1gyl - Revision history

OCA at 07:26, 7 February 2024

OCA — Wed, 07 Feb 2024 07:26:50 GMT

←Older revision		Revision as of 07:26, 7 February 2024
Line 3:		Line 3:
	<StructureSection load='1gyl' size='340' side='right'caption='[[1gyl]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1gyl' size='340' side='right'caption='[[1gyl]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gyl]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Spiol Spiol~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1GYL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gyl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GYL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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]] 3Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>GLYCOLATE OXIDASE FROM SPINACH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~3562 SPIOL])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/(S)-2-hydroxy-acid_oxidase (S)-2-hydroxy-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.15 1.1.3.15]~~ </~~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=1gyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyl OCA], [https://pdbe.org/1gyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gyl RCSB], [https://www.ebi.ac.uk/pdbsum/1gyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gyl ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1gyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyl OCA], [~~http~~://pdbe.org/1gyl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1gyl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1gyl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1gyl ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GOX_SPIOL GOX_SPIOL]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</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=1gyl 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=1gyl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Tyr24 and Trp108 are located in the active site of spinach glycolate oxidase. To elucidate their function in substrate binding and catalysis, they were replaced by phenylalanine and serine, respectively. The [Y24F]glycolate oxidase mutant enzyme showed a tenfold higher Km value for glycolate. L-lactate and DL-2-hydroxybutyrate also showed higher Km values, however, the substrate specificity was unchanged as compared to the wild-type enzyme (Km increases in the order glycolate < DL-2-hydroxybutyrate < L-lactate < L-mandelate). The turnover number and the rate of reduction, found to be rate limiting in catalysis, were only slightly affected by the deletion of the hydroxyl group. These findings suggest that Tyr24 is mostly involved in substrate binding. The spectral features of the [Y24F]glycolate oxidase suggest that a fraction (50-80%) of the protein bears a flavin N(5) adduct instead of the oxidized cofactor. Crystals obtained from the isolated [Y24F]glycolate oxidase mutant protein allowed the determination of the three-dimensional structure. Although the structure was low resolution (0.3 nm), it is evident that the structure determined is that of the N(5) adduct species. In addition to the lacking hydroxyl group of Tyr24, we also observed movements of the amino acid side chains of Arg164 and Trp108, the latter replacing a water molecule in the substrate-binding pocket. Other features predominantly found in the class of flavoprotein oxidases, such as stabilization of the covalent N(5)-sulfite adduct and of the paraquinoid form of 8-mercapto-FMN, were found to be conserved. [W108S]Glycolate oxidase, in contrast, showed dramatic effects on both the Km of substrates as well as the turnover number. The Km for glycolate was increased some hundred fold and the turnover number was decreased 500-fold. In addition, it was found that the higher homologs of glycolate, L-lactate and DL-2-hydroxybutyrate had turnover numbers similar to those found with the wild-type enzyme, although the Km values also increased dramatically. These results indicate that Trp108 is of major importance in catalysis and that this residue is involved in determining the substrate specificity of glycolate oxidase.
-
-	Involvement of Tyr24 and Trp108 in substrate binding and substrate specificity of glycolate oxidase.,Stenberg K, Clausen T, Lindqvist Y, Macheroux P Eur J Biochem. 1995 Mar 1;228(2):408-16. PMID:7705356<ref>PMID:7705356</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1gyl" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Glycolate oxidase 3D structures\|Glycolate oxidase 3D structures]]		*[[Glycolate oxidase 3D structures\|Glycolate oxidase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Spiol~~]]	+	[[Category: Spinacia oleracea]]
-	[[Category: Lindqvist, Y]]	+	[[Category: Lindqvist Y]]
-	[[Category: Stenberg, K]]	+	[[Category: Stenberg K]]

OCA at 10:30, 18 November 2020

OCA — Wed, 18 Nov 2020 10:30:47 GMT

←Older revision		Revision as of 10:30, 18 November 2020
Line 1:		Line 1:

