6urf - Revision history

OCA at 07:56, 11 October 2023

OCA — Wed, 11 Oct 2023 07:56:57 GMT

←Older revision		Revision as of 07:56, 11 October 2023
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	<StructureSection load='6urf' size='340' side='right'caption='[[6urf]], [[Resolution\|resolution]] 3.60Å' scene=''>		<StructureSection load='6urf' size='340' side='right'caption='[[6urf]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6urf]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6URF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6URF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6urf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6URF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6URF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 3.6Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">mez, mez_2, DSI35_04950, ERS007657_00054, ERS007661_01303, ERS007665_00385, ERS007670_00245, ERS007672_00340, ERS007681_00703, ERS007703_00793, ERS007720_02108, ERS007722_00150, ERS007741_00458, ERS023446_00378, ERS024276_00123, ERS027644_00794, ERS027646_00126, ERS027651_00016, ERS027652_00738, ERS027654_00055, ERS027659_00902, ERS027661_00290, ERS027666_00475, ERS031537_00346, ERS124361_01639, FDK60_04380, SAMEA2682835_05736, SAMEA2682864_03296, SAMEA2683035_01163 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1773~~ "~~Bacillus tuberculosis~~" ~~(Zopf 1883) Klein 1884])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[http://en.wikipedia.org/wiki/Malate_dehydrogenase_(oxaloacetate-decarboxylating) Malate dehydrogenase (oxaloacetate-decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.38 1.1.1.38] </~~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=6urf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6urf OCA], [https://pdbe.org/6urf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6urf RCSB], [https://www.ebi.ac.uk/pdbsum/6urf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6urf 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=6urf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6urf OCA], [~~http~~://pdbe.org/6urf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6urf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6urf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6urf ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MAOX_MYCTU MAOX_MYCTU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Beste, D J~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Burley, K H~~]]	+	[[Category: Beste DJ]]
-	[[Category: ~~Cuthbert, B J~~]]	+	[[Category: Burley KH]]
-	[[Category: ~~Goulding, C W~~]]	+	[[Category: Cuthbert BJ]]
-	[[Category: ~~Mathews, E I~~]]	+	[[Category: Goulding CW]]
-	[[Category: ~~Cytosolic protein]]~~	+	[[Category: Mathews EI]]
-	~~[[Category: Fatty acid synthesis]]~~	+
-	~~[[Category: Glucose metabolism]]~~	+
-	~~[[Category: Malic enzyme]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 06:00, 20 January 2021

