1qcw - Revision history

OCA at 08:15, 14 February 2024

OCA — Wed, 14 Feb 2024 08:15:08 GMT

←Older revision		Revision as of 08:15, 14 February 2024
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	<StructureSection load='1qcw' size='340' side='right'caption='[[1qcw]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='1qcw' size='340' side='right'caption='[[1qcw]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qcw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QCW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qcw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QCW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FNS:N~~-~~SULFO-FLAVIN+MONONUCLEOTIDE'>FNS</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]] 2.75Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1fcb\|1fcb]], [[1lco\|1lco]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FNS:N-SULFO-FLAVIN+MONONUCLEOTIDE'>FNS</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/L~~-~~lactate_dehydrogenase_(cytochrome) L~~-~~lactate dehydrogenase (cytochrome)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.2.3 1.1.2.3]~~ </~~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=1qcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qcw OCA], [https://pdbe.org/1qcw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qcw RCSB], [https://www.ebi.ac.uk/pdbsum/1qcw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qcw 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=1qcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qcw OCA], [https://pdbe.org/1qcw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qcw RCSB], [https://www.ebi.ac.uk/pdbsum/1qcw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qcw ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CYB2_YEAST CYB2_YEAST]
	== 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=1qcw 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=1qcw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Flavocytochrome b(2) from Saccharomyces cerevisiae couples L-lactate dehydrogenation to cytochrome c reduction. The crystal structure of the native yeast enzyme has been determined [Xia, Z.-X., and Mathews, F. S. (1990) J. Mol. Biol. 212, 837-863] as well as that of the sulfite adduct of the recombinant enzyme produced in Escherichia coli [Tegoni, M., and Cambillau, C. (1994) Protein Sci. 3, 303-313]; several key active site residues were identified. In the sulfite adduct crystal structure, Arg289 adopts two alternative conformations. In one of them, its side chain is stacked against that of Arg376, which interacts with the substrate; in the second orientation, the R289 side chain points toward the active site. This residue has now been mutated to lysine and the mutant enzyme, R289K-b(2), characterized kinetically. Under steady-state conditions, kinetic parameters (including the deuterium kinetic isotope effect) indicate the mutation affects k(cat) by a factor of about 10 and k(cat)/K(M) by up to nearly 10(2). Pre-steady-state kinetic analysis of flavin and heme reduction by lactate demonstrates that the latter is entirely limited by flavin reduction. Inhibition studies on R289K-b(2) with a range of compounds show a general rise in K(i) values relative to that of wild-type enzyme, in line with the elevation of the K(M) for L-lactate in R289K-b(2); they also show a change in the pattern of inhibition by pyruvate and oxalate, as well as a loss of the inhibition by excess substrate. Altogether, the kinetic studies indicate that the mutation has altered the first step of the catalytic cycle, namely, flavin reduction; they suggest that R289 plays a role both in Michaelis complex and transition-state stabilization, as well as in ligand binding to the active site when the flavin is in the semiquinone state. In addition, it appears that the mutation has not affected electron transfer from fully reduced flavin to heme, but may have slowed the second intramolecular ET step, namely, transfer from flavin semiquinone to heme b(2). Finally, the X-ray crystal structure of R289K-b(2), with sulfite bound at the active site, has been determined to 2.75 A resolution. The lysine side chain at position 289 is well-defined and in an orientation that corresponds approximately to one of the alternative conformations observed in the structure of the recombinant enzyme-sulfite complex [Tegoni, M., and Cambillau, C. (1994) Protein Sci. 3, 303-313]. Comparisons between the R289K-b(2) and wild-type structures allow the kinetic results to be interpreted in a structural context.
-
-	Kinetic and crystallographic studies on the active site Arg289Lys mutant of flavocytochrome b2 (yeast L-lactate dehydrogenase).,Mowat CG, Beaudoin I, Durley RC, Barton JD, Pike AD, Chen ZW, Reid GA, Chapman SK, Mathews FS, Lederer F Biochemistry. 2000 Mar 28;39(12):3266-75. PMID:10727218<ref>PMID:10727218</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1qcw" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Flavocytochrome 3D structures\|Flavocytochrome 3D structures]]		*[[Flavocytochrome 3D structures\|Flavocytochrome 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Barton~~, J D~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Chapman~~, S K~~]]	+	[[Category: Barton JD]]
-	[[Category: Chen, Z W]]	+	[[Category: Chapman SK]]
-	[[Category: Durley~~, R C.E~~]]	+	[[Category: Chen Z-W]]
-	[[Category: Lederer, F]]	+	[[Category: Durley RCE]]
-	[[Category: Mathews~~, F S~~]]	+	[[Category: Lederer F]]
-	[[Category: Mowat~~, C G~~]]	+	[[Category: Mathews FS]]
-	[[Category: Pike~~, A D~~]]	+	[[Category: Mowat CG]]
-	[[Category: Reid~~, G A]]~~	+	[[Category: Pike AD]]
-	~~[[Category: Flavoprotein electron transfer mutagenisis]]~~	+	[[Category: Reid GA]]
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:53, 15 September 2021

