6dvi - Revision history

OCA at 14:37, 13 March 2024

OCA — Wed, 13 Mar 2024 14:37:11 GMT

←Older revision		Revision as of 14:37, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6dvi' size='340' side='right'caption='[[6dvi]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6dvi' size='340' side='right'caption='[[6dvi]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dvi]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_smegmatis"_trevisan_1889 "bacillus~~ smegmatis~~" trevisan 1889~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DVI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dvi]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DVI 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~~>, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.3Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http:~~/~~/en.wikipedia.org/wiki/Lactate_2-monooxygenase Lactate 2-monooxygenase]~~, ~~with EC number [http~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.4 1.13.12.4]~~ </~~span~~></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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6dvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dvi OCA], [~~http~~://pdbe.org/6dvi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dvi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dvi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dvi 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=6dvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dvi OCA], [https://pdbe.org/6dvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dvi RCSB], [https://www.ebi.ac.uk/pdbsum/6dvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dvi ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/LMO_MYCSM LMO_MYCSM] Catalyzes the oxidative decarboxylation of (S)-lactate (L-lactate) to acetate and carbon dioxide. Its physiological role remains unknown.<ref>PMID:4640938</ref>
-	Lactate monooxygenase (LMO) catalyzes the FMN-dependent "coupled" oxidation of lactate and O2 to acetate, carbon dioxide and water, involving pyruvate and hydrogen peroxide as enzyme-bound intermediates. ~~Other alpha-hydroxy acid oxidase family members follow an "uncoupled pathway," wherein the alpha-keto acid product quickly dissociates before the reduced flavin reacts with oxygen~~. ~~Here, we report~~ the ~~structures~~ of ~~Mycobacterium smegmatis wild~~-~~type LMO and a wild~~-type-like C203A variant at 2.1 A and 1.7 A resolution, respectively. The overall LMO fold and active site organization, including a bound sulfate mimicking substrate, resemble those of other alpha-hydroxy acid oxidases. Based on structural similarity, LMO is similarly distant from lactate oxidase, glycolate oxidase, mandelate dehydrogenase, and flavocytochrome b2 and is the first representative enzyme of its type. Comparisons with other alpha-hydroxy acid oxidases reveal that LMO has a longer and more compact folded active site loop (loop 4)~~, which is known in related flavoenzymes~~ to ~~undergo order/disorder transitions to allow substrate/product binding~~ and ~~release~~. We propose that LMO's loop 4 has an enhanced stability that is responsible for the slow product release requisite for the coupled pathway. We also note electrostatic features of the LMO active site that promote substrate binding. Whereas the physiological role ~~of LMO~~ remains unknown, we document what can currently be assessed of LMO's distribution in nature, including its unexpected occurrence, presumably through horizontal gene transfer, in halophilic archaea and in a limited group of fungi of the genus Beauveria. ~~This article is protected by copyright. All rights reserved.~~	+
-		+
-	~~Structure and role for active site lid of lactate monooxygenase from Mycobacterium smegmatis.,Kean KM, Karplus PA Protein Sci. 2018 Sep 11. doi: 10.1002/pro.3506. PMID:30207005~~<ref>PMID:~~30207005~~</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6dvi" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 24:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus smegmatis trevisan 1889]]
-	[[Category: Lactate 2-monooxygenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Karplus, P A~~]]	+	[[Category: Mycolicibacterium smegmatis]]
-	[[Category: ~~Kean, K M~~]]	+	[[Category: Karplus PA]]
-	[[Category: ~~Alpha-hydroxy acid oxidase]]~~	+	[[Category: Kean KM]]
-	~~[[Category: Flavoenzyme]]~~	+
-	~~[[Category: Lactate metabolism]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 08:35, 27 November 2019

OCA — Wed, 27 Nov 2019 08:35:25 GMT

←Older revision		Revision as of 08:35, 27 November 2019
Line 1:		Line 1:

	==Wild-type Lactate Monooxygenase from Mycobacterium smegmatis==		==Wild-type Lactate Monooxygenase from Mycobacterium smegmatis==
-	<StructureSection load='6dvi' size='340' side='right' caption='[[6dvi]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='6dvi' size='340' side='right'caption='[[6dvi]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dvi]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DVI FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dvi]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DVI FirstGlance]. <br>
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 6dvi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6dvi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monooxygenase 3D structures\|Monooxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 26:
	[[Category: Bacillus smegmatis trevisan 1889]]		[[Category: Bacillus smegmatis trevisan 1889]]
	[[Category: Lactate 2-monooxygenase]]		[[Category: Lactate 2-monooxygenase]]
		+	[[Category: Large Structures]]
	[[Category: Karplus, P A]]		[[Category: Karplus, P A]]
	[[Category: Kean, K M]]		[[Category: Kean, K M]]

OCA at 08:38, 26 December 2018

OCA — Wed, 26 Dec 2018 08:38:12 GMT

←Older revision		Revision as of 08:38, 26 December 2018
Line 3:		Line 3:
	<StructureSection load='6dvi' size='340' side='right' caption='[[6dvi]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6dvi' size='340' side='right' caption='[[6dvi]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dvi]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DVI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dvi]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DVI 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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lactate_2-monooxygenase Lactate 2-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.4 1.13.12.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lactate_2-monooxygenase Lactate 2-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.4 1.13.12.4] </span></td></tr>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus smegmatis trevisan 1889]]
	[[Category: Lactate 2-monooxygenase]]		[[Category: Lactate 2-monooxygenase]]
	[[Category: Karplus, P A]]		[[Category: Karplus, P A]]

