1s8a - Revision history

OCA at 08:28, 14 February 2024

2024-02-14T08:28:58Z

← Older revision		Revision as of 08:28, 14 February 2024
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	<StructureSection load='1s8a' size='340' side='right'caption='[[1s8a]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1s8a' size='340' side='right'caption='[[1s8a]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1s8a]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[1s8a]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S8A FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PGA:2~~-~~PHOSPHOGLYCOLIC+ACID'>PGA</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]] 2.2Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em~~;~~'>[[1s89\|1s89]]</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>MGSA, B0963, Z1314, ECS1047, SF0965, S1031 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</td~~><~~/tr>~~
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Methylglyoxal_synthase Methylglyoxal synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.3 4.2.3.3]~~ </~~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=1s8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s8a OCA], [https://pdbe.org/1s8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s8a RCSB], [https://www.ebi.ac.uk/pdbsum/1s8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s8a 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=1s8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s8a OCA], [https://pdbe.org/1s8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s8a RCSB], [https://www.ebi.ac.uk/pdbsum/1s8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s8a ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/MGSA_ECOLI MGSA_ECOLI]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1s8a 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=1s8a ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Two detailed mechanisms [Marks et al. (2001) Biochemistry 40, 6805] have been proposed to explain the activity of methylglyoxal synthase (MGS), a homohexameric allosterically regulated enzyme that catalyzes the elimination of phosphate from DHAP to form enol pyruvaldehyde. This enol then tautomerizes to methylglyoxal in solution. In one of these mechanisms His 98 plays an obligate role in the transfer of a proton from the O(3) oxygen of DHAP to the O2 oxygen. To test this hypothesized mechanism, the variants H98N and H98Q were expressed and purified. Relative to the wild-type enzyme, the H98N variant shows a 50-fold decrease in k(cat) with all other kinetic parameters (i.e., K(m), K(PGA), etc.) being nearly the same. By contrast, the apparent catalytic rate for the H98Q variant is 250-fold lower than that of the wild-type enzyme. Inorganic phosphate acts as a competitive inhibitor (with a K(i) of 15 microM) rather than as an allosteric-type inhibitor as it does in the wild-type enzyme, and the competitive inhibitor phosphoglyolate (PGA) acts as an activator of this variant. These facts are explained by a shift in the conformational equilibrium toward an "inactive" state. When activation by PGA is accounted for, the catalytic rate for the "active" state of H98Q is estimated to be only 6-fold less than that of the wild-type enzyme, and thus His 98 is not essential for catalysis. Primary deuterium isotope effect data were measured for the wild-type enzyme and the two variants. At pH 7.0, the (D)V isotope effect (1.5) and the absence of a (D)(V/K) isotope effect for the wild-type enzyme suggest that the rate for the isotopically sensitive step is partially rate limiting but greater than the rate of substrate dissociation. Both the (D)V (2.0) and (D)(V/K) (3.4) isotope effects were more pronounced in the H98N variant, while the H98Q variant displayed an unusual inverse (D)V (0.8) isotope effect and a normal (D)(V/K) (1.5) isotope effect. The X-ray crystal structures of PGA bound to the H98Q and H98N variants were both determined to a resolution of 2.2 A. These mutations had little effect on the overall structure. However, the pattern of hydrogen bonding in the active site suggests an explanation as to how in the wild-type and H98N mutated enzymes the "inactive to active" equilibrium lies toward the active state, while with the H98Q mutated enzyme the equilibrium lies toward the inactive state. Thus, the role of His 98 appears to be more as a regulator of the enzyme's conformation rather than as a critical contributor to the catalytic mechanism.