	==INVOLVEMENT OF TYR24 AND TRP108 IN SUBSTRATE BINDING AND SUBSTRATE SPECIFICITY OF GLYCOLATE OXIDASE==		==INVOLVEMENT OF TYR24 AND TRP108 IN SUBSTRATE BINDING AND SUBSTRATE SPECIFICITY OF GLYCOLATE OXIDASE==
-	<StructureSection load='1gyl' size='340' side='right' caption='[[1gyl]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='1gyl' size='340' side='right'caption='[[1gyl]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gyl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Spiol Spiol]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1GYL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gyl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Spiol Spiol]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1GYL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLYCOLATE OXIDASE FROM SPINACH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3562 SPIOL])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLYCOLATE OXIDASE FROM SPINACH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3562 SPIOL])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(S)-2-hydroxy-acid_oxidase (S)-2-hydroxy-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.15 1.1.3.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(S)-2-hydroxy-acid_oxidase (S)-2-hydroxy-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.15 1.1.3.15] </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=1gyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyl OCA], [http://pdbe.org/1gyl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gyl RCSB], [http://www.ebi.ac.uk/pdbsum/1gyl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gyl ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1gyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyl OCA], [http://pdbe.org/1gyl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gyl RCSB], [http://www.ebi.ac.uk/pdbsum/1gyl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gyl ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1gyl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1gyl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glycolate oxidase 3D structures\|Glycolate oxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Spiol]]		[[Category: Spiol]]
	[[Category: Lindqvist, Y]]		[[Category: Lindqvist, Y]]
	[[Category: Stenberg, K]]		[[Category: Stenberg, K]]

OCA at 06:36, 3 January 2018

OCA — Wed, 03 Jan 2018 06:36:41 GMT

←Older revision		Revision as of 06:36, 3 January 2018
Line 1:		Line 1:
		+
	==INVOLVEMENT OF TYR24 AND TRP108 IN SUBSTRATE BINDING AND SUBSTRATE SPECIFICITY OF GLYCOLATE OXIDASE==		==INVOLVEMENT OF TYR24 AND TRP108 IN SUBSTRATE BINDING AND SUBSTRATE SPECIFICITY OF GLYCOLATE OXIDASE==
	<StructureSection load='1gyl' size='340' side='right' caption='[[1gyl]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1gyl' size='340' side='right' caption='[[1gyl]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLYCOLATE OXIDASE FROM SPINACH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3562 SPIOL])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLYCOLATE OXIDASE FROM SPINACH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3562 SPIOL])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(S)-2-hydroxy-acid_oxidase (S)-2-hydroxy-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.15 1.1.3.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(S)-2-hydroxy-acid_oxidase (S)-2-hydroxy-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.15 1.1.3.15] </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=1gyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyl OCA], [http://pdbe.org/1gyl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gyl RCSB], [http://www.ebi.ac.uk/pdbsum/1gyl 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=1gyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyl OCA], [http://pdbe.org/1gyl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gyl RCSB], [http://www.ebi.ac.uk/pdbsum/1gyl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gyl ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gy/1gyl_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gy/1gyl_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 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1gyl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1gyl" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Glycolate oxidase\|Glycolate oxidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:20, 7 February 2016

OCA — Sun, 07 Feb 2016 13:20:25 GMT

←Older revision		Revision as of 13:20, 7 February 2016
Line 16:		Line 16:
	<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=1gyl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:50, 10 September 2015