OCA — Wed, 15 Sep 2021 09:53:55 GMT

←Older revision		Revision as of 09:53, 15 September 2021
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	<StructureSection load='1qcw' size='340' side='right'caption='[[1qcw]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='1qcw' size='340' side='right'caption='[[1qcw]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qcw]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1QCW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qcw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QCW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FNS:N-SULFO-FLAVIN+MONONUCLEOTIDE'>FNS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FNS:N-SULFO-FLAVIN+MONONUCLEOTIDE'>FNS</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fcb\|1fcb]], [[1lco\|1lco]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fcb\|1fcb]], [[1lco\|1lco]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/L-lactate_dehydrogenase_(cytochrome) L-lactate dehydrogenase (cytochrome)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.2.3 1.1.2.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/L-lactate_dehydrogenase_(cytochrome) L-lactate dehydrogenase (cytochrome)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.2.3 1.1.2.3] </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=1qcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qcw OCA], [~~http~~://pdbe.org/1qcw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1qcw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1qcw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1qcw 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=1qcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qcw OCA], [https://pdbe.org/1qcw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qcw RCSB], [https://www.ebi.ac.uk/pdbsum/1qcw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qcw ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 09:58, 27 November 2019

OCA — Wed, 27 Nov 2019 09:58:02 GMT

←Older revision		Revision as of 09:58, 27 November 2019
Line 1:		Line 1:

	==Flavocytochrome B2, ARG289LYS mutant==		==Flavocytochrome B2, ARG289LYS mutant==
-	<StructureSection load='1qcw' size='340' side='right' caption='[[1qcw]], [[Resolution\|resolution]] 2.75Å' scene=''>	+	<StructureSection load='1qcw' size='340' side='right'caption='[[1qcw]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qcw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QCW FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qcw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QCW FirstGlance]. <br>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1qcw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1qcw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Flavocytochrome 3D structures\|Flavocytochrome 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Barton, J D]]		[[Category: Barton, J D]]
	[[Category: Chapman, S K]]		[[Category: Chapman, S K]]

OCA at 08:00, 24 February 2018

OCA — Sat, 24 Feb 2018 08:00:14 GMT

←Older revision		Revision as of 08:00, 24 February 2018
Line 1:		Line 1:
		+
	==Flavocytochrome B2, ARG289LYS mutant==		==Flavocytochrome B2, ARG289LYS mutant==
	<StructureSection load='1qcw' size='340' side='right' caption='[[1qcw]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='1qcw' size='340' side='right' caption='[[1qcw]], [[Resolution\|resolution]] 2.75Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fcb\|1fcb]], [[1lco\|1lco]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fcb\|1fcb]], [[1lco\|1lco]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase_(cytochrome) L-lactate dehydrogenase (cytochrome)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.2.3 1.1.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase_(cytochrome) L-lactate dehydrogenase (cytochrome)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.2.3 1.1.2.3] </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=1qcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qcw OCA], [http://pdbe.org/1qcw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qcw RCSB], [http://www.ebi.ac.uk/pdbsum/1qcw 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=1qcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qcw OCA], [http://pdbe.org/1qcw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qcw RCSB], [http://www.ebi.ac.uk/pdbsum/1qcw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qcw ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qc/1qcw_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qc/1qcw_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 1qcw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1qcw" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Flavocytochrome\|Flavocytochrome]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:46, 10 February 2016