	Mutagenic studies on histidine 98 of methylglyoxal synthase: effects on mechanism and conformational change.,Marks GT, Susler M, Harrison DH Biochemistry. 2004 Apr 6;43(13):3802-13. PMID:15049687<ref>PMID:15049687</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 1s8a" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]		[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Methylglyoxal synthase]]~~		[[Category: Harrison DH]]
	[[Category: Harrison~~, D H~~]]		[[Category: Marks GT]]
	[[Category: Marks~~, G T~~]]		[[Category: Susler M]]
	[[Category: Susler, M]]
	~~[[Category: Glycolytic bypass]]~~
	~~[[Category: Lyase]]~~
	~~[[Category: Methylglyoxal~~]]

OCA at 15:31, 27 October 2021

2021-10-27T15:31:22Z

← Older revision		Revision as of 15:31, 27 October 2021
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	<StructureSection load='1s8a' size='340' side='right'caption='[[1s8a]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1s8a' size='340' side='right'caption='[[1s8a]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1s8a]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S8A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1S8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[1s8a]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S8A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1s89\|1s89]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1s89\|1s89]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MGSA, B0963, Z1314, ECS1047, SF0965, S1031 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MGSA, B0963, Z1314, ECS1047, SF0965, S1031 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Methylglyoxal_synthase Methylglyoxal synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.3 4.2.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Methylglyoxal_synthase Methylglyoxal synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.3 4.2.3.3] </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=1s8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s8a OCA], [~~http~~://pdbe.org/1s8a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1s8a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1s8a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1s8a 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=1s8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s8a OCA], [https://pdbe.org/1s8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s8a RCSB], [https://www.ebi.ac.uk/pdbsum/1s8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s8a ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 13:43, 16 December 2020

2020-12-16T13:43:23Z

← Older revision		Revision as of 13:43, 16 December 2020
Line 1:		Line 1:

	==H98Q Mutant of Methylglyoxal Synthase from E. coli complexed with Phosphoglycolic Acid==		==H98Q Mutant of Methylglyoxal Synthase from E. coli complexed with Phosphoglycolic Acid==
	<StructureSection load='1s8a' size='340' side='right' caption='[[1s8a]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1s8a' size='340' side='right'caption='[[1s8a]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1s8a]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S8A OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1S8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[1s8a]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S8A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1S8A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s89\|1s89]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1s89\|1s89]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MGSA, B0963, Z1314, ECS1047, SF0965, S1031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MGSA, B0963, Z1314, ECS1047, SF0965, S1031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylglyoxal_synthase Methylglyoxal synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.3 4.2.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylglyoxal_synthase Methylglyoxal synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.3 4.2.3.3] </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=1s8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s8a OCA], [http://pdbe.org/1s8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s8a RCSB], [http://www.ebi.ac.uk/pdbsum/1s8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s8a 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=1s8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s8a OCA], [http://pdbe.org/1s8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s8a RCSB], [http://www.ebi.ac.uk/pdbsum/1s8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s8a ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
			[[Category: Large Structures]]
	[[Category: Methylglyoxal synthase]]		[[Category: Methylglyoxal synthase]]
	[[Category: Harrison, D H]]		[[Category: Harrison, D H]]

OCA at 06:56, 8 March 2018

2018-03-08T06:56:58Z

← Older revision		Revision as of 06:56, 8 March 2018
Line 1:		Line 1:

	==H98Q Mutant of Methylglyoxal Synthase from E. coli complexed with Phosphoglycolic Acid==		==H98Q Mutant of Methylglyoxal Synthase from E. coli complexed with Phosphoglycolic Acid==
	<StructureSection load='1s8a' size='340' side='right' caption='[[1s8a]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1s8a' size='340' side='right' caption='[[1s8a]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MGSA, B0963, Z1314, ECS1047, SF0965, S1031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MGSA, B0963, Z1314, ECS1047, SF0965, S1031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylglyoxal_synthase Methylglyoxal synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.3 4.2.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylglyoxal_synthase Methylglyoxal synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.3 4.2.3.3] </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=1s8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s8a OCA], [http://pdbe.org/1s8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s8a RCSB], [http://www.ebi.ac.uk/pdbsum/1s8a 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=1s8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s8a OCA], [http://pdbe.org/1s8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s8a RCSB], [http://www.ebi.ac.uk/pdbsum/1s8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s8a ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s8/1s8a_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s8/1s8a_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>