OCA — Thu, 10 Sep 2015 01:50:29 GMT

←Older revision		Revision as of 01:50, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1gyl' size='340' side='right' caption='[[1gyl]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1gyl' size='340' side='right' caption='[[1gyl]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gyl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Spinacia_oleracea Spinacia oleracea~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GYL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gyl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Spiol Spiol]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GYL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLYCOLATE OXIDASE FROM SPINACH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3562 ~~Spinacia oleracea~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLYCOLATE OXIDASE FROM SPINACH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3562 SPIOL])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(S)-2-hydroxy-acid_oxidase (S)-2-hydroxy-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.15 1.1.3.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(S)-2-hydroxy-acid_oxidase (S)-2-hydroxy-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.15 1.1.3.15] </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=1gyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gyl RCSB], [http://www.ebi.ac.uk/pdbsum/1gyl 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=1gyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyl OCA], [http://pdbe.org/1gyl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gyl RCSB], [http://www.ebi.ac.uk/pdbsum/1gyl PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1gyl" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Spinacia oleracea~~]]	+	[[Category: Spiol]]
	[[Category: Lindqvist, Y]]		[[Category: Lindqvist, Y]]
	[[Category: Stenberg, K]]		[[Category: Stenberg, K]]

OCA at 23:00, 22 December 2014

OCA — Mon, 22 Dec 2014 23:00:12 GMT

←Older revision		Revision as of 23:00, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gyl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GYL FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gyl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GYL FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLYCOLATE OXIDASE FROM SPINACH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3562 Spinacia oleracea])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLYCOLATE OXIDASE FROM SPINACH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3562 Spinacia oleracea])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(S)-2-hydroxy-acid_oxidase (S)-2-hydroxy-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.15 1.1.3.15] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(S)-2-hydroxy-acid_oxidase (S)-2-hydroxy-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.15 1.1.3.15] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gyl RCSB], [http://www.ebi.ac.uk/pdbsum/1gyl 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=1gyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gyl RCSB], [http://www.ebi.ac.uk/pdbsum/1gyl PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Spinacia oleracea]]		[[Category: Spinacia oleracea]]
-	[[Category: Lindqvist, Y.]]	+	[[Category: Lindqvist, Y]]
-	[[Category: Stenberg, K.]]	+	[[Category: Stenberg, K]]

OCA at 12:45, 28 September 2014

OCA — Sun, 28 Sep 2014 12:45:08 GMT

←Older revision		Revision as of 12:45, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1gyl.~~png~~\|~~left~~\|200px]]	+	==INVOLVEMENT OF TYR24 AND TRP108 IN SUBSTRATE BINDING AND SUBSTRATE SPECIFICITY OF GLYCOLATE OXIDASE==
		+	<StructureSection load='1gyl' size='340' side='right' caption='[[1gyl]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1gyl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GYL FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLYCOLATE OXIDASE FROM SPINACH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3562 Spinacia oleracea])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(S)-2-hydroxy-acid_oxidase (S)-2-hydroxy-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.15 1.1.3.15] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gyl RCSB], [http://www.ebi.ac.uk/pdbsum/1gyl 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/gy/1gyl_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 ==
		+	Tyr24 and Trp108 are located in the active site of spinach glycolate oxidase. To elucidate their function in substrate binding and catalysis, they were replaced by phenylalanine and serine, respectively. The [Y24F]glycolate oxidase mutant enzyme showed a tenfold higher Km value for glycolate. L-lactate and DL-2-hydroxybutyrate also showed higher Km values, however, the substrate specificity was unchanged as compared to the wild-type enzyme (Km increases in the order glycolate < DL-2-hydroxybutyrate < L-lactate < L-mandelate). The turnover number and the rate of reduction, found to be rate limiting in catalysis, were only slightly affected by the deletion of the hydroxyl group. These findings suggest that Tyr24 is mostly involved in substrate binding. The spectral features of the [Y24F]glycolate oxidase suggest that a fraction (50-80%) of the protein bears a flavin N(5) adduct instead of the oxidized cofactor. Crystals obtained from the isolated [Y24F]glycolate oxidase mutant protein allowed the determination of the three-dimensional structure. Although the structure was low resolution (0.3 nm), it is evident that the structure determined is that of the N(5) adduct species. In addition to the lacking hydroxyl group of Tyr24, we also observed movements of the amino acid side chains of Arg164 and Trp108, the latter replacing a water molecule in the substrate-binding pocket. Other features predominantly found in the class of flavoprotein oxidases, such as stabilization of the covalent N(5)-sulfite adduct and of the paraquinoid form of 8-mercapto-FMN, were found to be conserved. [W108S]Glycolate oxidase, in contrast, showed dramatic effects on both the Km of substrates as well as the turnover number. The Km for glycolate was increased some hundred fold and the turnover number was decreased 500-fold. In addition, it was found that the higher homologs of glycolate, L-lactate and DL-2-hydroxybutyrate had turnover numbers similar to those found with the wild-type enzyme, although the Km values also increased dramatically. These results indicate that Trp108 is of major importance in catalysis and that this residue is involved in determining the substrate specificity of glycolate oxidase.