OCA — Wed, 10 Feb 2016 02:46:34 GMT

←Older revision		Revision as of 02:46, 10 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=1qcw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:37, 11 September 2015

OCA — Fri, 11 Sep 2015 04:37:06 GMT

←Older revision		Revision as of 04:37, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1qcw' size='340' side='right' caption='[[1qcw]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='1qcw' size='340' side='right' caption='[[1qcw]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qcw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QCW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qcw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QCW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FNS:N-SULFO-FLAVIN+MONONUCLEOTIDE'>FNS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FNS:N-SULFO-FLAVIN+MONONUCLEOTIDE'>FNS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fcb\|1fcb]], [[1lco\|1lco]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fcb\|1fcb]], [[1lco\|1lco]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase_(cytochrome) L-lactate dehydrogenase (cytochrome)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.2.3 1.1.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase_(cytochrome) L-lactate dehydrogenase (cytochrome)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.2.3 1.1.2.3] </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=1qcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qcw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qcw RCSB], [http://www.ebi.ac.uk/pdbsum/1qcw 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=1qcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qcw OCA], [http://pdbe.org/1qcw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qcw RCSB], [http://www.ebi.ac.uk/pdbsum/1qcw 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 1qcw" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: Barton, J D]]		[[Category: Barton, J D]]
	[[Category: Chapman, S K]]		[[Category: Chapman, S K]]

OCA at 06:50, 6 January 2015

OCA — Tue, 06 Jan 2015 06:50:59 GMT

←Older revision		Revision as of 06:50, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qcw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QCW FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qcw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QCW FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FNS:N-SULFO-FLAVIN+MONONUCLEOTIDE'>FNS</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FNS:N-SULFO-FLAVIN+MONONUCLEOTIDE'>FNS</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fcb\|1fcb]], [[1lco\|1lco]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fcb\|1fcb]], [[1lco\|1lco]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase_(cytochrome) L-lactate dehydrogenase (cytochrome)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.2.3 1.1.2.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase_(cytochrome) L-lactate dehydrogenase (cytochrome)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.2.3 1.1.2.3] </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=1qcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qcw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qcw RCSB], [http://www.ebi.ac.uk/pdbsum/1qcw 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=1qcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qcw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qcw RCSB], [http://www.ebi.ac.uk/pdbsum/1qcw 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: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Barton, J D.]]	+	[[Category: Barton, J D]]
-	[[Category: Chapman, S K.]]	+	[[Category: Chapman, S K]]
-	[[Category: Chen, Z W.]]	+	[[Category: Chen, Z W]]
-	[[Category: Durley, R C.E.]]	+	[[Category: Durley, R C.E]]
-	[[Category: Lederer, F.]]	+	[[Category: Lederer, F]]
-	[[Category: Mathews, F S.]]	+	[[Category: Mathews, F S]]
-	[[Category: Mowat, C G.]]	+	[[Category: Mowat, C G]]
-	[[Category: Pike, A D.]]	+	[[Category: Pike, A D]]
-	[[Category: Reid, G A.]]	+	[[Category: Reid, G A]]
	[[Category: Flavoprotein electron transfer mutagenisis]]		[[Category: Flavoprotein electron transfer mutagenisis]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 19:25, 28 September 2014

