1m2w - Revision history

OCA at 08:30, 10 April 2024

OCA — Wed, 10 Apr 2024 08:30:39 GMT

←Older revision		Revision as of 08:30, 10 April 2024
Line 3:		Line 3:
	<StructureSection load='1m2w' size='340' side='right'caption='[[1m2w]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1m2w' size='340' side='right'caption='[[1m2w]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m2w]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus~~ fluorescens ~~liquefaciens" flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1M2W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m2w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M2W FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MTL:D~~-~~MANNITOL'>MTL</scene>~~, ~~<scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 1.8Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=MTL:D-MANNITOL'>MTL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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;~~'>~~[[1lj8\|1lj8]]~~</~~div~~><~~/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=1m2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2w OCA], [https://pdbe.org/1m2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m2w RCSB], [https://www.ebi.ac.uk/pdbsum/1m2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2w ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </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=1m2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2w OCA], [~~http~~://pdbe.org/1m2w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1m2w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1m2w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2w ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O08355_PSEFL O08355_PSEFL]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m2w 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=1m2w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Long-chain mannitol dehydrogenases are secondary alcohol dehydrogenases that are of wide interest because of their involvement in metabolism and potential applications in agriculture, medicine, and industry. They differ from other alcohol and polyol dehydrogenases because they do not contain a conserved tyrosine and are not dependent on Zn(2+) or other metal cofactors. The structures of the long-chain mannitol 2-dehydrogenase (54 kDa) from Pseudomonas fluorescens in a binary complex with NAD(+) and ternary complex with NAD(+) and d-mannitol have been determined to resolutions of 1.7 and 1.8 A and R-factors of 0.171 and 0.176, respectively. These results show an N-terminal domain that includes a typical Rossmann fold. The C-terminal domain is primarily alpha-helical and mediates mannitol binding. The electron lone pair of Lys-295 is steered by hydrogen-bonding interactions with the amide oxygen of Asn-300 and the main-chain carbonyl oxygen of Val-229 to act as the general base. Asn-191 and Asn-300 are involved in a web of hydrogen bonding, which precisely orients the mannitol O2 proton for abstraction. These residues also aid in stabilizing a negative charge in the intermediate state and in preventing the formation of nonproductive complexes with the substrate. The catalytic lysine may be returned to its unprotonated state using a rectifying proton tunnel driven by Glu-292 oscillating among different environments. Despite low sequence homology, the closest structural neighbors are glycerol-3-phosphate dehydrogenase, N-(1-d-carboxylethyl)-l-norvaline dehydrogenase, UDP-glucose dehydrogenase, and 6-phosphogluconate dehydrogenase, indicating a possible evolutionary relationship among these enzymes.
-
-	Crystal structure of Pseudomonas fluorescens mannitol 2-dehydrogenase binary and ternary complexes. Specificity and catalytic mechanism.,Kavanagh KL, Klimacek M, Nidetzky B, Wilson DK J Biol Chem. 2002 Nov 8;277(45):43433-42. Epub 2002 Aug 23. PMID:12196534<ref>PMID:12196534</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1m2w" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Alcohol dehydrogenase 3D structures\|Alcohol dehydrogenase 3D structures]]		*[[Alcohol dehydrogenase 3D structures\|Alcohol dehydrogenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Mannitol 2-dehydrogenase~~]]	+	[[Category: Pseudomonas fluorescens]]
-	[[Category: Kavanagh~~, K L~~]]	+	[[Category: Kavanagh KL]]
-	[[Category: Klimacek, M]]	+	[[Category: Klimacek M]]
-	[[Category: Nidetzky, B]]	+	[[Category: Nidetzky B]]
-	[[Category: Wilson~~, D K]]~~	+	[[Category: Wilson DK]]
-	~~[[Category: Di-nucleotide binding motif]]~~	+
-	~~[[Category: Long-chain dehydrogenase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Polyol dehydrogenase]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Secondary alcohol dehydrogenase~~]]	+

OCA at 08:32, 2 December 2020

OCA — Wed, 02 Dec 2020 08:32:31 GMT

←Older revision		Revision as of 08:32, 2 December 2020
Line 1:		Line 1:

	==Pseudomonas fluorescens mannitol 2-dehydrogenase ternary complex with NAD and D-mannitol==		==Pseudomonas fluorescens mannitol 2-dehydrogenase ternary complex with NAD and D-mannitol==
-	<StructureSection load='1m2w' size='340' side='right' caption='[[1m2w]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1m2w' size='340' side='right'caption='[[1m2w]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m2w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2W OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1M2W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m2w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1M2W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTL:D-MANNITOL'>MTL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTL:D-MANNITOL'>MTL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lj8\|1lj8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1lj8\|1lj8]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </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=1m2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2w OCA], [http://pdbe.org/1m2w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m2w RCSB], [http://www.ebi.ac.uk/pdbsum/1m2w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2w 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=1m2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2w OCA], [http://pdbe.org/1m2w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m2w RCSB], [http://www.ebi.ac.uk/pdbsum/1m2w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2w ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1m2w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1m2w" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alcohol dehydrogenase 3D structures\|Alcohol dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]		[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
		+	[[Category: Large Structures]]
	[[Category: Mannitol 2-dehydrogenase]]		[[Category: Mannitol 2-dehydrogenase]]
	[[Category: Kavanagh, K L]]		[[Category: Kavanagh, K L]]

OCA at 07:53, 31 January 2018

OCA — Wed, 31 Jan 2018 07:53:49 GMT

←Older revision		Revision as of 07:53, 31 January 2018
Line 1:		Line 1:
		+
	==Pseudomonas fluorescens mannitol 2-dehydrogenase ternary complex with NAD and D-mannitol==		==Pseudomonas fluorescens mannitol 2-dehydrogenase ternary complex with NAD and D-mannitol==
	<StructureSection load='1m2w' size='340' side='right' caption='[[1m2w]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1m2w' size='340' side='right' caption='[[1m2w]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </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=1m2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2w OCA], [http://pdbe.org/1m2w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m2w RCSB], [http://www.ebi.ac.uk/pdbsum/1m2w 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=1m2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2w OCA], [http://pdbe.org/1m2w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m2w RCSB], [http://www.ebi.ac.uk/pdbsum/1m2w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2w ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m2/1m2w_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m2/1m2w_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 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1m2w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1m2w" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:28, 8 February 2016

OCA — Mon, 08 Feb 2016 09:28:47 GMT

←Older revision		Revision as of 09:28, 8 February 2016
Line 18:		Line 18:
	<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=1m2w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:12, 10 September 2015

OCA — Thu, 10 Sep 2015 10:12:17 GMT

←Older revision		Revision as of 10:12, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1m2w' size='340' side='right' caption='[[1m2w]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1m2w' size='340' side='right' caption='[[1m2w]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m2w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_fluorescens Pseudomonas~~ fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m2w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTL:D-MANNITOL'>MTL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTL:D-MANNITOL'>MTL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lj8\|1lj8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lj8\|1lj8]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 ~~Pseudomonas~~ fluorescens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </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=1m2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m2w RCSB], [http://www.ebi.ac.uk/pdbsum/1m2w 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=1m2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2w OCA], [http://pdbe.org/1m2w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m2w RCSB], [http://www.ebi.ac.uk/pdbsum/1m2w PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 28:
	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 1m2w" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Mannitol 2-dehydrogenase]]		[[Category: Mannitol 2-dehydrogenase]]
-	[[Category: Pseudomonas fluorescens]]
	[[Category: Kavanagh, K L]]		[[Category: Kavanagh, K L]]
	[[Category: Klimacek, M]]		[[Category: Klimacek, M]]

OCA at 15:41, 5 January 2015

OCA — Mon, 05 Jan 2015 15:41:03 GMT

←Older revision		Revision as of 15:41, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m2w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2W FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m2w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2W FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTL:D-MANNITOL'>MTL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTL:D-MANNITOL'>MTL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lj8\|1lj8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lj8\|1lj8]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 Pseudomonas fluorescens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 Pseudomonas fluorescens])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </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=1m2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m2w RCSB], [http://www.ebi.ac.uk/pdbsum/1m2w 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=1m2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m2w RCSB], [http://www.ebi.ac.uk/pdbsum/1m2w 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 37:		Line 37:
	[[Category: Mannitol 2-dehydrogenase]]		[[Category: Mannitol 2-dehydrogenase]]
	[[Category: Pseudomonas fluorescens]]		[[Category: Pseudomonas fluorescens]]
-	[[Category: Kavanagh, K L.]]	+	[[Category: Kavanagh, K L]]
-	[[Category: Klimacek, M.]]	+	[[Category: Klimacek, M]]
-	[[Category: Nidetzky, B.]]	+	[[Category: Nidetzky, B]]
-	[[Category: Wilson, D K.]]	+	[[Category: Wilson, D K]]
	[[Category: Di-nucleotide binding motif]]		[[Category: Di-nucleotide binding motif]]
	[[Category: Long-chain dehydrogenase]]		[[Category: Long-chain dehydrogenase]]