-	~~{{STRUCTURE_1gyl\| PDB=1gyl \| SCENE= }}~~	+	Involvement of Tyr24 and Trp108 in substrate binding and substrate specificity of glycolate oxidase.,Stenberg K, Clausen T, Lindqvist Y, Macheroux P Eur J Biochem. 1995 Mar 1;228(2):408-16. PMID:7705356<ref>PMID:7705356</ref>

-	~~===INVOLVEMENT OF TYR24 AND TRP108 IN SUBSTRATE BINDING AND SUBSTRATE SPECIFICITY OF GLYCOLATE OXIDASE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_7705356}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1gyl]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Spinacia_oleracea Spinacia oleracea]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1GYL OCA].~~	+

	==See Also==		==See Also==
	*[[Glycolate oxidase\|Glycolate oxidase]]		*[[Glycolate oxidase\|Glycolate oxidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:007705356<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Spinacia oleracea]]		[[Category: Spinacia oleracea]]
	[[Category: Lindqvist, Y.]]		[[Category: Lindqvist, Y.]]
	[[Category: Stenberg, K.]]		[[Category: Stenberg, K.]]

OCA at 06:46, 20 October 2012

OCA — Sat, 20 Oct 2012 06:46:00 GMT

←Older revision		Revision as of 06:46, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1gyl]] is a 2 chain structure ~~of [[Glycolate oxidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYL OCA].	+	[[1gyl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYL OCA].

	==See Also==		==See Also==

OCA: Protected "1gyl" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 14:13:11 GMT

Protected "1gyl" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:13, 25 July 2012

OCA at 14:13, 25 July 2012

OCA — Wed, 25 Jul 2012 14:13:09 GMT

←Older revision		Revision as of 14:13, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1gyl.png\|left\|200px]]		[[Image:1gyl.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1gyl", 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_1gyl\| PDB=1gyl \| SCENE= }}		{{STRUCTURE_1gyl\| PDB=1gyl \| SCENE= }}

	===INVOLVEMENT OF TYR24 AND TRP108 IN SUBSTRATE BINDING AND SUBSTRATE SPECIFICITY OF GLYCOLATE OXIDASE===		===INVOLVEMENT OF TYR24 AND TRP108 IN SUBSTRATE BINDING AND SUBSTRATE SPECIFICITY OF GLYCOLATE OXIDASE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_7705356}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 7705356 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_7705356}}		{{ABSTRACT_PUBMED_7705356}}

	==About this Structure==		==About this Structure==
-	~~1GYL~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYL OCA].	+	[[1gyl]] is a 2 chain structure of [[Glycolate oxidase]] with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYL OCA].
		+
		+	==See Also==
		+	*[[Glycolate oxidase\|Glycolate oxidase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~7705356~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:007705356</ref><references group="xtra"/>
	[[Category: Spinacia oleracea]]		[[Category: Spinacia oleracea]]
	[[Category: Lindqvist, Y.]]		[[Category: Lindqvist, Y.]]
	[[Category: Stenberg, K.]]		[[Category: Stenberg, K.]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 14:04:40 2009''