OCA at 07:48, 3 October 2018

OCA — Wed, 03 Oct 2018 07:48:45 GMT

←Older revision		Revision as of 07:48, 3 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dvi is ~~ON HOLD~~	+	==Wild-type Lactate Monooxygenase from Mycobacterium smegmatis==
		+	<StructureSection load='6dvi' size='340' side='right' caption='[[6dvi]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6dvi]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DVI 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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lactate_2-monooxygenase Lactate 2-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.4 1.13.12.4] </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=6dvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dvi OCA], [http://pdbe.org/6dvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dvi RCSB], [http://www.ebi.ac.uk/pdbsum/6dvi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dvi ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lactate monooxygenase (LMO) catalyzes the FMN-dependent "coupled" oxidation of lactate and O2 to acetate, carbon dioxide and water, involving pyruvate and hydrogen peroxide as enzyme-bound intermediates. Other alpha-hydroxy acid oxidase family members follow an "uncoupled pathway," wherein the alpha-keto acid product quickly dissociates before the reduced flavin reacts with oxygen. Here, we report the structures of Mycobacterium smegmatis wild-type LMO and a wild-type-like C203A variant at 2.1 A and 1.7 A resolution, respectively. The overall LMO fold and active site organization, including a bound sulfate mimicking substrate, resemble those of other alpha-hydroxy acid oxidases. Based on structural similarity, LMO is similarly distant from lactate oxidase, glycolate oxidase, mandelate dehydrogenase, and flavocytochrome b2 and is the first representative enzyme of its type. Comparisons with other alpha-hydroxy acid oxidases reveal that LMO has a longer and more compact folded active site loop (loop 4), which is known in related flavoenzymes to undergo order/disorder transitions to allow substrate/product binding and release. We propose that LMO's loop 4 has an enhanced stability that is responsible for the slow product release requisite for the coupled pathway. We also note electrostatic features of the LMO active site that promote substrate binding. Whereas the physiological role of LMO remains unknown, we document what can currently be assessed of LMO's distribution in nature, including its unexpected occurrence, presumably through horizontal gene transfer, in halophilic archaea and in a limited group of fungi of the genus Beauveria. This article is protected by copyright. All rights reserved.

-	~~Authors:~~ Kean, K.M.~~, Karplus, P~~.A.	+	Structure and role for active site lid of lactate monooxygenase from Mycobacterium smegmatis.,Kean KM, Karplus PA Protein Sci. 2018 Sep 11. doi: 10.1002/pro.3506. PMID:30207005<ref>PMID:30207005</ref>

-	~~Description: Wild~~-~~type~~ Lactate ~~Monooxygenase from Mycobacterium smegmatis~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Kean, K.M]]	+	<div class="pdbe-citations 6dvi" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Karplus, P.A~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lactate 2-monooxygenase]]
		+	[[Category: Karplus, P A]]
		+	[[Category: Kean, K M]]
		+	[[Category: Alpha-hydroxy acid oxidase]]
		+	[[Category: Flavoenzyme]]
		+	[[Category: Lactate metabolism]]
		+	[[Category: Oxidoreductase]]

OCA at 06:06, 26 September 2018

OCA — Wed, 26 Sep 2018 06:06:27 GMT

←Older revision		Revision as of 06:06, 26 September 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6dvi is ON HOLD ~~until Paper Publication~~	+	The entry 6dvi is ON HOLD

	Authors: Kean, K.M., Karplus, P.A.		Authors: Kean, K.M., Karplus, P.A.

OCA at 05:50, 25 July 2018

OCA — Wed, 25 Jul 2018 05:50:15 GMT

←Older revision		Revision as of 05:50, 25 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6dvi is ON HOLD	+	The entry 6dvi is ON HOLD until Paper Publication

	Authors: Kean, K.M., Karplus, P.A.		Authors: Kean, K.M., Karplus, P.A.

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

OCA — Wed, 04 Jul 2018 05:44:53 GMT

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

←Older revision

Revision as of 05:44, 4 July 2018

OCA: New page: '''Unreleased structure''' The entry 6dvi is ON HOLD Authors: Kean, K.M., Karplus, P.A. Description: Wild-type Lactate Monooxygenase from Mycobacterium smegmatis [[Category: Unreleased...

OCA — Wed, 04 Jul 2018 05:44:52 GMT

New page: '''Unreleased structure''' The entry 6dvi is ON HOLD Authors: Kean, K.M., Karplus, P.A. Description: Wild-type Lactate Monooxygenase from Mycobacterium smegmatis [[Category: Unreleased...

New page

'''Unreleased structure'''

The entry 6dvi is ON HOLD

Authors: Kean, K.M., Karplus, P.A.

Description: Wild-type Lactate Monooxygenase from Mycobacterium smegmatis
[[Category: Unreleased Structures]]
[[Category: Kean, K.M]]
[[Category: Karplus, P.A]]