OCA — Wed, 20 Jan 2021 06:00:49 GMT

←Older revision		Revision as of 06:00, 20 January 2021
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	==Malic enzyme from Mycobacterium tuberculosis==		==Malic enzyme from Mycobacterium tuberculosis==
-	<StructureSection load='6urf' size='340' side='right'caption='[[6urf]]' scene=''>	+	<StructureSection load='6urf' size='340' side='right'caption='[[6urf]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6URF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6URF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6urf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6URF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6URF FirstGlance]. <br>
-	</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=6urf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6urf OCA], [http://pdbe.org/6urf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6urf RCSB], [http://www.ebi.ac.uk/pdbsum/6urf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6urf ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mez, mez_2, DSI35_04950, ERS007657_00054, ERS007661_01303, ERS007665_00385, ERS007670_00245, ERS007672_00340, ERS007681_00703, ERS007703_00793, ERS007720_02108, ERS007722_00150, ERS007741_00458, ERS023446_00378, ERS024276_00123, ERS027644_00794, ERS027646_00126, ERS027651_00016, ERS027652_00738, ERS027654_00055, ERS027659_00902, ERS027661_00290, ERS027666_00475, ERS031537_00346, ERS124361_01639, FDK60_04380, SAMEA2682835_05736, SAMEA2682864_03296, SAMEA2683035_01163 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malate_dehydrogenase_(oxaloacetate-decarboxylating) Malate dehydrogenase (oxaloacetate-decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.38 1.1.1.38] </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=6urf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6urf OCA], [http://pdbe.org/6urf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6urf RCSB], [http://www.ebi.ac.uk/pdbsum/6urf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6urf ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tuberculosis (TB) is the most lethal bacterial infectious disease worldwide. It is notoriously difficult to treat, requiring a cocktail of antibiotics administered over many months. The dense, waxy outer membrane of the TB-causing agent, Mycobacterium tuberculosis (Mtb), acts as a formidable barrier against uptake of antibiotics. Subsequently, enzymes involved in maintaining the integrity of the Mtb cell wall are promising drug targets. Recently, we demonstrated that Mtb lacking malic enzyme (MEZ) has altered cell wall lipid composition and attenuated uptake by macrophages. These results suggest that MEZ contributes to lipid biosynthesis by providing reductants in the form of NAD(P)H. Here, we present the X-ray crystal structure of MEZ to 3.6 A. We use biochemical assays to demonstrate MEZ is dimeric in solution and to evaluate the effects of pH and allosteric regulators on its kinetics and thermal stability. To assess the interactions between MEZ and its substrate malate and cofactors, Mn(2+) and NAD(P)(+), we ran a series of molecular dynamics (MD) simulations. First, the MD analysis corroborates our empirical observations that MEZ is unusually flexible, which persists even with the addition of substrate and cofactors. Second, the MD simulations reveal that dimeric MEZ subunits alternate between open and closed states, and that MEZ can stably bind its NAD(P)(+) cofactor in multiple conformations, including an inactive, compact NAD(+) form. Together the structure of MEZ and insights from its dynamics can be harnessed to inform the design of MEZ inhibitors that target Mtb and not human malic enzyme homologues.
		+
		+	Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target.,Burley KH, Cuthbert BJ, Basu P, Newcombe J, Irimpan EM, Quechol R, Foik IP, Mobley DL, Beste DJV, Goulding CW ACS Infect Dis. 2021 Jan 8;7(1):174-188. doi: 10.1021/acsinfecdis.0c00735. Epub, 2020 Dec 23. PMID:33356117<ref>PMID:33356117</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6urf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Beste DJ]]	+	[[Category: Beste, D J]]
-	[[Category: Burley KH]]	+	[[Category: Burley, K H]]
-	[[Category: Cuthbert BJ]]	+	[[Category: Cuthbert, B J]]
-	[[Category: Goulding CW]]	+	[[Category: Goulding, C W]]
-	[[Category: Mathews EI]]	+	[[Category: Mathews, E I]]
		+	[[Category: Cytosolic protein]]
		+	[[Category: Fatty acid synthesis]]
		+	[[Category: Glucose metabolism]]
		+	[[Category: Malic enzyme]]
		+	[[Category: Oxidoreductase]]

OCA at 20:33, 28 October 2020

OCA — Wed, 28 Oct 2020 20:33:06 GMT

←Older revision		Revision as of 20:33, 28 October 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6urf ~~is ON HOLD until Oct 23 2021~~	+	==Malic enzyme from Mycobacterium tuberculosis==
-		+	<StructureSection load='6urf' size='340' side='right'caption='[[6urf]]' scene=''>
-	~~Authors~~: ~~Cuthbert, B~~.J., ~~Burley, K~~.H., ~~Goulding~~, C.W., ~~Mathews, E~~.I., ~~Beste, D~~.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6URF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6URF FirstGlance]. <br>
-	~~Description: Malic enzyme from Mycobacterium tuberculosis~~	+	</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=6urf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6urf OCA], [http://pdbe.org/6urf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6urf RCSB], [http://www.ebi.ac.uk/pdbsum/6urf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6urf ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Goulding, C.W~~]]	+	__TOC__
-	[[Category: Burley~~, K.H~~]]	+	</StructureSection>
-	[[Category: ~~Mathews, E.I~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Cuthbert, B.J~~]]	+	[[Category: Beste DJ]]
-	[[Category: ~~Beste, D.J~~]]	+	[[Category: Burley KH]]
		+	[[Category: Cuthbert BJ]]
		+	[[Category: Goulding CW]]
		+	[[Category: Mathews EI]]

OCA at 03:55, 14 October 2020

OCA — Wed, 14 Oct 2020 03:55:29 GMT

←Older revision		Revision as of 03:55, 14 October 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6urf is ON HOLD	+	The entry 6urf is ON HOLD until Oct 23 2021

	Authors: Cuthbert, B.J., Burley, K.H., Goulding, C.W., Mathews, E.I., Beste, D.J.		Authors: Cuthbert, B.J., Burley, K.H., Goulding, C.W., Mathews, E.I., Beste, D.J.

