chains~~ structure with ~~sequences~~ 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].	+	[[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].
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Glycine oxidase]]		[[Category: Glycine oxidase]]
Line 24:		Line 18:
	[[Category: Savino, C.]]		[[Category: Savino, C.]]
	[[Category: Vallone, B.]]		[[Category: Vallone, B.]]
-	[[Category: Cytoplasm]]
	[[Category: Fad]]		[[Category: Fad]]
	[[Category: Flavoprotein]]		[[Category: Flavoprotein]]
Line 31:		Line 24:
	[[Category: Go structure]]		[[Category: Go structure]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 14:58:10 2010''

OCA at 12:58, 28 January 2010

OCA — Thu, 28 Jan 2010 12:58:11 GMT

←Older revision		Revision as of 12:58, 28 January 2010
Line 14:		Line 14:

	==About this Structure==		==About this Structure==
-	3IF9 is a 4 chains structure of sequences 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].	+	3IF9 is a 4 chains structure with sequences 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].
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Glycine oxidase]]		[[Category: Glycine oxidase]]
Line 32:		Line 32:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Nov 25 11~~:15:~~52 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 14:58:10 2010''

OCA at 09:15, 25 November 2009

OCA — Wed, 25 Nov 2009 09:15:53 GMT

←Older revision		Revision as of 09:15, 25 November 2009
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3if9.~~jpg~~\|left\|200px]]	+	[[Image:3if9.png\|left\|200px]]

	<!--		<!--
Line 32:		Line 32:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Oct 28 13~~:55:58 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 25 11:15:52 2009''