OCA at 22:19, 9 February 2016

2016-02-09T22:19:05Z

← Older revision		Revision as of 22:19, 9 February 2016
Line 17:		Line 17:
	<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=1s8a ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:35, 11 September 2015

2015-09-11T02:35:22Z

← Older revision		Revision as of 02:35, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1s8a' size='340' side='right' caption='[[1s8a]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1s8a' size='340' side='right' caption='[[1s8a]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1s8a]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[1s8a]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S8A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s89\|1s89]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s89\|1s89]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MGSA, B0963, Z1314, ECS1047, SF0965, S1031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MGSA, B0963, Z1314, ECS1047, SF0965, S1031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylglyoxal_synthase Methylglyoxal synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.3 4.2.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylglyoxal_synthase Methylglyoxal synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.3 4.2.3.3] </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=1s8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s8a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s8a RCSB], [http://www.ebi.ac.uk/pdbsum/1s8a 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=1s8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s8a OCA], [http://pdbe.org/1s8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s8a RCSB], [http://www.ebi.ac.uk/pdbsum/1s8a PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	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 1s8a" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia~~ coli]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Methylglyoxal synthase]]		[[Category: Methylglyoxal synthase]]
	[[Category: Harrison, D H]]		[[Category: Harrison, D H]]

OCA at 08:05, 6 January 2015

2015-01-06T08:05:20Z

← Older revision		Revision as of 08:05, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1s8a]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[1s8a]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S8A FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s89\|1s89]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s89\|1s89]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MGSA, B0963, Z1314, ECS1047, SF0965, S1031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MGSA, B0963, Z1314, ECS1047, SF0965, S1031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylglyoxal_synthase Methylglyoxal synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.3 4.2.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylglyoxal_synthase Methylglyoxal synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.3 4.2.3.3] </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=1s8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s8a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s8a RCSB], [http://www.ebi.ac.uk/pdbsum/1s8a 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=1s8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s8a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s8a RCSB], [http://www.ebi.ac.uk/pdbsum/1s8a 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 33:		Line 33:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Methylglyoxal synthase]]		[[Category: Methylglyoxal synthase]]
	[[Category: Harrison, D H.]]		[[Category: Harrison, D H]]
	[[Category: Marks, G T.]]		[[Category: Marks, G T]]
	[[Category: Susler, M.]]		[[Category: Susler, M]]
	[[Category: Glycolytic bypass]]		[[Category: Glycolytic bypass]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Methylglyoxal]]		[[Category: Methylglyoxal]]