OCA at 06:35, 16 September 2020

OCA — Wed, 16 Sep 2020 06:35:18 GMT

←Older revision		Revision as of 06:35, 16 September 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6urf is ON HOLD ~~until Oct 23 2021~~	+	The entry 6urf is ON HOLD

	Authors: Cuthbert, B.J., Burley, K.H., Goulding, C.W., Mathews, E.I., Beste, D.J.		Authors: Cuthbert, B.J., Burley, K.H., Goulding, C.W., Mathews, E.I., Beste, D.J.
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	Description: Malic enzyme from Mycobacterium tuberculosis		Description: Malic enzyme from Mycobacterium tuberculosis
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Burley, K.H]]
-	[[Category: Cuthbert, B.J]]
	[[Category: Goulding, C.W]]		[[Category: Goulding, C.W]]
		+	[[Category: Burley, K.H]]
	[[Category: Mathews, E.I]]		[[Category: Mathews, E.I]]
		+	[[Category: Cuthbert, B.J]]
	[[Category: Beste, D.J]]		[[Category: Beste, D.J]]

OCA at 09:32, 13 November 2019

OCA — Wed, 13 Nov 2019 09:32:53 GMT

←Older revision		Revision as of 09:32, 13 November 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6urf is ON HOLD	+	The entry 6urf is ON HOLD until Oct 23 2021

	Authors: Cuthbert, B.J., Burley, K.H., Goulding, C.W., Mathews, E.I., Beste, D.J.		Authors: Cuthbert, B.J., Burley, K.H., Goulding, C.W., Mathews, E.I., Beste, D.J.
Line 7:		Line 7:
	Description: Malic enzyme from Mycobacterium tuberculosis		Description: Malic enzyme from Mycobacterium tuberculosis
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Cuthbert, B.J]]
	[[Category: Burley, K.H]]		[[Category: Burley, K.H]]
		+	[[Category: Cuthbert, B.J]]
	[[Category: Goulding, C.W]]		[[Category: Goulding, C.W]]
	[[Category: Mathews, E.I]]		[[Category: Mathews, E.I]]
	[[Category: Beste, D.J]]		[[Category: Beste, D.J]]

OCA: Protected "6urf" [edit=sysop:move=sysop]

OCA — Wed, 30 Oct 2019 07:42:49 GMT

Protected "6urf" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:42, 30 October 2019

OCA: New page: '''Unreleased structure''' The entry 6urf is ON HOLD Authors: Cuthbert, B.J., Burley, K.H., Goulding, C.W., Mathews, E.I., Beste, D.J. Description: Malic enzyme from Mycobacterium tube...

OCA — Wed, 30 Oct 2019 07:42:48 GMT

New page: '''Unreleased structure''' The entry 6urf is ON HOLD Authors: Cuthbert, B.J., Burley, K.H., Goulding, C.W., Mathews, E.I., Beste, D.J. Description: Malic enzyme from Mycobacterium tube...

New page

'''Unreleased structure'''

The entry 6urf is ON HOLD

Authors: Cuthbert, B.J., Burley, K.H., Goulding, C.W., Mathews, E.I., Beste, D.J.

Description: Malic enzyme from Mycobacterium tuberculosis
[[Category: Unreleased Structures]]
[[Category: Cuthbert, B.J]]
[[Category: Burley, K.H]]
[[Category: Goulding, C.W]]
[[Category: Mathews, E.I]]
[[Category: Beste, D.J]]