OCA — Sun, 28 Sep 2014 19:25:15 GMT

←Older revision		Revision as of 19:25, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1qcw.~~png~~\|~~left~~\|200px]]	+	==Flavocytochrome B2, ARG289LYS mutant==
		+	<StructureSection load='1qcw' size='340' side='right' caption='[[1qcw]], [[Resolution\|resolution]] 2.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1qcw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QCW FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FNS:N-SULFO-FLAVIN+MONONUCLEOTIDE'>FNS</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fcb\|1fcb]], [[1lco\|1lco]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase_(cytochrome) L-lactate dehydrogenase (cytochrome)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.2.3 1.1.2.3] </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=1qcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qcw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qcw RCSB], [http://www.ebi.ac.uk/pdbsum/1qcw 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/qc/1qcw_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 ==
		+	Flavocytochrome b(2) from Saccharomyces cerevisiae couples L-lactate dehydrogenation to cytochrome c reduction. The crystal structure of the native yeast enzyme has been determined [Xia, Z.-X., and Mathews, F. S. (1990) J. Mol. Biol. 212, 837-863] as well as that of the sulfite adduct of the recombinant enzyme produced in Escherichia coli [Tegoni, M., and Cambillau, C. (1994) Protein Sci. 3, 303-313]; several key active site residues were identified. In the sulfite adduct crystal structure, Arg289 adopts two alternative conformations. In one of them, its side chain is stacked against that of Arg376, which interacts with the substrate; in the second orientation, the R289 side chain points toward the active site. This residue has now been mutated to lysine and the mutant enzyme, R289K-b(2), characterized kinetically. Under steady-state conditions, kinetic parameters (including the deuterium kinetic isotope effect) indicate the mutation affects k(cat) by a factor of about 10 and k(cat)/K(M) by up to nearly 10(2). Pre-steady-state kinetic analysis of flavin and heme reduction by lactate demonstrates that the latter is entirely limited by flavin reduction. Inhibition studies on R289K-b(2) with a range of compounds show a general rise in K(i) values relative to that of wild-type enzyme, in line with the elevation of the K(M) for L-lactate in R289K-b(2); they also show a change in the pattern of inhibition by pyruvate and oxalate, as well as a loss of the inhibition by excess substrate. Altogether, the kinetic studies indicate that the mutation has altered the first step of the catalytic cycle, namely, flavin reduction; they suggest that R289 plays a role both in Michaelis complex and transition-state stabilization, as well as in ligand binding to the active site when the flavin is in the semiquinone state. In addition, it appears that the mutation has not affected electron transfer from fully reduced flavin to heme, but may have slowed the second intramolecular ET step, namely, transfer from flavin semiquinone to heme b(2). Finally, the X-ray crystal structure of R289K-b(2), with sulfite bound at the active site, has been determined to 2.75 A resolution. The lysine side chain at position 289 is well-defined and in an orientation that corresponds approximately to one of the alternative conformations observed in the structure of the recombinant enzyme-sulfite complex [Tegoni, M., and Cambillau, C. (1994) Protein Sci. 3, 303-313]. Comparisons between the R289K-b(2) and wild-type structures allow the kinetic results to be interpreted in a structural context.

-	~~{{STRUCTURE_1qcw\| PDB=1qcw \| SCENE= }}~~	+	Kinetic and crystallographic studies on the active site Arg289Lys mutant of flavocytochrome b2 (yeast L-lactate dehydrogenase).,Mowat CG, Beaudoin I, Durley RC, Barton JD, Pike AD, Chen ZW, Reid GA, Chapman SK, Mathews FS, Lederer F Biochemistry. 2000 Mar 28;39(12):3266-75. PMID:10727218<ref>PMID:10727218</ref>

-	~~===Flavocytochrome B2~~, ~~ARG289LYS mutant===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10727218}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1qcw]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1QCW OCA].~~	+

	==See Also==		==See Also==
	*[[Flavocytochrome\|Flavocytochrome]]		*[[Flavocytochrome\|Flavocytochrome]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010727218<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Barton, J D.]]		[[Category: Barton, J D.]]

OCA at 16:03, 20 October 2012

OCA — Sat, 20 Oct 2012 16:03:33 GMT

←Older revision		Revision as of 16:03, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1qcw]] is a 2 chain structure ~~of [[Flavocytochrome]]~~ with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCW OCA].	+	[[1qcw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCW OCA].

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

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

OCA — Thu, 26 Jul 2012 20:27:33 GMT

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

←Older revision

Revision as of 20:27, 26 July 2012