OCA at 13:16, 28 September 2014

OCA — Sun, 28 Sep 2014 13:16:37 GMT

←Older revision		Revision as of 13:16, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1m2w.~~png~~\|~~left~~\|200px]]	+	==Pseudomonas fluorescens mannitol 2-dehydrogenase ternary complex with NAD and D-mannitol==
		+	<StructureSection load='1m2w' size='340' side='right' caption='[[1m2w]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1m2w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M2W FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTL:D-MANNITOL'>MTL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lj8\|1lj8]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtlD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 Pseudomonas fluorescens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannitol_2-dehydrogenase Mannitol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.67 1.1.1.67] </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=1m2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m2w RCSB], [http://www.ebi.ac.uk/pdbsum/1m2w 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/m2/1m2w_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 ==
		+	Long-chain mannitol dehydrogenases are secondary alcohol dehydrogenases that are of wide interest because of their involvement in metabolism and potential applications in agriculture, medicine, and industry. They differ from other alcohol and polyol dehydrogenases because they do not contain a conserved tyrosine and are not dependent on Zn(2+) or other metal cofactors. The structures of the long-chain mannitol 2-dehydrogenase (54 kDa) from Pseudomonas fluorescens in a binary complex with NAD(+) and ternary complex with NAD(+) and d-mannitol have been determined to resolutions of 1.7 and 1.8 A and R-factors of 0.171 and 0.176, respectively. These results show an N-terminal domain that includes a typical Rossmann fold. The C-terminal domain is primarily alpha-helical and mediates mannitol binding. The electron lone pair of Lys-295 is steered by hydrogen-bonding interactions with the amide oxygen of Asn-300 and the main-chain carbonyl oxygen of Val-229 to act as the general base. Asn-191 and Asn-300 are involved in a web of hydrogen bonding, which precisely orients the mannitol O2 proton for abstraction. These residues also aid in stabilizing a negative charge in the intermediate state and in preventing the formation of nonproductive complexes with the substrate. The catalytic lysine may be returned to its unprotonated state using a rectifying proton tunnel driven by Glu-292 oscillating among different environments. Despite low sequence homology, the closest structural neighbors are glycerol-3-phosphate dehydrogenase, N-(1-d-carboxylethyl)-l-norvaline dehydrogenase, UDP-glucose dehydrogenase, and 6-phosphogluconate dehydrogenase, indicating a possible evolutionary relationship among these enzymes.

-	~~{{STRUCTURE_1m2w\| PDB=1m2w \| SCENE= }}~~	+	Crystal structure of Pseudomonas fluorescens mannitol 2-dehydrogenase binary and ternary complexes. Specificity and catalytic mechanism.,Kavanagh KL, Klimacek M, Nidetzky B, Wilson DK J Biol Chem. 2002 Nov 8;277(45):43433-42. Epub 2002 Aug 23. PMID:12196534<ref>PMID:12196534</ref>

-	~~===Pseudomonas fluorescens mannitol 2-dehydrogenase ternary complex with NAD and D-mannitol===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12196534}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1m2w]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1M2W OCA].~~	+

	==See Also==		==See Also==
	*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]		*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012196534<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Mannitol 2-dehydrogenase]]		[[Category: Mannitol 2-dehydrogenase]]
	[[Category: Pseudomonas fluorescens]]		[[Category: Pseudomonas fluorescens]]

OCA at 09:42, 20 October 2012

OCA — Sat, 20 Oct 2012 09:42:26 GMT

←Older revision		Revision as of 09:42, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1m2w]] is a 2 chain structure ~~of [[Alcohol dehydrogenase]]~~ with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2W OCA].	+	[[1m2w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2W OCA].

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

OCA at 23:42, 25 July 2012

OCA — Wed, 25 Jul 2012 23:42:40 GMT

←Older revision		Revision as of 23:42, 25 July 2012
Line 1:		Line 1:
	[[Image:1m2w.png\|left\|200px]]		[[Image:1m2w.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1m2w", 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_1m2w\| PDB=1m2w \| SCENE= }}		{{STRUCTURE_1m2w\| PDB=1m2w \| SCENE= }}

	===Pseudomonas fluorescens mannitol 2-dehydrogenase ternary complex with NAD and D-mannitol===		===Pseudomonas fluorescens mannitol 2-dehydrogenase ternary complex with NAD and D-mannitol===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12196534}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12196534 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12196534}}		{{ABSTRACT_PUBMED_12196534}}

Line 22:		Line 11:

	==See Also==		==See Also==
-	*[[Alcohol dehydrogenase]]	+	*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]

	==Reference==		==Reference==

OCA: Protected "1m2w" [edit=sysop:move=sysop]

OCA — Wed, 16 Nov 2011 10:23:56 GMT

Protected "1m2w" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:23, 16 November 2011