OCA at 16:30, 29 September 2014

2014-09-29T16:30:26Z

← Older revision		Revision as of 16:30, 29 September 2014
Line 1:		Line 1:
	[[Image:~~1s8a~~.~~png~~\|~~left~~\|~~200px~~]]		==H98Q Mutant of Methylglyoxal Synthase from E. coli complexed with Phosphoglycolic Acid==
			<StructureSection load='1s8a' size='340' side='right' caption='[[1s8a]], [[Resolution\|resolution]] 2.20Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[1s8a]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S8A FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s89\|1s89]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MGSA, B0963, Z1314, ECS1047, SF0965, S1031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylglyoxal_synthase Methylglyoxal synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.3 4.2.3.3] </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=1s8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s8a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s8a RCSB], [http://www.ebi.ac.uk/pdbsum/1s8a 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/s8/1s8a_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 ==
			Two detailed mechanisms [Marks et al. (2001) Biochemistry 40, 6805] have been proposed to explain the activity of methylglyoxal synthase (MGS), a homohexameric allosterically regulated enzyme that catalyzes the elimination of phosphate from DHAP to form enol pyruvaldehyde. This enol then tautomerizes to methylglyoxal in solution. In one of these mechanisms His 98 plays an obligate role in the transfer of a proton from the O(3) oxygen of DHAP to the O2 oxygen. To test this hypothesized mechanism, the variants H98N and H98Q were expressed and purified. Relative to the wild-type enzyme, the H98N variant shows a 50-fold decrease in k(cat) with all other kinetic parameters (i.e., K(m), K(PGA), etc.) being nearly the same. By contrast, the apparent catalytic rate for the H98Q variant is 250-fold lower than that of the wild-type enzyme. Inorganic phosphate acts as a competitive inhibitor (with a K(i) of 15 microM) rather than as an allosteric-type inhibitor as it does in the wild-type enzyme, and the competitive inhibitor phosphoglyolate (PGA) acts as an activator of this variant. These facts are explained by a shift in the conformational equilibrium toward an "inactive" state. When activation by PGA is accounted for, the catalytic rate for the "active" state of H98Q is estimated to be only 6-fold less than that of the wild-type enzyme, and thus His 98 is not essential for catalysis. Primary deuterium isotope effect data were measured for the wild-type enzyme and the two variants. At pH 7.0, the (D)V isotope effect (1.5) and the absence of a (D)(V/K) isotope effect for the wild-type enzyme suggest that the rate for the isotopically sensitive step is partially rate limiting but greater than the rate of substrate dissociation. Both the (D)V (2.0) and (D)(V/K) (3.4) isotope effects were more pronounced in the H98N variant, while the H98Q variant displayed an unusual inverse (D)V (0.8) isotope effect and a normal (D)(V/K) (1.5) isotope effect. The X-ray crystal structures of PGA bound to the H98Q and H98N variants were both determined to a resolution of 2.2 A. These mutations had little effect on the overall structure. However, the pattern of hydrogen bonding in the active site suggests an explanation as to how in the wild-type and H98N mutated enzymes the "inactive to active" equilibrium lies toward the active state, while with the H98Q mutated enzyme the equilibrium lies toward the inactive state. Thus, the role of His 98 appears to be more as a regulator of the enzyme's conformation rather than as a critical contributor to the catalytic mechanism.

	~~{{STRUCTURE_1s8a\| PDB=1s8a \| SCENE= }}~~		Mutagenic studies on histidine 98 of methylglyoxal synthase: effects on mechanism and conformational change.,Marks GT, Susler M, Harrison DH Biochemistry. 2004 Apr 6;43(13):3802-13. PMID:15049687<ref>PMID:15049687</ref>

	~~===H98Q Mutant~~ of ~~Methylglyoxal Synthase from E~~. ~~coli complexed with Phosphoglycolic Acid===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_15049687}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[1s8a]] is a 6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S8A OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:015049687<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Methylglyoxal synthase]]		[[Category: Methylglyoxal synthase]]

OCA: Protected "1s8a" [edit=sysop:move=sysop]

2013-01-04T10:26:18Z

Protected "1s8a" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:26, 4 January 2013
(No difference)

OCA at 10:26, 4 January 2013

2013-01-04T10:26:17Z

← Older revision		Revision as of 10:26, 4 January 2013
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:1s8a.png\|left\|200px]]		[[Image:1s8a.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_1s8a", 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_1s8a\| PDB=1s8a \| SCENE= }}		{{STRUCTURE_1s8a\| PDB=1s8a \| SCENE= }}

	===H98Q Mutant of Methylglyoxal Synthase from E. coli complexed with Phosphoglycolic Acid===		===H98Q Mutant of Methylglyoxal Synthase from E. coli complexed with Phosphoglycolic Acid===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_15049687}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 15049687 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_15049687}}		{{ABSTRACT_PUBMED_15049687}}

	==About this Structure==		==About this Structure==
	~~1S8A~~ is a 6 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S8A OCA].		[[1s8a]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S8A OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~15049687~~</ref><references group="xtra"/>		<ref group="xtra">PMID:015049687</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Methylglyoxal synthase]]		[[Category: Methylglyoxal synthase]]
Line 32:		Line 20:
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Methylglyoxal]]		[[Category: Methylglyoxal]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:11:06 2009''~~